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version 1.37, 2002/03/29 15:31:59 version 1.78, 2003/05/27 17:26:53
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 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, 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
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
      movingaverage()
     varevsij() 
 int erreur; /* Error number */    if popbased==1 varevsij(,popbased)
 int nvar;    total life expectancies
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Variance of stable prevalence
 int npar=NPARMAX;   end
 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;  
    
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <math.h>
 int maxwav; /* Maxim number of waves */  #include <stdio.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdlib.h>
 int mle, weightopt;  #include <unistd.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define MAXLINE 256
 double jmean; /* Mean space between 2 waves */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define FILENAMELENGTH 80
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define DEBUG*/
 FILE *ficgp,*ficresprob,*ficpop;  #define windows
 FILE *ficreseij;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
  FILE  *ficresvpl;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   char fileresvpl[FILENAMELENGTH];  
   #define NINTERVMAX 8
 #define NR_END 1  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FREE_ARG char*  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FTOL 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 #define NRANSI  #define YEARM 12. /* Number of months per year */
 #define ITMAX 200  #define AGESUP 130
   #define AGEBASE 40
 #define TOL 2.0e-4  #ifdef windows
   #define DIRSEPARATOR '\\'
 #define CGOLD 0.3819660  #define ODIRSEPARATOR '/'
 #define ZEPS 1.0e-10  #else
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 #define GOLD 1.618034  #endif
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";
   int erreur; /* Error number */
 static double maxarg1,maxarg2;  int nvar;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int ndeath=1; /* Number of dead states */
 #define rint(a) floor(a+0.5)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int *wav; /* Number of waves for this individuual 0 is possible */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 int imx;  int mle, weightopt;
 int stepm;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /* Stepm, step in month: minimum step interpolation*/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 int estepm;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 int m,nb;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  FILE *ficlog, *ficrespow;
 double **pmmij, ***probs, ***mobaverage;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double dateintmean=0;  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 double *weight;  FILE *ficreseij;
 int **s; /* Status */  char filerese[FILENAMELENGTH];
 double *agedc, **covar, idx;  FILE  *ficresvij;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char fileresvpl[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /**************** split *************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    char *s;                             /* pointer */  char filelog[FILENAMELENGTH]; /* Log file */
    int  l1, l2;                         /* length counters */  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  char popfile[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  
 #else  #define NR_END 1
    s = strrchr( path, '/' );            /* find last / */  #define FREE_ARG char*
 #endif  #define FTOL 1.0e-10
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  #define NRANSI 
       extern char       *getwd( );  #define ITMAX 200 
   
       if ( getwd( dirc ) == NULL ) {  #define TOL 2.0e-4 
 #else  
       extern char       *getcwd( );  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #endif  
          return( GLOCK_ERROR_GETCWD );  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
       strcpy( name, path );             /* we've got it */  #define TINY 1.0e-20 
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  static double maxarg1,maxarg2;
       l2 = strlen( s );                 /* length of filename */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       strcpy( name, s );                /* save file name */    
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       dirc[l1-l2] = 0;                  /* add zero */  #define rint(a) floor(a+0.5)
    }  
    l1 = strlen( dirc );                 /* length of directory */  static double sqrarg;
 #ifdef windows  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int imx; 
 #endif  int stepm;
    s = strrchr( name, '.' );            /* find last / */  /* Stepm, step in month: minimum step interpolation*/
    s++;  
    strcpy(ext,s);                       /* save extension */  int estepm;
    l1= strlen( name);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  int m,nb;
    finame[l1-l2]= 0;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    return( 0 );                         /* we're done */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double dateintmean=0;
   
 /******************************************/  double *weight;
   int **s; /* Status */
 void replace(char *s, char*t)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int i;  
   int lg=20;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   i=0;  double ftolhess; /* Tolerance for computing hessian */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  /**************** split *************************/
     (s[i] = t[i]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     if (t[i]== '\\') s[i]='/';  {
   }    char  *ss;                            /* pointer */
 }    int   l1, l2;                         /* length counters */
   
 int nbocc(char *s, char occ)    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,j=0;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int lg=20;    if ( ss == NULL ) {                   /* no directory, so use current */
   i=0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   lg=strlen(s);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(i=0; i<= lg; i++) {      /* get current working directory */
   if  (s[i] == occ ) j++;      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   return j;        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 void cutv(char *u,char *v, char*t, char occ)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   int i,lg,j,p=0;      l2 = strlen( ss );                  /* length of filename */
   i=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<=strlen(t)-1; j++) {      strcpy( name, ss );         /* save file name */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
     }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(j=0; j<p; j++) {  #ifdef windows
     (u[j] = t[j]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      u[p]='\0';    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
    for(j=0; j<= lg; j++) {    ss = strrchr( name, '.' );            /* find last / */
     if (j>=(p+1))(v[j-p-1] = t[j]);    ss++;
   }    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /********************** nrerror ********************/    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 void nrerror(char error_text[])    return( 0 );                          /* we're done */
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /******************************************/
 }  
 /*********************** vector *******************/  void replace(char *s, char*t)
 double *vector(int nl, int nh)  {
 {    int i;
   double *v;    int lg=20;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ivector *******************************/    int lg=20;
 int *ivector(long nl,long nh)    i=0;
 {    lg=strlen(s);
   int *v;    for(i=0; i<= lg; i++) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    if  (s[i] == occ ) j++;
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;    return j;
 }  }
   
 /******************free ivector **************************/  void cutv(char *u,char *v, char*t, char occ)
 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
   free((FREE_ARG)(v+nl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************* imatrix *******************************/    i=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<=strlen(t)-1; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* allocate pointers to rows */      (u[j] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");       u[p]='\0';
   m += NR_END;  
   m -= nrl;     for(j=0; j<= lg; j++) {
        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)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   /* return pointer to array of pointers to rows */    exit(EXIT_FAILURE);
   return m;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    double *v;
       int **m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       long nch,ncl,nrh,nrl;    if (!v) nrerror("allocation failure in vector");
      /* free an int matrix allocated by imatrix() */    return v-nl+NR_END;
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* matrix *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /************************ivector *******************************/
   double **m;  char *cvector(long nl,long nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    char *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   m += NR_END;    if (!v) nrerror("allocation failure in cvector");
   m -= nrl;    return v-nl+NR_END;
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_cvector(char *v, long nl, long nh)
   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;  
 }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 /*************************free matrix ************************/  {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!v) nrerror("allocation failure in ivector");
   free((FREE_ARG)(m+nrl-NR_END));    return v-nl+NR_END;
 }  }
   
 /******************* ma3x *******************************/  /******************free ivector **************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  void free_ivector(int *v, long nl, long nh)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    free((FREE_ARG)(v+nl-NR_END));
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /******************* imatrix *******************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   m += NR_END;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m -= nrl;  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int **m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* allocate pointers to rows */ 
   m[nrl] -= ncl;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    m += NR_END; 
     m -= nrl; 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    
   m[nrl][ncl] += NR_END;    /* allocate rows and set pointers to them */ 
   m[nrl][ncl] -= nll;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (j=ncl+1; j<=nch; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl][j]=m[nrl][j-1]+nlay;    m[nrl] += NR_END; 
      m[nrl] -= ncl; 
   for (i=nrl+1; i<=nrh; i++) {    
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for (j=ncl+1; j<=nch; j++)    
       m[i][j]=m[i][j-1]+nlay;    /* return pointer to array of pointers to rows */ 
   }    return m; 
   return m;  } 
 }  
   /****************** free_imatrix *************************/
 /*************************free ma3x ************************/  void free_imatrix(m,nrl,nrh,ncl,nch)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)        int **m;
 {        long nch,ncl,nrh,nrl; 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));       /* free an int matrix allocated by imatrix() */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  { 
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /***************** f1dim *************************/  
 extern int ncom;  /******************* matrix *******************************/
 extern double *pcom,*xicom;  double **matrix(long nrl, long nrh, long ncl, long nch)
 extern double (*nrfunc)(double []);  {
      long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 double f1dim(double x)    double **m;
 {  
   int j;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double f;    if (!m) nrerror("allocation failure 1 in matrix()");
   double *xt;    m += NR_END;
      m -= nrl;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   f=(*nrfunc)(xt);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_vector(xt,1,ncom);    m[nrl] += NR_END;
   return f;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /*****************brent *************************/    return m;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 {     */
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /*************************free matrix ************************/
   double ftemp;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   a=(ax < cx ? ax : cx);  }
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /******************* ma3x *******************************/
   fw=fv=fx=(*f)(x);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (iter=1;iter<=ITMAX;iter++) {  {
     xm=0.5*(a+b);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double ***m;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()");
     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);    m += NR_END;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    m -= nrl;
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       *xmin=x;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       return fx;    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     ftemp=fu;  
     if (fabs(e) > tol1) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       p=(x-v)*q-(x-w)*r;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       q=2.0*(q-r);    m[nrl][ncl] += NR_END;
       if (q > 0.0) p = -p;    m[nrl][ncl] -= nll;
       q=fabs(q);    for (j=ncl+1; j<=nch; j++) 
       etemp=e;      m[nrl][j]=m[nrl][j-1]+nlay;
       e=d;    
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    for (i=nrl+1; i<=nrh; i++) {
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       else {      for (j=ncl+1; j<=nch; j++) 
         d=p/q;        m[i][j]=m[i][j-1]+nlay;
         u=x+d;    }
         if (u-a < tol2 || b-u < tol2)    return m; 
           d=SIGN(tol1,xm-x);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     } else {    */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /*************************free ma3x ************************/
     fu=(*f)(u);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     if (fu <= fx) {  {
       if (u >= x) a=x; else b=x;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       SHFT(v,w,x,u)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         SHFT(fv,fw,fx,fu)    free((FREE_ARG)(m+nrl-NR_END));
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /***************** f1dim *************************/
             v=w;  extern int ncom; 
             w=u;  extern double *pcom,*xicom;
             fv=fw;  extern double (*nrfunc)(double []); 
             fw=fu;   
           } else if (fu <= fv || v == x || v == w) {  double f1dim(double x) 
             v=u;  { 
             fv=fu;    int j; 
           }    double f;
         }    double *xt; 
   }   
   nrerror("Too many iterations in brent");    xt=vector(1,ncom); 
   *xmin=x;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   return fx;    f=(*nrfunc)(xt); 
 }    free_vector(xt,1,ncom); 
     return f; 
 /****************** mnbrak ***********************/  } 
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /*****************brent *************************/
             double (*func)(double))  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 {  { 
   double ulim,u,r,q, dum;    int iter; 
   double fu;    double a,b,d,etemp;
      double fu,fv,fw,fx;
   *fa=(*func)(*ax);    double ftemp;
   *fb=(*func)(*bx);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   if (*fb > *fa) {    double e=0.0; 
     SHFT(dum,*ax,*bx,dum)   
       SHFT(dum,*fb,*fa,dum)    a=(ax < cx ? ax : cx); 
       }    b=(ax > cx ? ax : cx); 
   *cx=(*bx)+GOLD*(*bx-*ax);    x=w=v=bx; 
   *fc=(*func)(*cx);    fw=fv=fx=(*f)(x); 
   while (*fb > *fc) {    for (iter=1;iter<=ITMAX;iter++) { 
     r=(*bx-*ax)*(*fb-*fc);      xm=0.5*(a+b); 
     q=(*bx-*cx)*(*fb-*fa);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      printf(".");fflush(stdout);
     ulim=(*bx)+GLIMIT*(*cx-*bx);      fprintf(ficlog,".");fflush(ficlog);
     if ((*bx-u)*(u-*cx) > 0.0) {  #ifdef DEBUG
       fu=(*func)(u);      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);
     } else if ((*cx-u)*(u-ulim) > 0.0) {      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);
       fu=(*func)(u);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if (fu < *fc) {  #endif
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           SHFT(*fb,*fc,fu,(*func)(u))        *xmin=x; 
           }        return fx; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      } 
       u=ulim;      ftemp=fu;
       fu=(*func)(u);      if (fabs(e) > tol1) { 
     } else {        r=(x-w)*(fx-fv); 
       u=(*cx)+GOLD*(*cx-*bx);        q=(x-v)*(fx-fw); 
       fu=(*func)(u);        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     SHFT(*ax,*bx,*cx,u)        if (q > 0.0) p = -p; 
       SHFT(*fa,*fb,*fc,fu)        q=fabs(q); 
       }        etemp=e; 
 }        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 /*************** linmin ************************/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
 int ncom;          d=p/q; 
 double *pcom,*xicom;          u=x+d; 
 double (*nrfunc)(double []);          if (u-a < tol2 || b-u < tol2) 
              d=SIGN(tol1,xm-x); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        } 
 {      } else { 
   double brent(double ax, double bx, double cx,        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                double (*f)(double), double tol, double *xmin);      } 
   double f1dim(double x);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      fu=(*f)(u); 
               double *fc, double (*func)(double));      if (fu <= fx) { 
   int j;        if (u >= x) a=x; else b=x; 
   double xx,xmin,bx,ax;        SHFT(v,w,x,u) 
   double fx,fb,fa;          SHFT(fv,fw,fx,fu) 
            } else { 
   ncom=n;            if (u < x) a=u; else b=u; 
   pcom=vector(1,n);            if (fu <= fw || w == x) { 
   xicom=vector(1,n);              v=w; 
   nrfunc=func;              w=u; 
   for (j=1;j<=n;j++) {              fv=fw; 
     pcom[j]=p[j];              fw=fu; 
     xicom[j]=xi[j];            } else if (fu <= fv || v == x || v == w) { 
   }              v=u; 
   ax=0.0;              fv=fu; 
   xx=1.0;            } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);          } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    } 
 #ifdef DEBUG    nrerror("Too many iterations in brent"); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *xmin=x; 
 #endif    return fx; 
   for (j=1;j<=n;j++) {  } 
     xi[j] *= xmin;  
     p[j] += xi[j];  /****************** mnbrak ***********************/
   }  
   free_vector(xicom,1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   free_vector(pcom,1,n);              double (*func)(double)) 
 }  { 
     double ulim,u,r,q, dum;
 /*************** powell ************************/    double fu; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   
             double (*func)(double []))    *fa=(*func)(*ax); 
 {    *fb=(*func)(*bx); 
   void linmin(double p[], double xi[], int n, double *fret,    if (*fb > *fa) { 
               double (*func)(double []));      SHFT(dum,*ax,*bx,dum) 
   int i,ibig,j;        SHFT(dum,*fb,*fa,dum) 
   double del,t,*pt,*ptt,*xit;        } 
   double fp,fptt;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double *xits;    *fc=(*func)(*cx); 
   pt=vector(1,n);    while (*fb > *fc) { 
   ptt=vector(1,n);      r=(*bx-*ax)*(*fb-*fc); 
   xit=vector(1,n);      q=(*bx-*cx)*(*fb-*fa); 
   xits=vector(1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   *fret=(*func)(p);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for (j=1;j<=n;j++) pt[j]=p[j];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (*iter=1;;++(*iter)) {      if ((*bx-u)*(u-*cx) > 0.0) { 
     fp=(*fret);        fu=(*func)(u); 
     ibig=0;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     del=0.0;        fu=(*func)(u); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        if (fu < *fc) { 
     for (i=1;i<=n;i++)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       printf(" %d %.12f",i, p[i]);            SHFT(*fb,*fc,fu,(*func)(u)) 
     printf("\n");            } 
     for (i=1;i<=n;i++) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        u=ulim; 
       fptt=(*fret);        fu=(*func)(u); 
 #ifdef DEBUG      } else { 
       printf("fret=%lf \n",*fret);        u=(*cx)+GOLD*(*cx-*bx); 
 #endif        fu=(*func)(u); 
       printf("%d",i);fflush(stdout);      } 
       linmin(p,xit,n,fret,func);      SHFT(*ax,*bx,*cx,u) 
       if (fabs(fptt-(*fret)) > del) {        SHFT(*fa,*fb,*fc,fu) 
         del=fabs(fptt-(*fret));        } 
         ibig=i;  } 
       }  
 #ifdef DEBUG  /*************** linmin ************************/
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  int ncom; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  double *pcom,*xicom;
         printf(" x(%d)=%.12e",j,xit[j]);  double (*nrfunc)(double []); 
       }   
       for(j=1;j<=n;j++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         printf(" p=%.12e",p[j]);  { 
       printf("\n");    double brent(double ax, double bx, double cx, 
 #endif                 double (*f)(double), double tol, double *xmin); 
     }    double f1dim(double x); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #ifdef DEBUG                double *fc, double (*func)(double)); 
       int k[2],l;    int j; 
       k[0]=1;    double xx,xmin,bx,ax; 
       k[1]=-1;    double fx,fb,fa;
       printf("Max: %.12e",(*func)(p));   
       for (j=1;j<=n;j++)    ncom=n; 
         printf(" %.12e",p[j]);    pcom=vector(1,n); 
       printf("\n");    xicom=vector(1,n); 
       for(l=0;l<=1;l++) {    nrfunc=func; 
         for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      pcom[j]=p[j]; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      xicom[j]=xi[j]; 
         }    } 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    ax=0.0; 
       }    xx=1.0; 
 #endif    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
       free_vector(xit,1,n);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       free_vector(xits,1,n);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       free_vector(ptt,1,n);  #endif
       free_vector(pt,1,n);    for (j=1;j<=n;j++) { 
       return;      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    } 
     for (j=1;j<=n;j++) {    free_vector(xicom,1,n); 
       ptt[j]=2.0*p[j]-pt[j];    free_vector(pcom,1,n); 
       xit[j]=p[j]-pt[j];  } 
       pt[j]=p[j];  
     }  /*************** powell ************************/
     fptt=(*func)(ptt);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     if (fptt < fp) {              double (*func)(double [])) 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  { 
       if (t < 0.0) {    void linmin(double p[], double xi[], int n, double *fret, 
         linmin(p,xit,n,fret,func);                double (*func)(double [])); 
         for (j=1;j<=n;j++) {    int i,ibig,j; 
           xi[j][ibig]=xi[j][n];    double del,t,*pt,*ptt,*xit;
           xi[j][n]=xit[j];    double fp,fptt;
         }    double *xits;
 #ifdef DEBUG    pt=vector(1,n); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    ptt=vector(1,n); 
         for(j=1;j<=n;j++)    xit=vector(1,n); 
           printf(" %.12e",xit[j]);    xits=vector(1,n); 
         printf("\n");    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
       }    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
   }      ibig=0; 
 }      del=0.0; 
       printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 /**** Prevalence limit ****************/      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficrespow,"%d %.12f",*iter,*fret);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      for (i=1;i<=n;i++) {
 {        printf(" %d %.12f",i, p[i]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        fprintf(ficlog," %d %.12lf",i, p[i]);
      matrix by transitions matrix until convergence is reached */        fprintf(ficrespow," %.12lf", p[i]);
       }
   int i, ii,j,k;      printf("\n");
   double min, max, maxmin, maxmax,sumnew=0.;      fprintf(ficlog,"\n");
   double **matprod2();      fprintf(ficrespow,"\n");
   double **out, cov[NCOVMAX], **pmij();      for (i=1;i<=n;i++) { 
   double **newm;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double agefin, delaymax=50 ; /* Max number of years to converge */        fptt=(*fret); 
   #ifdef DEBUG
   for (ii=1;ii<=nlstate+ndeath;ii++)        printf("fret=%lf \n",*fret);
     for (j=1;j<=nlstate+ndeath;j++){        fprintf(ficlog,"fret=%lf \n",*fret);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #endif
     }        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
    cov[1]=1.;        linmin(p,xit,n,fret,func); 
          if (fabs(fptt-(*fret)) > del) { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          del=fabs(fptt-(*fret)); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){          ibig=i; 
     newm=savm;        } 
     /* Covariates have to be included here again */  #ifdef DEBUG
      cov[2]=agefin;        printf("%d %.12e",i,(*fret));
          fprintf(ficlog,"%d %.12e",i,(*fret));
       for (k=1; k<=cptcovn;k++) {        for (j=1;j<=n;j++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        }
       for (k=1; k<=cptcovprod;k++)        for(j=1;j<=n;j++) {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        printf("\n");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        fprintf(ficlog,"\n");
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #endif
       } 
     savm=oldm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     oldm=newm;  #ifdef DEBUG
     maxmax=0.;        int k[2],l;
     for(j=1;j<=nlstate;j++){        k[0]=1;
       min=1.;        k[1]=-1;
       max=0.;        printf("Max: %.12e",(*func)(p));
       for(i=1; i<=nlstate; i++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
         sumnew=0;        for (j=1;j<=n;j++) {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf(" %.12e",p[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog," %.12e",p[j]);
         max=FMAX(max,prlim[i][j]);        }
         min=FMIN(min,prlim[i][j]);        printf("\n");
       }        fprintf(ficlog,"\n");
       maxmin=max-min;        for(l=0;l<=1;l++) {
       maxmax=FMAX(maxmax,maxmin);          for (j=1;j<=n;j++) {
     }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     if(maxmax < ftolpl){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       return prlim;            fprintf(ficlog,"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)));
 }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
 /*************** transition probabilities ***************/  #endif
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {        free_vector(xit,1,n); 
   double s1, s2;        free_vector(xits,1,n); 
   /*double t34;*/        free_vector(ptt,1,n); 
   int i,j,j1, nc, ii, jj;        free_vector(pt,1,n); 
         return; 
     for(i=1; i<= nlstate; i++){      } 
     for(j=1; j<i;j++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      for (j=1;j<=n;j++) { 
         /*s2 += param[i][j][nc]*cov[nc];*/        ptt[j]=2.0*p[j]-pt[j]; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        xit[j]=p[j]-pt[j]; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        pt[j]=p[j]; 
       }      } 
       ps[i][j]=s2;      fptt=(*func)(ptt); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      if (fptt < fp) { 
     }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(j=i+1; j<=nlstate+ndeath;j++){        if (t < 0.0) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          linmin(p,xit,n,fret,func); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          for (j=1;j<=n;j++) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/            xi[j][ibig]=xi[j][n]; 
       }            xi[j][n]=xit[j]; 
       ps[i][j]=s2;          }
     }  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     /*ps[3][2]=1;*/          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]);
      s1=0;            fprintf(ficlog," %.12e",xit[j]);
     for(j=1; j<i; j++)          }
       s1+=exp(ps[i][j]);          printf("\n");
     for(j=i+1; j<=nlstate+ndeath; j++)          fprintf(ficlog,"\n");
       s1+=exp(ps[i][j]);  #endif
     ps[i][i]=1./(s1+1.);        }
     for(j=1; j<i; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    } 
     for(j=i+1; j<=nlstate+ndeath; j++)  } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /**** Prevalence limit (stable prevalence)  ****************/
   } /* end i */  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       ps[ii][jj]=0;       matrix by transitions matrix until convergence is reached */
       ps[ii][ii]=1;  
     }    int i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double **newm;
     for(jj=1; jj<= nlstate+ndeath; jj++){    double agefin, delaymax=50 ; /* Max number of years to converge */
      printf("%lf ",ps[ii][jj]);  
    }    for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("\n ");      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n ");printf("%lf ",cov[2]);*/      }
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);     cov[1]=1.;
   goto end;*/   
     return ps;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /**************** Product of 2 matrices ******************/      /* Covariates have to be included here again */
        cov[2]=agefin;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    
 {        for (k=1; k<=cptcovn;k++) {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          /*      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]]);*/
   /* in, b, out are matrice of pointers which should have been initialized        }
      before: only the contents of out is modified. The function returns        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      a pointer to pointers identical to out */        for (k=1; k<=cptcovprod;k++)
   long i, j, k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         out[i][k] +=in[i][j]*b[j][k];        /*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);
   return out;  
 }      savm=oldm;
       oldm=newm;
       maxmax=0.;
 /************* Higher Matrix Product ***************/      for(j=1;j<=nlstate;j++){
         min=1.;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        max=0.;
 {        for(i=1; i<=nlstate; i++) {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          sumnew=0;
      duration (i.e. until          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          prlim[i][j]= newm[i][j]/(1-sumnew);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          max=FMAX(max,prlim[i][j]);
      (typically every 2 years instead of every month which is too big).          min=FMIN(min,prlim[i][j]);
      Model is determined by parameters x and covariates have to be        }
      included manually here.        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
      */      }
       if(maxmax < ftolpl){
   int i, j, d, h, k;        return prlim;
   double **out, cov[NCOVMAX];      }
   double **newm;    }
   }
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /*************** transition probabilities ***************/ 
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       po[i][j][0]=(i==j ? 1.0 : 0.0);  {
     }    double s1, s2;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /*double t34;*/
   for(h=1; h <=nhstepm; h++){    int i,j,j1, nc, ii, jj;
     for(d=1; d <=hstepm; d++){  
       newm=savm;      for(i=1; i<= nlstate; i++){
       /* Covariates have to be included here again */      for(j=1; j<i;j++){
       cov[1]=1.;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          /*s2 += param[i][j][nc]*cov[nc];*/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (k=1; k<=cptcovage;k++)          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        }
       for (k=1; k<=cptcovprod;k++)        ps[i][j]=s2;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
       for(j=i+1; j<=nlstate+ndeath;j++){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        }
       savm=oldm;        ps[i][j]=s2;
       oldm=newm;      }
     }    }
     for(i=1; i<=nlstate+ndeath; i++)      /*ps[3][2]=1;*/
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];    for(i=1; i<= nlstate; i++){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);       s1=0;
          */      for(j=1; j<i; j++)
       }        s1+=exp(ps[i][j]);
   } /* end h */      for(j=i+1; j<=nlstate+ndeath; j++)
   return po;        s1+=exp(ps[i][j]);
 }      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 /*************** log-likelihood *************/      for(j=i+1; j<=nlstate+ndeath; j++)
 double func( double *x)        ps[i][j]= exp(ps[i][j])*ps[i][i];
 {      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   int i, ii, j, k, mi, d, kk;    } /* end i */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double sw; /* Sum of weights */      for(jj=1; jj<= nlstate+ndeath; jj++){
   double lli; /* Individual log likelihood */        ps[ii][jj]=0;
   long ipmx;        ps[ii][ii]=1;
   /*extern weight */      }
   /* We are differentiating ll according to initial status */    }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   */      for(jj=1; jj<= nlstate+ndeath; jj++){
   cov[1]=1.;       printf("%lf ",ps[ii][jj]);
      }
   for(k=1; k<=nlstate; k++) ll[k]=0.;      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("\n ");printf("%lf ",cov[2]);*/
     for(mi=1; mi<= wav[i]-1; mi++){  /*
       for (ii=1;ii<=nlstate+ndeath;ii++)    for(i=1; i<= npar; i++) printf("%f ",x[i]);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    goto end;*/
       for(d=0; d<dh[mi][i]; d++){      return ps;
         newm=savm;  }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /**************** Product of 2 matrices ******************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         savm=oldm;    /* in, b, out are matrice of pointers which should have been initialized 
         oldm=newm;       before: only the contents of out is modified. The function returns
               a pointer to pointers identical to out */
            long i, j, k;
       } /* end mult */    for(i=nrl; i<= nrh; i++)
            for(k=ncolol; k<=ncoloh; k++)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          out[i][k] +=in[i][j]*b[j][k];
       ipmx +=1;  
       sw += weight[i];    return out;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  }
     } /* end of wave */  
   } /* end of individual */  
   /************* Higher Matrix Product ***************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  {
   return -l;    /* Computes the transition matrix starting at age 'age' over 
 }       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
 /*********** Maximum Likelihood Estimation ***************/       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 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       for the memory).
 {       Model is determined by parameters x and covariates have to be 
   int i,j, iter;       included manually here. 
   double **xi,*delti;  
   double fret;       */
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)    int i, j, d, h, k;
     for (j=1;j<=npar;j++)    double **out, cov[NCOVMAX];
       xi[i][j]=(i==j ? 1.0 : 0.0);    double **newm;
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
 }      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /**** Computes Hessian and covariance matrix ***/    for(h=1; h <=nhstepm; h++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(d=1; d <=hstepm; d++){
 {        newm=savm;
   double  **a,**y,*x,pd;        /* Covariates have to be included here again */
   double **hess;        cov[1]=1.;
   int i, j,jk;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int *indx;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
   double hessii(double p[], double delta, int theta, double delti[]);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double hessij(double p[], double delti[], int i, int j);        for (k=1; k<=cptcovprod;k++)
   void lubksb(double **a, int npar, int *indx, double b[]) ;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   
   hess=matrix(1,npar,1,npar);        /*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("\nCalculation of the hessian matrix. Wait...\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   for (i=1;i<=npar;i++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("%d",i);fflush(stdout);        savm=oldm;
     hess[i][i]=hessii(p,ftolhess,i,delti);        oldm=newm;
     /*printf(" %f ",p[i]);*/      }
     /*printf(" %lf ",hess[i][i]);*/      for(i=1; i<=nlstate+ndeath; i++)
   }        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   for (i=1;i<=npar;i++) {          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     for (j=1;j<=npar;j++)  {           */
       if (j>i) {        }
         printf(".%d%d",i,j);fflush(stdout);    } /* end h */
         hess[i][j]=hessij(p,delti,i,j);    return po;
         hess[j][i]=hess[i][j];      }
         /*printf(" %lf ",hess[i][j]);*/  
       }  
     }  /*************** log-likelihood *************/
   }  double func( double *x)
   printf("\n");  {
     int i, ii, j, k, mi, d, kk;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   a=matrix(1,npar,1,npar);    double sw; /* Sum of weights */
   y=matrix(1,npar,1,npar);    double lli; /* Individual log likelihood */
   x=vector(1,npar);    int s1, s2;
   indx=ivector(1,npar);    double bbh, survp;
   for (i=1;i<=npar;i++)    long ipmx;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    /*extern weight */
   ludcmp(a,npar,indx,&pd);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (j=1;j<=npar;j++) {    /*for(i=1;i<imx;i++) 
     for (i=1;i<=npar;i++) x[i]=0;      printf(" %d\n",s[4][i]);
     x[j]=1;    */
     lubksb(a,npar,indx,x);    cov[1]=1.;
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
   }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("\n#Hessian matrix#\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (i=1;i<=npar;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (j=1;j<=npar;j++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       printf("%.3e ",hess[i][j]);            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
           for(d=0; d<dh[mi][i]; d++){
   /* Recompute Inverse */            newm=savm;
   for (i=1;i<=npar;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            for (kk=1; kk<=cptcovage;kk++) {
   ludcmp(a,npar,indx,&pd);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   /*  printf("\n#Hessian matrix recomputed#\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (j=1;j<=npar;j++) {            savm=oldm;
     for (i=1;i<=npar;i++) x[i]=0;            oldm=newm;
     x[j]=1;          } /* end mult */
     lubksb(a,npar,indx,x);        
     for (i=1;i<=npar;i++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       y[i][j]=x[i];          /* But now since version 0.9 we anticipate for bias and large stepm.
       printf("%.3e ",y[i][j]);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     printf("\n");           * 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
            * probability in order to take into account the bias as a fraction of the way
   free_matrix(a,1,npar,1,npar);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   free_matrix(y,1,npar,1,npar);           * -stepm/2 to stepm/2 .
   free_vector(x,1,npar);           * For stepm=1 the results are the same as for previous versions of Imach.
   free_ivector(indx,1,npar);           * For stepm > 1 the results are less biased than in previous versions. 
   free_matrix(hess,1,npar,1,npar);           */
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 /*************** hessian matrix ****************/           * is higher than the multiple of stepm and negative otherwise.
 double hessii( double x[], double delta, int theta, double delti[])           */
 {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int i;          if( s2 > nlstate){ 
   int l=1, lmax=20;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   double k1,k2;               to the likelihood is the probability to die between last step unit time and current 
   double p2[NPARMAX+1];               step unit time, which is also the differences between probability to die before dh 
   double res;               and probability to die before dh-stepm . 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;               In version up to 0.92 likelihood was computed
   double fx;          as if date of death was unknown. Death was treated as any other
   int k=0,kmax=10;          health state: the date of the interview describes the actual state
   double l1;          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
   fx=func(x);          (healthy, disable or death) and IMaCh was corrected; but when we
   for (i=1;i<=npar;i++) p2[i]=x[i];          introduced the exact date of death then we should have modified
   for(l=0 ; l <=lmax; l++){          the contribution of an exact death to the likelihood. This new
     l1=pow(10,l);          contribution is smaller and very dependent of the step unit
     delts=delt;          stepm. It is no more the probability to die between last interview
     for(k=1 ; k <kmax; k=k+1){          and month of death but the probability to survive from last
       delt = delta*(l1*k);          interview up to one month before death multiplied by the
       p2[theta]=x[theta] +delt;          probability to die within a month. Thanks to Chris
       k1=func(p2)-fx;          Jackson for correcting this bug.  Former versions increased
       p2[theta]=x[theta]-delt;          mortality artificially. The bad side is that we add another loop
       k2=func(p2)-fx;          which slows down the processing. The difference can be up to 10%
       /*res= (k1-2.0*fx+k2)/delt/delt; */          lower mortality.
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            */
                  lli=log(out[s1][s2] - savm[s1][s2]);
 #ifdef DEBUG          }else{
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 #endif            /*  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 */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         k=kmax;          /*if(lli ==000.0)*/
       }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          ipmx +=1;
         k=kmax; l=lmax*10.;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        } /* end of wave */
         delts=delt;      } /* end of individual */
       }    }  else if(mle==2){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   delti[theta]=delts;        for(mi=1; mi<= wav[i]-1; mi++){
   return res;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 double hessij( double x[], double delti[], int thetai,int thetaj)            }
 {          for(d=0; d<=dh[mi][i]; d++){
   int i;            newm=savm;
   int l=1, l1, lmax=20;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double k1,k2,k3,k4,res,fx;            for (kk=1; kk<=cptcovage;kk++) {
   double p2[NPARMAX+1];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int k;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fx=func(x);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=1; k<=2; k++) {            savm=oldm;
     for (i=1;i<=npar;i++) p2[i]=x[i];            oldm=newm;
     p2[thetai]=x[thetai]+delti[thetai]/k;          } /* end mult */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        
     k1=func(p2)-fx;          /*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.
     p2[thetai]=x[thetai]+delti[thetai]/k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     k2=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * probability in order to take into account the bias as a fraction of the way
     k3=func(p2)-fx;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
             * -stepm/2 to stepm/2 .
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     k4=func(p2)-fx;           */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          s1=s[mw[mi][i]][i];
 #ifdef DEBUG          s2=s[mw[mi+1][i]][i];
     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);          bbh=(double)bh[mi][i]/(double)stepm; 
 #endif          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   return res;           */
 }          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 */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 /************** Inverse of matrix **************/          /*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 */
 void ludcmp(double **a, int n, int *indx, double *d)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i,imax,j,k;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   double big,dum,sum,temp;          ipmx +=1;
   double *vv;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   vv=vector(1,n);        } /* end of wave */
   *d=1.0;      } /* end of individual */
   for (i=1;i<=n;i++) {    }  else if(mle==3){  /* exponential inter-extrapolation */
     big=0.0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (j=1;j<=n;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(mi=1; mi<= wav[i]-1; mi++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          for (ii=1;ii<=nlstate+ndeath;ii++)
     vv[i]=1.0/big;            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<j;i++) {            }
       sum=a[i][j];          for(d=0; d<dh[mi][i]; d++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            newm=savm;
       a[i][j]=sum;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     big=0.0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=j;i<=n;i++) {            }
       sum=a[i][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=1;k<j;k++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         sum -= a[i][k]*a[k][j];            savm=oldm;
       a[i][j]=sum;            oldm=newm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {          } /* end mult */
         big=dum;        
         imax=i;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       }          /* But now since version 0.9 we anticipate for bias and large stepm.
     }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (j != imax) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for (k=1;k<=n;k++) {           * the nearest (and in case of equal distance, to the lowest) interval but now
         dum=a[imax][k];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         a[imax][k]=a[j][k];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         a[j][k]=dum;           * 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
       *d = -(*d);           * -stepm/2 to stepm/2 .
       vv[imax]=vv[j];           * 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. 
     indx[j]=imax;           */
     if (a[j][j] == 0.0) a[j][j]=TINY;          s1=s[mw[mi][i]][i];
     if (j != n) {          s2=s[mw[mi+1][i]][i];
       dum=1.0/(a[j][j]);          bbh=(double)bh[mi][i]/(double)stepm; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          /* bias is positive if real duration
     }           * is higher than the multiple of stepm and negative otherwise.
   }           */
   free_vector(vv,1,n);  /* Doesn't work */          /* 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 */
 ;          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)*/
 void lubksb(double **a, int n, int *indx, double b[])          /*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;
   int i,ii=0,ip,j;          sw += weight[i];
   double sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   for (i=1;i<=n;i++) {      } /* end of individual */
     ip=indx[i];    }else{  /* ml=4 no inter-extrapolation */
     sum=b[ip];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     b[ip]=b[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if (ii)        for(mi=1; mi<= wav[i]-1; mi++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          for (ii=1;ii<=nlstate+ndeath;ii++)
     else if (sum) ii=i;            for (j=1;j<=nlstate+ndeath;j++){
     b[i]=sum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=n;i>=1;i--) {            }
     sum=b[i];          for(d=0; d<dh[mi][i]; d++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            newm=savm;
     b[i]=sum/a[i][i];            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];
             }
 /************ 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)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {  /* Some frequencies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            oldm=newm;
   double ***freq; /* Frequencies */          } /* end mult */
   double *pp;        
   double pos, k2, dateintsum=0,k2cpt=0;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   FILE *ficresp;          ipmx +=1;
   char fileresp[FILENAMELENGTH];          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);        } /* end of wave */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of individual */
   strcpy(fileresp,"p");    } /* End of if */
   strcat(fileresp,fileres);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   if((ficresp=fopen(fileresp,"w"))==NULL) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     printf("Problem with prevalence resultfile: %s\n", fileresp);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     exit(0);    return -l;
   }  }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  
    /*********** Maximum Likelihood Estimation ***************/
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
   for(k1=1; k1<=j;k1++){    int i,j, iter;
     for(i1=1; i1<=ncodemax[k1];i1++){    double **xi;
       j1++;    double fret;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    char filerespow[FILENAMELENGTH];
         scanf("%d", i);*/    xi=matrix(1,npar,1,npar);
       for (i=-1; i<=nlstate+ndeath; i++)      for (i=1;i<=npar;i++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)        for (j=1;j<=npar;j++)
           for(m=agemin; m <= agemax+3; m++)        xi[i][j]=(i==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
          strcpy(filerespow,"pow"); 
       dateintsum=0;    strcat(filerespow,fileres);
       k2cpt=0;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       for (i=1; i<=imx; i++) {      printf("Problem with resultfile: %s\n", filerespow);
         bool=1;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         if  (cptcovn>0) {    }
           for (z1=1; z1<=cptcoveff; z1++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (i=1;i<=nlstate;i++)
               bool=0;      for(j=1;j<=nlstate+ndeath;j++)
         }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         if (bool==1) {    fprintf(ficrespow,"\n");
           for(m=firstpass; m<=lastpass; m++){    powell(p,xi,npar,ftol,&iter,&fret,func);
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    fclose(ficrespow);
               if(agev[m][i]==0) agev[m][i]=agemax+1;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
               if(agev[m][i]==1) agev[m][i]=agemax+2;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if (m<lastpass) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  }
               }  
                /**** Computes Hessian and covariance matrix ***/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                 dateintsum=dateintsum+k2;  {
                 k2cpt++;    double  **a,**y,*x,pd;
               }    double **hess;
             }    int i, j,jk;
           }    int *indx;
         }  
       }    double hessii(double p[], double delta, int theta, double delti[]);
            double hessij(double p[], double delti[], int i, int j);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");    hess=matrix(1,npar,1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");    printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      printf("%d",i);fflush(stdout);
       fprintf(ficresp, "\n");      fprintf(ficlog,"%d",i);fflush(ficlog);
            hess[i][i]=hessii(p,ftolhess,i,delti);
       for(i=(int)agemin; i <= (int)agemax+3; i++){      /*printf(" %f ",p[i]);*/
         if(i==(int)agemax+3)      /*printf(" %lf ",hess[i][i]);*/
           printf("Total");    }
         else    
           printf("Age %d", i);    for (i=1;i<=npar;i++) {
         for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++)  {
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        if (j>i) { 
             pp[jk] += freq[jk][m][i];          printf(".%d%d",i,j);fflush(stdout);
         }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(jk=1; jk <=nlstate ; jk++){          hess[i][j]=hessij(p,delti,i,j);
           for(m=-1, pos=0; m <=0 ; m++)          hess[j][i]=hess[i][j];    
             pos += freq[jk][m][i];          /*printf(" %lf ",hess[i][j]);*/
           if(pp[jk]>=1.e-10)        }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      }
           else    }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    printf("\n");
         }    fprintf(ficlog,"\n");
   
         for(jk=1; jk <=nlstate ; jk++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             pp[jk] += freq[jk][m][i];    
         }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
         for(jk=1,pos=0; jk <=nlstate ; jk++)    x=vector(1,npar);
           pos += pp[jk];    indx=ivector(1,npar);
         for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++)
           if(pos>=1.e-5)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    ludcmp(a,npar,indx,&pd);
           else  
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (j=1;j<=npar;j++) {
           if( i <= (int) agemax){      for (i=1;i<=npar;i++) x[i]=0;
             if(pos>=1.e-5){      x[j]=1;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      lubksb(a,npar,indx,x);
               probs[i][jk][j1]= pp[jk]/pos;      for (i=1;i<=npar;i++){ 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        matcov[i][j]=x[i];
             }      }
             else    }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  
           }    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
            for (i=1;i<=npar;i++) { 
         for(jk=-1; jk <=nlstate+ndeath; jk++)      for (j=1;j<=npar;j++) { 
           for(m=-1; m <=nlstate+ndeath; m++)        printf("%.3e ",hess[i][j]);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        fprintf(ficlog,"%.3e ",hess[i][j]);
         if(i <= (int) agemax)      }
           fprintf(ficresp,"\n");      printf("\n");
         printf("\n");      fprintf(ficlog,"\n");
       }    }
     }  
   }    /* Recompute Inverse */
   dateintmean=dateintsum/k2cpt;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   fclose(ficresp);    ludcmp(a,npar,indx,&pd);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    /*  printf("\n#Hessian matrix recomputed#\n");
    
   /* End of Freq */    for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 /************ Prevalence ********************/      lubksb(a,npar,indx,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++){ 
 {  /* Some frequencies */        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fprintf(ficlog,"%.3e ",y[i][j]);
   double ***freq; /* Frequencies */      }
   double *pp;      printf("\n");
   double pos, k2;      fprintf(ficlog,"\n");
     }
   pp=vector(1,nlstate);    */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
      free_matrix(a,1,npar,1,npar);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    free_matrix(y,1,npar,1,npar);
   j1=0;    free_vector(x,1,npar);
      free_ivector(indx,1,npar);
   j=cptcoveff;    free_matrix(hess,1,npar,1,npar);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    
  for(k1=1; k1<=j;k1++){  }
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;  /*************** hessian matrix ****************/
    double hessii( double x[], double delta, int theta, double delti[])
       for (i=-1; i<=nlstate+ndeath; i++)    {
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int i;
           for(m=agemin; m <= agemax+3; m++)    int l=1, lmax=20;
             freq[i][jk][m]=0;    double k1,k2;
          double p2[NPARMAX+1];
       for (i=1; i<=imx; i++) {    double res;
         bool=1;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         if  (cptcovn>0) {    double fx;
           for (z1=1; z1<=cptcoveff; z1++)    int k=0,kmax=10;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double l1;
               bool=0;  
         }    fx=func(x);
         if (bool==1) {    for (i=1;i<=npar;i++) p2[i]=x[i];
           for(m=firstpass; m<=lastpass; m++){    for(l=0 ; l <=lmax; l++){
             k2=anint[m][i]+(mint[m][i]/12.);      l1=pow(10,l);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      delts=delt;
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for(k=1 ; k <kmax; k=k+1){
               if(agev[m][i]==1) agev[m][i]=agemax+2;        delt = delta*(l1*k);
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        p2[theta]=x[theta] +delt;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        k1=func(p2)-fx;
             }        p2[theta]=x[theta]-delt;
           }        k2=func(p2)-fx;
         }        /*res= (k1-2.0*fx+k2)/delt/delt; */
       }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        
           for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        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);
               pp[jk] += freq[jk][m][i];        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(jk=1; jk <=nlstate ; jk++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             for(m=-1, pos=0; m <=0 ; m++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
             pos += freq[jk][m][i];          k=kmax;
         }        }
                else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
          for(jk=1; jk <=nlstate ; jk++){          k=kmax; l=lmax*10.;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        }
              pp[jk] += freq[jk][m][i];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
          }          delts=delt;
                  }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      }
     }
          for(jk=1; jk <=nlstate ; jk++){              delti[theta]=delts;
            if( i <= (int) agemax){    return res; 
              if(pos>=1.e-5){    
                probs[i][jk][j1]= pp[jk]/pos;  }
              }  
            }  double hessij( double x[], double delti[], int thetai,int thetaj)
          }  {
              int i;
         }    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
   }    double p2[NPARMAX+1];
      int k;
    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    fx=func(x);
   free_vector(pp,1,nlstate);    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
 }  /* End of Freq */      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 /************* Waves Concatenation ***************/      k1=func(p2)-fx;
     
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      p2[thetai]=x[thetai]+delti[thetai]/k;
 {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      k2=func(p2)-fx;
      Death is a valid wave (if date is known).    
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      p2[thetai]=x[thetai]-delti[thetai]/k;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      and mw[mi+1][i]. dh depends on stepm.      k3=func(p2)-fx;
      */    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   int i, mi, m;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      k4=func(p2)-fx;
      double sum=0., jmean=0.;*/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
   int j, k=0,jk, ju, jl;      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);
   double sum=0.;      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);
   jmin=1e+5;  #endif
   jmax=-1;    }
   jmean=0.;    return res;
   for(i=1; i<=imx; i++){  }
     mi=0;  
     m=firstpass;  /************** Inverse of matrix **************/
     while(s[m][i] <= nlstate){  void ludcmp(double **a, int n, int *indx, double *d) 
       if(s[m][i]>=1)  { 
         mw[++mi][i]=m;    int i,imax,j,k; 
       if(m >=lastpass)    double big,dum,sum,temp; 
         break;    double *vv; 
       else   
         m++;    vv=vector(1,n); 
     }/* end while */    *d=1.0; 
     if (s[m][i] > nlstate){    for (i=1;i<=n;i++) { 
       mi++;     /* Death is another wave */      big=0.0; 
       /* if(mi==0)  never been interviewed correctly before death */      for (j=1;j<=n;j++) 
          /* Only death is a correct wave */        if ((temp=fabs(a[i][j])) > big) big=temp; 
       mw[mi][i]=m;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }      vv[i]=1.0/big; 
     } 
     wav[i]=mi;    for (j=1;j<=n;j++) { 
     if(mi==0)      for (i=1;i<j;i++) { 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        sum=a[i][j]; 
   }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   for(i=1; i<=imx; i++){      } 
     for(mi=1; mi<wav[i];mi++){      big=0.0; 
       if (stepm <=0)      for (i=j;i<=n;i++) { 
         dh[mi][i]=1;        sum=a[i][j]; 
       else{        for (k=1;k<j;k++) 
         if (s[mw[mi+1][i]][i] > nlstate) {          sum -= a[i][k]*a[k][j]; 
           if (agedc[i] < 2*AGESUP) {        a[i][j]=sum; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           if(j==0) j=1;  /* Survives at least one month after exam */          big=dum; 
           k=k+1;          imax=i; 
           if (j >= jmax) jmax=j;        } 
           if (j <= jmin) jmin=j;      } 
           sum=sum+j;      if (j != imax) { 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for (k=1;k<=n;k++) { 
           }          dum=a[imax][k]; 
         }          a[imax][k]=a[j][k]; 
         else{          a[j][k]=dum; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        } 
           k=k+1;        *d = -(*d); 
           if (j >= jmax) jmax=j;        vv[imax]=vv[j]; 
           else if (j <= jmin)jmin=j;      } 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      indx[j]=imax; 
           sum=sum+j;      if (a[j][j] == 0.0) a[j][j]=TINY; 
         }      if (j != n) { 
         jk= j/stepm;        dum=1.0/(a[j][j]); 
         jl= j -jk*stepm;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         ju= j -(jk+1)*stepm;      } 
         if(jl <= -ju)    } 
           dh[mi][i]=jk;    free_vector(vv,1,n);  /* Doesn't work */
         else  ;
           dh[mi][i]=jk+1;  } 
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
     }    int i,ii=0,ip,j; 
   }    double sum; 
   jmean=sum/k;   
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    for (i=1;i<=n;i++) { 
  }      ip=indx[i]; 
 /*********** Tricode ****************************/      sum=b[ip]; 
 void tricode(int *Tvar, int **nbcode, int imx)      b[ip]=b[i]; 
 {      if (ii) 
   int Ndum[20],ij=1, k, j, i;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int cptcode=0;      else if (sum) ii=i; 
   cptcoveff=0;      b[i]=sum; 
      } 
   for (k=0; k<19; k++) Ndum[k]=0;    for (i=n;i>=1;i--) { 
   for (k=1; k<=7; k++) ncodemax[k]=0;      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      b[i]=sum/a[i][i]; 
     for (i=1; i<=imx; i++) {    } 
       ij=(int)(covar[Tvar[j]][i]);  } 
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  /************ Frequencies ********************/
       if (ij > cptcode) cptcode=ij;  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)
     }  {  /* Some frequencies */
     
     for (i=0; i<=cptcode; i++) {    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       if(Ndum[i]!=0) ncodemax[j]++;    int first;
     }    double ***freq; /* Frequencies */
     ij=1;    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
     for (i=1; i<=ncodemax[j]; i++) {    char fileresp[FILENAMELENGTH];
       for (k=0; k<=19; k++) {    
         if (Ndum[k] != 0) {    pp=vector(1,nlstate);
           nbcode[Tvar[j]][ij]=k;    prop=matrix(1,nlstate,iagemin,iagemax+3);
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    strcpy(fileresp,"p");
           ij++;    strcat(fileresp,fileres);
         }    if((ficresp=fopen(fileresp,"w"))==NULL) {
         if (ij > ncodemax[j]) break;      printf("Problem with prevalence resultfile: %s\n", fileresp);
       }        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
   }      }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
  for (k=0; k<19; k++) Ndum[k]=0;    j1=0;
     
  for (i=1; i<=ncovmodel-2; i++) {    j=cptcoveff;
       ij=Tvar[i];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       Ndum[ij]++;  
     }    first=1;
   
  ij=1;    for(k1=1; k1<=j;k1++){
  for (i=1; i<=10; i++) {      for(i1=1; i1<=ncodemax[k1];i1++){
    if((Ndum[i]!=0) && (i<=ncovcol)){        j1++;
      Tvaraff[ij]=i;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      ij++;          scanf("%d", i);*/
    }        for (i=-1; i<=nlstate+ndeath; i++)  
  }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
              for(m=iagemin; m <= iagemax+3; m++)
     cptcoveff=ij-1;              freq[i][jk][m]=0;
 }  
       for (i=1; i<=nlstate; i++)  
 /*********** Health Expectancies ****************/        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)        
 {        dateintsum=0;
   /* Health expectancies */        k2cpt=0;
   int i, j, nhstepm, hstepm, h, nstepm;        for (i=1; i<=imx; i++) {
   double age, agelim, hf;          bool=1;
   double ***p3mat;          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficreseij,"# Health expectancies\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(ficreseij,"# Age");                bool=0;
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=nlstate;j++)          if (bool==1){
       fprintf(ficreseij," %1d-%1d",i,j);            for(m=firstpass; m<=lastpass; m++){
   fprintf(ficreseij,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
   if(estepm < stepm){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf ("Problem %d lower than %d\n",estepm, stepm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   else  hstepm=estepm;                  if (m<lastpass) {
   /* We compute the life expectancy from trapezoids spaced every estepm months                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    * This is mainly to measure the difference between two models: for example                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    * if stepm=24 months pijx are given only every 2 years and by summing them                }
    * we are calculating an estimate of the Life Expectancy assuming a linear                
    * progression inbetween and thus overestimating or underestimating according                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
    * to the curvature of the survival function. If, for the same date, we                  dateintsum=dateintsum+k2;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months                  k2cpt++;
    * to compare the new estimate of Life expectancy with the same linear                }
    * hypothesis. A more precise result, taking into account a more precise              }
    * curvature will be obtained if estepm is as small as stepm. */            }
           }
   /* For example we decided to compute the life expectancy with the smallest unit */        }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.         
      nhstepm is the number of hstepm from age to agelim        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size        if  (cptcovn>0) {
      and note for a fixed period like estepm months */          fprintf(ficresp, "\n#********** Variable "); 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      survival function given by stepm (the optimization length). Unfortunately it          fprintf(ficresp, "**********\n#");
      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        for(i=1; i<=nlstate;i++) 
      results. So we changed our mind and took the option of the best precision.          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   */        fprintf(ficresp, "\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        
         for(i=iagemin; i <= iagemax+3; i++){
   agelim=AGESUP;          if(i==iagemax+3){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            fprintf(ficlog,"Total");
     /* nhstepm age range expressed in number of stepm */          }else{
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            if(first==1){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              first=0;
     /* if (stepm >= YEARM) hstepm=1;*/              printf("See log file for details...\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog,"Age %d", i);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(jk=1; jk <=nlstate ; jk++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              pp[jk] += freq[jk][m][i]; 
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            for(m=-1, pos=0; m <=0 ; m++)
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;              pos += freq[jk][m][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]);*/            if(pp[jk]>=1.e-10){
         }              if(first==1){
     fprintf(ficreseij,"%3.0f",age );              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(i=1; i<=nlstate;i++)              }
       for(j=1; j<=nlstate;j++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            }else{
       }              if(first==1)
     fprintf(ficreseij,"\n");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
 }          }
   
 /************ Variance ******************/          for(jk=1; jk <=nlstate ; jk++){
 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)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 {              pp[jk] += freq[jk][m][i];
   /* Variance of health expectancies */          }       
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double **newm;            pos += pp[jk];
   double **dnewm,**doldm;            posprop += prop[jk][i];
   int i, j, nhstepm, hstepm, h, nstepm ;          }
   int k, cptcode;          for(jk=1; jk <=nlstate ; jk++){
   double *xp;            if(pos>=1.e-5){
   double **gp, **gm;              if(first==1)
   double ***gradg, ***trgradg;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double ***p3mat;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double age,agelim, hf;            }else{
   int theta;              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    fprintf(ficresvij,"# Covariances of life expectancies\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresvij,"# Age");            }
   for(i=1; i<=nlstate;i++)            if( i <= iagemax){
     for(j=1; j<=nlstate;j++)              if(pos>=1.e-5){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   fprintf(ficresvij,"\n");                probs[i][jk][j1]= pp[jk]/pos;
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   xp=vector(1,npar);              }
   dnewm=matrix(1,nlstate,1,npar);              else
   doldm=matrix(1,nlstate,1,nlstate);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
              }
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          
   }          for(jk=-1; jk <=nlstate+ndeath; jk++)
   else  hstepm=estepm;              for(m=-1; m <=nlstate+ndeath; m++)
   /* For example we decided to compute the life expectancy with the smallest unit */              if(freq[jk][m][i] !=0 ) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              if(first==1)
      nhstepm is the number of hstepm from age to agelim                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      nstepm is the number of stepm from age to agelin.                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      Look at hpijx to understand the reason of that which relies in memory size              }
      and note for a fixed period like k years */          if(i <= iagemax)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            fprintf(ficresp,"\n");
      survival function given by stepm (the optimization length). Unfortunately it          if(first==1)
      means that if the survival funtion is printed only each two years of age and if            printf("Others in log...\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          fprintf(ficlog,"\n");
      results. So we changed our mind and took the option of the best precision.        }
   */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    }
   agelim = AGESUP;    dateintmean=dateintsum/k2cpt; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fclose(ficresp);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(pp,1,nlstate);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     gp=matrix(0,nhstepm,1,nlstate);    /* End of Freq */
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /************ Prevalence ********************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  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)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {  
       }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         in each health status at the date of interview (if between dateprev1 and dateprev2).
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       We still use firstpass and lastpass as another selection.
     */
       if (popbased==1) {   
         for(i=1; i<=nlstate;i++)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           prlim[i][i]=probs[(int)age][i][ij];    double ***freq; /* Frequencies */
       }    double *pp, **prop;
      double pos,posprop; 
       for(j=1; j<= nlstate; j++){    double  y2; /* in fractional years */
         for(h=0; h<=nhstepm; h++){    int iagemin, iagemax;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    iagemin= (int) agemin;
         }    iagemax= (int) agemax;
       }    /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin,iagemax+3); 
       for(i=1; i<=npar; i++) /* Computes gradient */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    j1=0;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    for(k1=1; k1<=j;k1++){
           prlim[i][i]=probs[(int)age][i][ij];      for(i1=1; i1<=ncodemax[k1];i1++){
       }        j1++;
         
       for(j=1; j<= nlstate; j++){        for (i=1; i<=nlstate; i++)  
         for(h=0; h<=nhstepm; h++){          for(m=iagemin; m <= iagemax+3; m++)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            prop[i][m]=0.0;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];       
         }        for (i=1; i<=imx; i++) { /* Each individual */
       }          bool=1;
           if  (cptcovn>0) {
       for(j=1; j<= nlstate; j++)            for (z1=1; z1<=cptcoveff; z1++) 
         for(h=0; h<=nhstepm; h++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                bool=0;
         }          } 
     } /* End theta */          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     for(h=0; h<=nhstepm; h++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(j=1; j<=nlstate;j++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         for(theta=1; theta <=npar; theta++)                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); 
           trgradg[h][j][theta]=gradg[h][theta][j];                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]]);*/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1;i<=nlstate;i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for(j=1;j<=nlstate;j++)                } 
         vareij[i][j][(int)age] =0.;              }
             } /* end selection of waves */
     for(h=0;h<=nhstepm;h++){          }
       for(k=0;k<=nhstepm;k++){        }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        for(i=iagemin; i <= iagemax+3; i++){  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          
         for(i=1;i<=nlstate;i++)          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           for(j=1;j<=nlstate;j++)            posprop += prop[jk][i]; 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          } 
       }  
     }          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
     fprintf(ficresvij,"%.0f ",age );              if(posprop>=1.e-5){ 
     for(i=1; i<=nlstate;i++)                probs[i][jk][j1]= prop[jk][i]/posprop;
       for(j=1; j<=nlstate;j++){              } 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            } 
       }          }/* end jk */ 
     fprintf(ficresvij,"\n");        }/* end i */ 
     free_matrix(gp,0,nhstepm,1,nlstate);      } /* end i1 */
     free_matrix(gm,0,nhstepm,1,nlstate);    } /* end k1 */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*free_vector(pp,1,nlstate);*/
   } /* End age */    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  /* End of prevalence */
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  /************* Waves Concatenation ***************/
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   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 of prevlim ******************/       Death is a valid wave (if date is known).
 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)       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 prevalence limit */       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;    /* 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 age,agelim;    first=0;
   int theta;    jmin=1e+5;
        jmax=-1;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    jmean=0.;
   fprintf(ficresvpl,"# Age");    for(i=1; i<=imx; i++){
   for(i=1; i<=nlstate;i++)      mi=0;
       fprintf(ficresvpl," %1d-%1d",i,i);      m=firstpass;
   fprintf(ficresvpl,"\n");      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
   xp=vector(1,npar);          mw[++mi][i]=m;
   dnewm=matrix(1,nlstate,1,npar);        if(m >=lastpass)
   doldm=matrix(1,nlstate,1,nlstate);          break;
          else
   hstepm=1*YEARM; /* Every year of age */          m++;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      }/* end while */
   agelim = AGESUP;      if (s[m][i] > nlstate){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        mi++;     /* Death is another wave */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /* if(mi==0)  never been interviewed correctly before death */
     if (stepm >= YEARM) hstepm=1;           /* Only death is a correct wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        mw[mi][i]=m;
     gradg=matrix(1,npar,1,nlstate);      }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);      wav[i]=mi;
       if(mi==0){
     for(theta=1; theta <=npar; theta++){        if(first==0){
       for(i=1; i<=npar; i++){ /* Computes gradient */          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          first=1;
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if(first==1){
       for(i=1;i<=nlstate;i++)          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         gp[i] = prlim[i][i];        }
          } /* end mi==0 */
       for(i=1; i<=npar; i++) /* Computes gradient */    } /* End individuals */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(i=1; i<=imx; i++){
       for(i=1;i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
         gm[i] = prlim[i][i];        if (stepm <=0)
           dh[mi][i]=1;
       for(i=1;i<=nlstate;i++)        else{
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     } /* End theta */            if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     trgradg =matrix(1,nlstate,1,npar);            if(j==0) j=1;  /* Survives at least one month after exam */
             k=k+1;
     for(j=1; j<=nlstate;j++)            if (j >= jmax) jmax=j;
       for(theta=1; theta <=npar; theta++)            if (j <= jmin) jmin=j;
         trgradg[j][theta]=gradg[theta][j];            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     for(i=1;i<=nlstate;i++)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       varpl[i][(int)age] =0.;            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          }
     for(i=1;i<=nlstate;i++)          else{
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     fprintf(ficresvpl,"%.0f ",age );            k=k+1;
     for(i=1; i<=nlstate;i++)            if (j >= jmax) jmax=j;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            else if (j <= jmin)jmin=j;
     fprintf(ficresvpl,"\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_vector(gp,1,nlstate);            /*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]);*/
     free_vector(gm,1,nlstate);            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     free_matrix(gradg,1,npar,1,nlstate);            sum=sum+j;
     free_matrix(trgradg,1,nlstate,1,npar);          }
   } /* End age */          jk= j/stepm;
           jl= j -jk*stepm;
   free_vector(xp,1,npar);          ju= j -(jk+1)*stepm;
   free_matrix(doldm,1,nlstate,1,npar);          if(mle <=1){ 
   free_matrix(dnewm,1,nlstate,1,nlstate);            if(jl==0){
               dh[mi][i]=jk;
 }              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
 /************ Variance of one-step probabilities  ******************/                    * at the price of an extra matrix product in likelihood */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)              dh[mi][i]=jk+1;
 {              bh[mi][i]=ju;
   int i, j;            }
   int k=0, cptcode;          }else{
   double **dnewm,**doldm;            if(jl <= -ju){
   double *xp;              dh[mi][i]=jk;
   double *gp, *gm;              bh[mi][i]=jl;       /* bias is positive if real duration
   double **gradg, **trgradg;                                   * is higher than the multiple of stepm and negative otherwise.
   double age,agelim, cov[NCOVMAX];                                   */
   int theta;            }
   char fileresprob[FILENAMELENGTH];            else{
               dh[mi][i]=jk+1;
   strcpy(fileresprob,"prob");              bh[mi][i]=ju;
   strcat(fileresprob,fileres);            }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            if(dh[mi][i]==0){
     printf("Problem with resultfile: %s\n", fileresprob);              dh[mi][i]=1; /* At least one step */
   }              bh[mi][i]=ju; /* At least one step */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              /*  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);*/
              }
           }
   xp=vector(1,npar);        } /* end if mle */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      } /* end wave */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    }
      jmean=sum/k;
   cov[1]=1;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   for (age=bage; age<=fage; age ++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     cov[2]=age;   }
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  /*********** Tricode ****************************/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  void tricode(int *Tvar, int **nbcode, int imx)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {
        
     for(theta=1; theta <=npar; theta++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
       for(i=1; i<=npar; i++)    int cptcode=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    cptcoveff=0; 
         
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    for (k=0; k<maxncov; k++) Ndum[k]=0;
        for (k=1; k<=7; k++) ncodemax[k]=0;
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         for(j=1; j<=(nlstate+ndeath);j++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
            k=k+1;                                 modality*/ 
           gp[k]=pmmij[i][j];        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         }        Ndum[ij]++; /*store the modality */
       }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       for(i=1; i<=npar; i++)                                         Tvar[j]. If V=sex and male is 0 and 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                                         female is 1, then  cptcode=1.*/
          }
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=0; i<=cptcode; i++) {
       k=0;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       for(i=1; i<=(nlstate+ndeath); i++){      }
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;      ij=1; 
           gm[k]=pmmij[i][j];      for (i=1; i<=ncodemax[j]; i++) {
         }        for (k=0; k<= maxncov; k++) {
       }          if (Ndum[k] != 0) {
                  nbcode[Tvar[j]][ij]=k; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              
     }            ij++;
           }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          if (ij > ncodemax[j]) break; 
       for(theta=1; theta <=npar; theta++)        }  
       trgradg[j][theta]=gradg[theta][j];      } 
      }  
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
      pmij(pmmij,cov,ncovmodel,x,nlstate);   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      k=0;     ij=Tvar[i];
      for(i=1; i<=(nlstate+ndeath); i++){     Ndum[ij]++;
        for(j=1; j<=(nlstate+ndeath);j++){   }
          k=k+1;  
          gm[k]=pmmij[i][j];   ij=1;
         }   for (i=1; i<= maxncov; i++) {
      }     if((Ndum[i]!=0) && (i<=ncovcol)){
             Tvaraff[ij]=i; /*For printing */
      /*printf("\n%d ",(int)age);       ij++;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){     }
           }
    
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));   cptcoveff=ij-1; /*Number of simple covariates*/
      }*/  }
   
   fprintf(ficresprob,"\n%d ",(int)age);  /*********** Health Expectancies ****************/
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  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 )
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  {
   }    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double age, agelim, hf;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double ***p3mat,***varhe;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double **dnewm,**doldm;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double *xp;
 }    double **gp, **gm;
  free_vector(xp,1,npar);    double ***gradg, ***trgradg;
 fclose(ficresprob);    int theta;
   
 }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
 /******************* Printing html file ***********/    dnewm=matrix(1,nlstate*nlstate,1,npar);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  int lastpass, int stepm, int weightopt, char model[],\    
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    fprintf(ficreseij,"# Health expectancies\n");
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    fprintf(ficreseij,"# Age");
  char version[], int popforecast, int estepm ){    for(i=1; i<=nlstate;i++)
   int jj1, k1, i1, cpt;      for(j=1; j<=nlstate;j++)
   FILE *fichtm;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   /*char optionfilehtm[FILENAMELENGTH];*/    fprintf(ficreseij,"\n");
   
   strcpy(optionfilehtm,optionfile);    if(estepm < stepm){
   strcat(optionfilehtm,".htm");      printf ("Problem %d lower than %d\n",estepm, stepm);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm), exit(0);    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n     * if stepm=24 months pijx are given only every 2 years and by summing them
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n     * we are calculating an estimate of the Life Expectancy assuming a linear 
 \n     * progression in between and thus overestimating or underestimating according
 Total number of observations=%d <br>\n     * to the curvature of the survival function. If, for the same date, we 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 <hr  size=\"2\" color=\"#EC5E5E\">     * to compare the new estimate of Life expectancy with the same linear 
  <ul><li>Outputs files<br>\n     * hypothesis. A more precise result, taking into account a more precise
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n     * curvature will be obtained if estepm is as small as stepm. */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n  
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    /* For example we decided to compute the life expectancy with the smallest unit */
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n       nhstepm is the number of hstepm from age to agelim 
  - 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,fileres,fileres,estepm);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
  fprintf(fichtm,"\n       and note for a fixed period like estepm months */
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n       survival function given by stepm (the optimization length). Unfortunately it
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n       means that if the survival funtion is printed only each two years of age and if
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);       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.
  if(popforecast==1) fprintf(fichtm,"\n    */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    agelim=AGESUP;
  else    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    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);      /* nhstepm age range expressed in number of stepm */
 fprintf(fichtm," <li>Graphs</li><p>");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  m=cptcoveff;      /* if (stepm >= YEARM) hstepm=1;*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  jj1=0;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
  for(k1=1; k1<=m;k1++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
    for(i1=1; i1<=ncodemax[k1];i1++){      gm=matrix(0,nhstepm,1,nlstate*nlstate);
        jj1++;  
        if (cptcovn > 0) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          for (cpt=1; cpt<=cptcoveff;cpt++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);   
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          /* Computing Variances of health expectancies */
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       for(theta=1; theta <=npar; theta++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i=1; i<=npar; i++){ 
        }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 interval) in state (%d): v%s%d%d.gif <br>    
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          cptj=0;
      }        for(j=1; j<= nlstate; j++){
      for(cpt=1; cpt<=nlstate;cpt++) {          for(i=1; i<=nlstate; i++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            cptj=cptj+1;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
      }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
 fprintf(fichtm,"\n</body>");       
    }       
    }        for(i=1; i<=npar; i++) 
 fclose(fichtm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
 /******************* Gnuplot file **************/        cptj=0;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp.txt");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            }
     printf("Problem with file %s",optionfilegnuplot);          }
   }        }
         for(j=1; j<= nlstate*nlstate; j++)
 #ifdef windows          for(h=0; h<=nhstepm-1; h++){
     fprintf(ficgp,"cd \"%s\" \n",pathc);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 #endif          }
 m=pow(2,cptcoveff);       } 
       
  /* 1eme*/  /* End theta */
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
 #ifdef windows       for(h=0; h<=nhstepm-1; h++)
     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);        for(j=1; j<=nlstate*nlstate;j++)
 #endif          for(theta=1; theta <=npar; theta++)
 #ifdef unix            trgradg[h][j][theta]=gradg[h][theta][j];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);       
 #endif  
        for(i=1;i<=nlstate*nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {        for(j=1;j<=nlstate*nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          varhe[i][j][(int)age] =0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for (i=1; i<= nlstate ; i ++) {       for(h=0;h<=nhstepm-1;h++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(k=0;k<=nhstepm-1;k++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(i=1;i<=nlstate*nlstate;i++)
      for (i=1; i<= nlstate ; i ++) {            for(j=1;j<=nlstate*nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      /* Computing expectancies */
 #ifdef unix      for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter gif small size 400,300");        for(j=1; j<=nlstate;j++)
 #endif          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
    }            
   }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   /*2 eme*/  
           }
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      fprintf(ficreseij,"%3.0f",age );
          cptj=0;
     for (i=1; i<= nlstate+1 ; i ++) {      for(i=1; i<=nlstate;i++)
       k=2*i;        for(j=1; j<=nlstate;j++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          cptj++;
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficreseij,"\n");
 }       
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      printf("\n");
       fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(ficlog,"\n");
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    free_vector(xp,1,npar);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 }      free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  }
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }  /************ Variance ******************/
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  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)
   }  {
      /* Variance of health expectancies */
   /*3eme*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   for (k1=1; k1<= m ; k1 ++) {    double **dnewm,**doldm;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double **dnewmp,**doldmp;
       k=2+nlstate*(cpt-1);    int i, j, nhstepm, hstepm, h, nstepm ;
       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);    int k, cptcode;
       for (i=1; i< nlstate ; i ++) {    double *xp;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    double **gp, **gm;  /* for var eij */
       }    double ***gradg, ***trgradg; /*for var eij */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double **gradgp, **trgradgp; /* for var p point j */
     }    double *gpp, *gmp; /* for var p point j */
     }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
   /* CV preval stat */    double age,agelim, hf;
     for (k1=1; k1<= m ; k1 ++) {    double ***mobaverage;
     for (cpt=1; cpt<nlstate ; cpt ++) {    int theta;
       k=3;    char digit[4];
       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);    char digitp[25];
   
       for (i=1; i< nlstate ; i ++)    char fileresprobmorprev[FILENAMELENGTH];
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    if(popbased==1){
            if(mobilav!=0)
       l=3+(nlstate+ndeath)*cpt;        strcpy(digitp,"-populbased-mobilav-");
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      else strcpy(digitp,"-populbased-nomobil-");
       for (i=1; i< nlstate ; i ++) {    }
         l=3+(nlstate+ndeath)*cpt;    else 
         fprintf(ficgp,"+$%d",l+i+1);      strcpy(digitp,"-stablbased-");
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      if (mobilav!=0) {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      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);
   /* proba elementaires */      }
    for(i=1,jk=1; i <=nlstate; i++){    }
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    strcpy(fileresprobmorprev,"prmorprev"); 
         for(j=1; j <=ncovmodel; j++){    sprintf(digit,"%-d",ij);
            /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           jk++;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           fprintf(ficgp,"\n");    strcat(fileresprobmorprev,fileres);
         }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for(jk=1; jk <=m; jk++) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    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);
    i=1;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(k2=1; k2<=nlstate; k2++) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      k3=i;      fprintf(ficresprobmorprev," p.%-d SE",j);
      for(k=1; k<=(nlstate+ndeath); k++) {      for(i=1; i<=nlstate;i++)
        if (k != k2){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    }  
 ij=1;    fprintf(ficresprobmorprev,"\n");
         for(j=3; j <=ncovmodel; j++) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
             ij++;      exit(0);
           }    }
           else    else{
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      fprintf(ficgp,"\n# Routine varevsij");
         }    }
           fprintf(ficgp,")/(1");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
              printf("Problem with html file: %s\n", optionfilehtm);
         for(k1=1; k1 <=nlstate; k1++){        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      exit(0);
 ij=1;    }
           for(j=3; j <=ncovmodel; j++){    else{
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      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");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
             ij++;    }
           }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    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(ficgp,")");    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=nlstate;j++)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    fprintf(ficresvij,"\n");
         i=i+ncovmodel;  
        }    xp=vector(1,npar);
      }    dnewm=matrix(1,nlstate,1,npar);
    }    doldm=matrix(1,nlstate,1,nlstate);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
    }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
   fclose(ficgp);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 }  /* end gnuplot */    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 /*************** Moving average **************/    
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   int i, cpt, cptcod;    }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    else  hstepm=estepm;   
       for (i=1; i<=nlstate;i++)    /* For example we decided to compute the life expectancy with the smallest unit */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           mobaverage[(int)agedeb][i][cptcod]=0.;       nhstepm is the number of hstepm from age to agelim 
           nstepm is the number of stepm from age to agelin. 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){       Look at hpijx to understand the reason of that which relies in memory size
       for (i=1; i<=nlstate;i++){       and note for a fixed period like k years */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           for (cpt=0;cpt<=4;cpt++){       survival function given by stepm (the optimization length). Unfortunately it
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];       means that if the survival funtion is printed every two years of age and if
           }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;       results. So we changed our mind and took the option of the best precision.
         }    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }    agelim = AGESUP;
        for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /************** Forecasting ******************/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 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){      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for(theta=1; theta <=npar; theta++){
   double *popeffectif,*popcount;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   double ***p3mat;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char fileresf[FILENAMELENGTH];        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  agelim=AGESUP;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
         if (popbased==1) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
   strcpy(fileresf,"f");          }else{ /* mobilav */ 
   strcat(fileresf,fileres);            for(i=1; i<=nlstate;i++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {              prlim[i][i]=mobaverage[(int)age][i][ij];
     printf("Problem with forecast resultfile: %s\n", fileresf);          }
   }        }
   printf("Computing forecasting: result on file '%s' \n", fileresf);    
         for(j=1; j<= nlstate; j++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   if (mobilav==1) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
     movingaverage(agedeb, fage, ageminpar, mobaverage);        }
   }        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   stepsize=(int) (stepm+YEARM-1)/YEARM;           as a weighted average of prlim.
   if (stepm<=12) stepsize=1;        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   hstepm=1;        }    
   hstepm=hstepm/stepm;        /* end probability of death */
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   yp2=modf((yp1*12),&yp);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   mprojmean=yp;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   yp1=modf((yp2*30.5),&yp);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   jprojmean=yp;   
   if(jprojmean==0) jprojmean=1;        if (popbased==1) {
   if(mprojmean==0) jprojmean=1;          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   for(cptcov=1;cptcov<=i2;cptcov++){            for(i=1; i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              prlim[i][i]=mobaverage[(int)age][i][ij];
       k=k+1;          }
       fprintf(ficresf,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<= nlstate; j++){
       }          for(h=0; h<=nhstepm; h++){
       fprintf(ficresf,"******\n");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fprintf(ficresf,"# StartingAge FinalAge");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          }
              }
              /* This for computing probability of death (h=1 means
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           computed over hstepm matrices product = hstepm*stepm months) 
         fprintf(ficresf,"\n");           as a weighted average of prlim.
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           nhstepm = nhstepm/hstepm;        }    
                  /* end probability of death */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;        for(j=1; j<= nlstate; j++) /* vareij */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(h=0; h<=nhstepm; h++){
                    gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           for (h=0; h<=nhstepm; h++){          }
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
             }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                    } /* End theta */
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      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];
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                                for(theta=1; theta <=npar; theta++)
               }          trgradgp[j][theta]=gradgp[theta][j];
             }    
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         }      for(i=1;i<=nlstate;i++)
       }        for(j=1;j<=nlstate;j++)
     }          vareij[i][j][(int)age] =0.;
   }  
              for(h=0;h<=nhstepm;h++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   fclose(ficresf);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 }          for(i=1;i<=nlstate;i++)
 /************** Forecasting ******************/            for(j=1;j<=nlstate;j++)
 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){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      }
   int *popage;    
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      /* pptj */
   double *popeffectif,*popcount;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   double ***p3mat,***tabpop,***tabpopprev;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   char filerespop[FILENAMELENGTH];      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          varppt[j][i]=doldmp[j][i];
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* end ppptj */
   agelim=AGESUP;      /*  x centered again */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   
        if (popbased==1) {
          if(mobilav ==0){
   strcpy(filerespop,"pop");          for(i=1; i<=nlstate;i++)
   strcat(filerespop,fileres);            prlim[i][i]=probs[(int)age][i][ij];
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }else{ /* mobilav */ 
     printf("Problem with forecast resultfile: %s\n", filerespop);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=mobaverage[(int)age][i][ij];
   printf("Computing forecasting: result on file '%s' \n", filerespop);        }
       }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;               
       /* This for computing probability of death (h=1 means
   if (mobilav==1) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         as a weighted average of prlim.
     movingaverage(agedeb, fage, ageminpar, mobaverage);      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   stepsize=(int) (stepm+YEARM-1)/YEARM;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   if (stepm<=12) stepsize=1;      }    
        /* end probability of death */
   agelim=AGESUP;  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   hstepm=1;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   hstepm=hstepm/stepm;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   if (popforecast==1) {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     if((ficpop=fopen(popfile,"r"))==NULL) {        }
       printf("Problem with population file : %s\n",popfile);exit(0);      } 
     }      fprintf(ficresprobmorprev,"\n");
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      fprintf(ficresvij,"%.0f ",age );
     popcount=vector(0,AGESUP);      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++){
     i=1;            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }
          fprintf(ficresvij,"\n");
     imx=i;      free_matrix(gp,0,nhstepm,1,nlstate);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      free_matrix(gm,0,nhstepm,1,nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    } /* End age */
       k=k+1;    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fprintf(ficrespop,"\n#******");    free_vector(gmp,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++) {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    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");
       fprintf(ficrespop,"******\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficrespop,"# Age");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
        /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for (cpt=0; cpt<=0;cpt++) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
            fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    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);
           nhstepm = nhstepm/hstepm;    /*  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);
            */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_vector(xp,1,npar);
            free_matrix(doldm,1,nlstate,1,nlstate);
           for (h=0; h<=nhstepm; h++){    free_matrix(dnewm,1,nlstate,1,npar);
             if (h==(int) (calagedate+YEARM*cpt)) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             for(j=1; j<=nlstate+ndeath;j++) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               kk1=0.;kk2=0;    fclose(ficresprobmorprev);
               for(i=1; i<=nlstate;i++) {                  fclose(ficgp);
                 if (mobilav==1)    fclose(fichtm);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  }  
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  /************ 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)
               }  {
               if (h==(int)(calagedate+12*cpt)){    /* Variance of prevalence limit */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   /*fprintf(ficrespop," %.3f", kk1);    double **newm;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    double **dnewm,**doldm;
               }    int i, j, nhstepm, hstepm;
             }    int k, cptcode;
             for(i=1; i<=nlstate;i++){    double *xp;
               kk1=0.;    double *gp, *gm;
                 for(j=1; j<=nlstate;j++){    double **gradg, **trgradg;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double age,agelim;
                 }    int theta;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];     
             }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    for(i=1; i<=nlstate;i++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        fprintf(ficresvpl," %1d-%1d",i,i);
           }    fprintf(ficresvpl,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
   /******/    
     hstepm=1*YEARM; /* Every year of age */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      agelim = AGESUP;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm;      if (stepm >= YEARM) hstepm=1;
                nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gradg=matrix(1,npar,1,nlstate);
           oldm=oldms;savm=savms;      gp=vector(1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        gm=vector(1,nlstate);
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      for(theta=1; theta <=npar; theta++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(i=1; i<=npar; i++){ /* Computes gradient */
             }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               for(i=1; i<=nlstate;i++) {                      for(i=1;i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              gp[i] = prlim[i][i];
               }      
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        for(i=1; i<=npar; i++) /* Computes gradient */
             }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1;i<=nlstate;i++)
         }          gm[i] = prlim[i][i];
       }  
    }        for(i=1;i<=nlstate;i++)
   }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       trgradg =matrix(1,nlstate,1,npar);
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);      for(j=1; j<=nlstate;j++)
     free_vector(popeffectif,0,AGESUP);        for(theta=1; theta <=npar; theta++)
     free_vector(popcount,0,AGESUP);          trgradg[j][theta]=gradg[theta][j];
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1;i<=nlstate;i++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        varpl[i][(int)age] =0.;
   fclose(ficrespop);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
 /***********************************************/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 /**************** Main Program *****************/  
 /***********************************************/      fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
 int main(int argc, char *argv[])        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 {      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      free_vector(gm,1,nlstate);
   double agedeb, agefin,hf;      free_matrix(gradg,1,npar,1,nlstate);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   double fret;  
   double **xi,tmp,delta;    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
   double dum; /* Dummy variable */    free_matrix(dnewm,1,nlstate,1,nlstate);
   double ***p3mat;  
   int *indx;  }
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  /************ Variance of one-step probabilities  ******************/
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  {
      int i, j=0,  i1, k1, l1, t, tj;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   char filerest[FILENAMELENGTH];    int first=1, first1;
   char fileregp[FILENAMELENGTH];    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   char popfile[FILENAMELENGTH];    double **dnewm,**doldm;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double *xp;
   int firstobs=1, lastobs=10;    double *gp, *gm;
   int sdeb, sfin; /* Status at beginning and end */    double **gradg, **trgradg;
   int c,  h , cpt,l;    double **mu;
   int ju,jl, mi;    double age,agelim, cov[NCOVMAX];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int theta;
   int mobilav=0,popforecast=0;    char fileresprob[FILENAMELENGTH];
   int hstepm, nhstepm;    char fileresprobcov[FILENAMELENGTH];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    char fileresprobcor[FILENAMELENGTH];
   
   double bage, fage, age, agelim, agebase;    double ***varpij;
   double ftolpl=FTOL;  
   double **prlim;    strcpy(fileresprob,"prob"); 
   double *severity;    strcat(fileresprob,fileres);
   double ***param; /* Matrix of parameters */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   double  *p;      printf("Problem with resultfile: %s\n", fileresprob);
   double **matcov; /* Matrix of covariance */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   double ***delti3; /* Scale */    }
   double *delti; /* Scale */    strcpy(fileresprobcov,"probcov"); 
   double ***eij, ***vareij;    strcat(fileresprobcov,fileres);
   double **varpl; /* Variances of prevalence limits by age */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   double *epj, vepp;      printf("Problem with resultfile: %s\n", fileresprobcov);
   double kk1, kk2;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    }
      strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   char *alph[]={"a","a","b","c","d","e"}, str[4];      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   char z[1]="c", occ;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 #include <sys/time.h>    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 #include <time.h>    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    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);
   /* long total_usecs;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   struct timeval start_time, end_time;    
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficresprob,"# Age");
   getcwd(pathcd, size);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
   printf("\n%s",version);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if(argc <=1){    fprintf(ficresprobcov,"# Age");
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);  
   }    for(i=1; i<=nlstate;i++)
   else{      for(j=1; j<=(nlstate+ndeath);j++){
     strcpy(pathtot,argv[1]);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   /*cygwin_split_path(pathtot,path,optionfile);      }  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/   /* fprintf(ficresprob,"\n");
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);   */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   xp=vector(1,npar);
   chdir(path);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   replace(pathc,path);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
 /*-------- arguments in the command line --------*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
   strcpy(fileres,"r");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   strcat(fileres, optionfilefiname);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   strcat(fileres,".txt");    /* Other files have txt extension */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
   /*---------arguments file --------*/    }
     else{
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      fprintf(ficgp,"\n# Routine varprob");
     printf("Problem with optionfile %s\n",optionfile);    }
     goto end;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   strcpy(filereso,"o");      exit(0);
   strcat(filereso,fileres);    }
   if((ficparo=fopen(filereso,"w"))==NULL) {    else{
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   }      fprintf(fichtm,"\n");
   
   /* Reads comments: lines beginning with '#' */      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   while((c=getc(ficpar))=='#' && c!= EOF){      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");
     ungetc(c,ficpar);      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");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    }
     fputs(line,ficparo);  
   }    cov[1]=1;
   ungetc(c,ficpar);    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    j1=0;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);    for(t=1; t<=tj;t++){
   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);      for(i1=1; i1<=ncodemax[t];i1++){ 
 while((c=getc(ficpar))=='#' && c!= EOF){        j1++;
     ungetc(c,ficpar);        if  (cptcovn>0) {
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprob, "\n#********** Variable "); 
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcov, "**********\n#\n");
              
   covar=matrix(0,NCOVMAX,1,n);          fprintf(ficgp, "\n#********** Variable "); 
   cptcovn=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          fprintf(ficgp, "**********\n#\n");
           
   ncovmodel=2+cptcovn;          
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Read guess parameters */          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcor, "\n#********** Variable ");    
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor, "**********\n#");    
     puts(line);        }
     fputs(line,ficparo);        
   }        for (age=bage; age<=fage; age ++){ 
   ungetc(c,ficpar);          cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     for(i=1; i <=nlstate; i++)          }
     for(j=1; j <=nlstate+ndeath-1; j++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for (k=1; k<=cptcovprod;k++)
       fprintf(ficparo,"%1d%1d",i1,j1);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("%1d%1d",i,j);          
       for(k=1; k<=ncovmodel;k++){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         fscanf(ficpar," %lf",&param[i][j][k]);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         printf(" %lf",param[i][j][k]);          gp=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficparo," %lf",param[i][j][k]);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       }      
       fscanf(ficpar,"\n");          for(theta=1; theta <=npar; theta++){
       printf("\n");            for(i=1; i<=npar; i++)
       fprintf(ficparo,"\n");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     }            
              pmij(pmmij,cov,ncovmodel,xp,nlstate);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            
             k=0;
   p=param[1][1];            for(i=1; i<= (nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
   /* Reads comments: lines beginning with '#' */                k=k+1;
   while((c=getc(ficpar))=='#' && c!= EOF){                gp[k]=pmmij[i][j];
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);            }
     puts(line);            
     fputs(line,ficparo);            for(i=1; i<=npar; i++)
   }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   ungetc(c,ficpar);      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            k=0;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            for(i=1; i<=(nlstate); i++){
   for(i=1; i <=nlstate; i++){              for(j=1; j<=(nlstate+ndeath);j++){
     for(j=1; j <=nlstate+ndeath-1; j++){                k=k+1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);                gm[k]=pmmij[i][j];
       printf("%1d%1d",i,j);              }
       fprintf(ficparo,"%1d%1d",i1,j1);            }
       for(k=1; k<=ncovmodel;k++){       
         fscanf(ficpar,"%le",&delti3[i][j][k]);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         printf(" %le",delti3[i][j][k]);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         fprintf(ficparo," %le",delti3[i][j][k]);          }
       }  
       fscanf(ficpar,"\n");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       printf("\n");            for(theta=1; theta <=npar; theta++)
       fprintf(ficparo,"\n");              trgradg[j][theta]=gradg[theta][j];
     }          
   }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   delti=delti3[1][1];          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   /* Reads comments: lines beginning with '#' */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     ungetc(c,ficpar);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     fputs(line,ficparo);          
   }          k=0;
   ungetc(c,ficpar);          for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
   matcov=matrix(1,npar,1,npar);              k=k+1;
   for(i=1; i <=npar; i++){              mu[k][(int) age]=pmmij[i][j];
     fscanf(ficpar,"%s",&str);            }
     printf("%s",str);          }
     fprintf(ficparo,"%s",str);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     for(j=1; j <=i; j++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fscanf(ficpar," %le",&matcov[i][j]);              varpij[i][j][(int)age] = doldm[i][j];
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);          /*printf("\n%d ",(int)age);
     }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fscanf(ficpar,"\n");            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     printf("\n");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fprintf(ficparo,"\n");            }*/
   }  
   for(i=1; i <=npar; i++)          fprintf(ficresprob,"\n%d ",(int)age);
     for(j=i+1;j<=npar;j++)          fprintf(ficresprobcov,"\n%d ",(int)age);
       matcov[i][j]=matcov[j][i];          fprintf(ficresprobcor,"\n%d ",(int)age);
      
   printf("\n");          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++){
     /*-------- Rewriting paramater file ----------*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
      strcpy(rfileres,"r");    /* "Rparameterfile */            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          }
      strcat(rfileres,".");    /* */          i=0;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          for (k=1; k<=(nlstate);k++){
     if((ficres =fopen(rfileres,"w"))==NULL) {            for (l=1; l<=(nlstate+ndeath);l++){ 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;              i=i++;
     }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     fprintf(ficres,"#%s\n",version);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                  for (j=1; j<=i;j++){
     /*-------- data file ----------*/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     if((fic=fopen(datafile,"r"))==NULL)    {                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       printf("Problem with datafile: %s\n", datafile);goto end;              }
     }            }
           }/* end of loop for state */
     n= lastobs;        } /* end of loop for age */
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);        /* Confidence intervalle of pij  */
     num=ivector(1,n);        /*
     moisnais=vector(1,n);          fprintf(ficgp,"\nset noparametric;unset label");
     annais=vector(1,n);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     moisdc=vector(1,n);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     andc=vector(1,n);          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);
     agedc=vector(1,n);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     cod=ivector(1,n);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     weight=vector(1,n);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     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);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     s=imatrix(1,maxwav+1,1,n);        first1=1;
     adl=imatrix(1,maxwav+1,1,n);            for (k2=1; k2<=(nlstate);k2++){
     tab=ivector(1,NCOVMAX);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     ncodemax=ivector(1,8);            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
     i=1;            for (k1=1; k1<=(nlstate);k1++){
     while (fgets(line, MAXLINE, fic) != NULL)    {              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       if ((i >= firstobs) && (i <=lastobs)) {                if(l1==k1) continue;
                        i=(k1-1)*(nlstate+ndeath)+l1;
         for (j=maxwav;j>=1;j--){                if(i<=j) continue;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                for (age=bage; age<=fage; age ++){ 
           strcpy(line,stra);                  if ((int)age %5==0){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                            mu1=mu[i][(int) age]/stepm*YEARM ;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    mu2=mu[j][(int) age]/stepm*YEARM;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         for (j=ncovcol;j>=1;j--){                    /*v21=sqrt(1.-v11*v11); *//* error */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    v21=(lc1-v1)/cv12*v11;
         }                    v12=-v21;
         num[i]=atol(stra);                    v22=v11;
                            tnalp=v21/v11;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    if(first1==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])); ij=ij+1;}*/                      first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         i=i+1;                    }
       }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     }                    /*printf(fignu*/
     /* printf("ii=%d", ij);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
        scanf("%d",i);*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   imx=i-1; /* Number of individuals */                    if(first==1){
                       first=0;
   /* for (i=1; i<=imx; i++){                      fprintf(ficgp,"\nset parametric;unset label");
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                      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);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                      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);
   /* for (i=1; i<=imx; i++){                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
      if (s[4][i]==9)  s[4][i]=-1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
      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]));}                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   */                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   /* Calculation of the number of parameter from char model*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   Tvar=ivector(1,15);                    }else{
   Tprod=ivector(1,15);                      first=0;
   Tvaraff=ivector(1,15);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   Tvard=imatrix(1,15,1,2);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   Tage=ivector(1,15);                            fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                          fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   if (strlen(model) >1){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     j=0, j1=0, k1=1, k2=1;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     j=nbocc(model,'+');                    }/* if first */
     j1=nbocc(model,'*');                  } /* age mod 5 */
     cptcovn=j+1;                } /* end loop age */
     cptcovprod=j1;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                    first=1;
     strcpy(modelsav,model);              } /*l12 */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            } /* k12 */
       printf("Error. Non available option model=%s ",model);          } /*l1 */
       goto end;        }/* k1 */
     }      } /* loop covariates */
        }
     for(i=(j+1); i>=1;i--){    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       cutv(stra,strb,modelsav,'+');    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    free_vector(xp,1,npar);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    fclose(ficresprob);
       /*scanf("%d",i);*/    fclose(ficresprobcov);
       if (strchr(strb,'*')) {    fclose(ficresprobcor);
         cutv(strd,strc,strb,'*');    fclose(ficgp);
         if (strcmp(strc,"age")==0) {    fclose(fichtm);
           cptcovprod--;  }
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);  
           cptcovage++;  /******************* Printing html file ***********/
             Tage[cptcovage]=i;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             /*printf("stre=%s ", stre);*/                    int lastpass, int stepm, int weightopt, char model[],\
         }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         else if (strcmp(strd,"age")==0) {                    int popforecast, int estepm ,\
           cptcovprod--;                    double jprev1, double mprev1,double anprev1, \
           cutv(strb,stre,strc,'V');                    double jprev2, double mprev2,double anprev2){
           Tvar[i]=atoi(stre);    int jj1, k1, i1, cpt;
           cptcovage++;    /*char optionfilehtm[FILENAMELENGTH];*/
           Tage[cptcovage]=i;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
         }      printf("Problem with %s \n",optionfilehtm), exit(0);
         else {      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V');     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
           Tprod[k1]=i;   - 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
           Tvard[k1][1]=atoi(strc);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
           Tvard[k1][2]=atoi(stre);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
           Tvar[cptcovn+k2]=Tvard[k1][1];   - Life expectancies by age and initial health status (estepm=%2d months): 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     <a href=\"e%s\">e%s</a> <br>\n</li>", \
           for (k=1; k<=lastobs;k++)    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           k2=k2+2;  
         }   m=cptcoveff;
       }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/   jj1=0;
        /*  scanf("%d",i);*/   for(k1=1; k1<=m;k1++){
       cutv(strd,strc,strb,'V');     for(i1=1; i1<=ncodemax[k1];i1++){
       Tvar[i]=atoi(strc);       jj1++;
       }       if (cptcovn > 0) {
       strcpy(modelsav,stra);           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);         for (cpt=1; cpt<=cptcoveff;cpt++) 
         scanf("%d",i);*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 }       }
         /* Pij */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);       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>
   printf("cptcovprod=%d ", cptcovprod);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   scanf("%d ",i);*/       /* Quasi-incidences */
     fclose(fic);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     /*  if(mle==1){*/         /* Stable prevalence in each health state */
     if (weightopt != 1) { /* Maximisation without weights*/         for(cpt=1; cpt<nlstate;cpt++){
       for(i=1;i<=n;i++) weight[i]=1.0;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
     }  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     /*-calculation of age at interview from date of interview and age at death -*/         }
     agev=matrix(1,maxwav,1,imx);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     for (i=1; i<=imx; i++) {  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       for(m=2; (m<= maxwav); m++) {       }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       fprintf(fichtm,"\n<br>- Total life expectancy by age and
          anint[m][i]=9999;  health expectancies in states (1) and (2): e%s%d.png<br>
          s[m][i]=-1;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
        }     } /* end i1 */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;   }/* End k1 */
       }   fprintf(fichtm,"</ul>");
     }  
   
     for (i=1; i<=imx; i++)  {   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
       for(m=1; (m<= maxwav); m++){   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
         if(s[m][i] >0){   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
           if (s[m][i] >= nlstate+1) {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
             if(agedc[i]>0)   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
               if(moisdc[i]!=99 && andc[i]!=9999)   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
                 agev[m][i]=agedc[i];   - 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);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {  /*  if(popforecast==1) fprintf(fichtm,"\n */
               if (andc[i]!=9999){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
               agev[m][i]=-1;  /*      <br>",fileres,fileres,fileres,fileres); */
               }  /*  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); */
           }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   m=cptcoveff;
             if(mint[m][i]==99 || anint[m][i]==9999)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){   jj1=0;
               agemin=agev[m][i];   for(k1=1; k1<=m;k1++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/     for(i1=1; i1<=ncodemax[k1];i1++){
             }       jj1++;
             else if(agev[m][i] >agemax){       if (cptcovn > 0) {
               agemax=agev[m][i];         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
             }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             /*agev[m][i]=anint[m][i]-annais[i];*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             /*   agev[m][i] = age[i]+2*m;*/       }
           }       for(cpt=1; cpt<=nlstate;cpt++) {
           else { /* =9 */         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
             agev[m][i]=1;  interval) in state (%d): v%s%d%d.png <br>
             s[m][i]=-1;  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           }       }
         }     } /* end i1 */
         else /*= 0 Unknown */   }/* End k1 */
           agev[m][i]=1;   fprintf(fichtm,"</ul>");
       }  fclose(fichtm);
      }
     }  
     for (i=1; i<=imx; i++)  {  /******************* Gnuplot file **************/
       for(m=1; (m<= maxwav); m++){  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");      int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           goto end;    int ng;
         }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       }      printf("Problem with file %s",optionfilegnuplot);
     }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
     /*#ifdef windows */
     free_vector(severity,1,maxwav);      fprintf(ficgp,"cd \"%s\" \n",pathc);
     free_imatrix(outcome,1,maxwav+1,1,n);      /*#endif */
     free_vector(moisnais,1,n);  m=pow(2,cptcoveff);
     free_vector(annais,1,n);    
     /* free_matrix(mint,1,maxwav,1,n);   /* 1eme*/
        free_matrix(anint,1,maxwav,1,n);*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
     free_vector(moisdc,1,n);     for (k1=1; k1<= m ; k1 ++) {
     free_vector(andc,1,n);       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);
      
     wav=ivector(1,imx);       for (i=1; i<= nlstate ; i ++) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }
     /* Concatenates waves */       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);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
       Tcode=ivector(1,100);       } 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
       ncodemax[1]=1;       for (i=1; i<= nlstate ; i ++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
               else fprintf(ficgp," \%%*lf (\%%*lf)");
    codtab=imatrix(1,100,1,10);       }  
    h=0;       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
    m=pow(2,cptcoveff);     }
      }
    for(k=1;k<=cptcoveff; k++){    /*2 eme*/
      for(i=1; i <=(m/pow(2,k));i++){    
        for(j=1; j <= ncodemax[k]; j++){    for (k1=1; k1<= m ; k1 ++) { 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
            h++;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
            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]);*/      for (i=1; i<= nlstate+1 ; i ++) {
          }        k=2*i;
        }        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)");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       codtab[1][2]=1;codtab[2][2]=2; */        }   
    /* for(i=1; i <=m ;i++){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       for(k=1; k <=cptcovn; k++){        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        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 ++) {
       printf("\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
       scanf("%d",i);*/        }   
            fprintf(ficgp,"\" t\"\" w l 0,");
    /* Calculates basic frequencies. Computes observed prevalence at single age        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
        and prints on file fileres'p'. */        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        else fprintf(ficgp,"\" t\"\" w l 0,");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
          /*3eme*/
     /* For Powell, parameters are in a vector p[] starting at p[1]    
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    for (k1=1; k1<= m ; k1 ++) { 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
     if(mle==1){        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     /*--------- results files --------------*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    jk=1;          
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for (i=1; i< nlstate ; i ++) {
    for(i=1,jk=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);
      for(k=1; k <=(nlstate+ndeath); k++){          
        if (k != i)        } 
          {      }
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    
            for(j=1; j <=ncovmodel; j++){    /* CV preval stable (period) */
              printf("%f ",p[jk]);    for (k1=1; k1<= m ; k1 ++) { 
              fprintf(ficres,"%f ",p[jk]);      for (cpt=1; cpt<=nlstate ; cpt ++) {
              jk++;        k=3;
            }        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
            printf("\n");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
            fprintf(ficres,"\n");        
          }        for (i=1; i<= nlstate ; i ++)
      }          fprintf(ficgp,"+$%d",k+i+1);
    }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
  if(mle==1){        
     /* Computing hessian and covariance matrix */        l=3+(nlstate+ndeath)*cpt;
     ftolhess=ftol; /* Usually correct */        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     hesscov(matcov, p, npar, delti, ftolhess, func);        for (i=1; i< nlstate ; i ++) {
  }          l=3+(nlstate+ndeath)*cpt;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          fprintf(ficgp,"+$%d",l+i+1);
     printf("# Scales (for hessian or gradient estimation)\n");        }
      for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       for(j=1; j <=nlstate+ndeath; j++){      } 
         if (j!=i) {    }  
           fprintf(ficres,"%1d%1d",i,j);    
           printf("%1d%1d",i,j);    /* proba elementaires */
           for(k=1; k<=ncovmodel;k++){    for(i=1,jk=1; i <=nlstate; i++){
             printf(" %.5e",delti[jk]);      for(k=1; k <=(nlstate+ndeath); k++){
             fprintf(ficres," %.5e",delti[jk]);        if (k != i) {
             jk++;          for(j=1; j <=ncovmodel; j++){
           }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           printf("\n");            jk++; 
           fprintf(ficres,"\n");            fprintf(ficgp,"\n");
         }          }
       }        }
      }      }
         }
     k=1;  
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     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(jk=1; jk <=m; jk++) {
     for(i=1;i<=npar;i++){         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       /*  if (k>nlstate) k=1;         if (ng==2)
       i1=(i-1)/(ncovmodel*nlstate)+1;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);         else
       printf("%s%d%d",alph[k],i1,tab[i]);*/           fprintf(ficgp,"\nset title \"Probability\"\n");
       fprintf(ficres,"%3d",i);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
       printf("%3d",i);         i=1;
       for(j=1; j<=i;j++){         for(k2=1; k2<=nlstate; k2++) {
         fprintf(ficres," %.5e",matcov[i][j]);           k3=i;
         printf(" %.5e",matcov[i][j]);           for(k=1; k<=(nlstate+ndeath); k++) {
       }             if (k != k2){
       fprintf(ficres,"\n");               if(ng==2)
       printf("\n");                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       k++;               else
     }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   ij=1;
     while((c=getc(ficpar))=='#' && c!= EOF){               for(j=3; j <=ncovmodel; j++) {
       ungetc(c,ficpar);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       fgets(line, MAXLINE, ficpar);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       puts(line);                   ij++;
       fputs(line,ficparo);                 }
     }                 else
     ungetc(c,ficpar);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     estepm=0;               }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);               fprintf(ficgp,")/(1");
     if (estepm==0 || estepm < stepm) estepm=stepm;               
     if (fage <= 2) {               for(k1=1; k1 <=nlstate; k1++){   
       bage = ageminpar;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       fage = agemaxpar;                 ij=1;
     }                 for(j=3; j <=ncovmodel; j++){
                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                     ij++;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                   }
                     else
     while((c=getc(ficpar))=='#' && c!= EOF){                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     ungetc(c,ficpar);                 }
     fgets(line, MAXLINE, ficpar);                 fprintf(ficgp,")");
     puts(line);               }
     fputs(line,ficparo);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   ungetc(c,ficpar);               i=i+ncovmodel;
               }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);           } /* end k */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         } /* end k2 */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       } /* end jk */
           } /* end ng */
   while((c=getc(ficpar))=='#' && c!= EOF){     fclose(ficgp); 
     ungetc(c,ficpar);  }  /* end gnuplot */
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  /*************** Moving average **************/
   }  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   ungetc(c,ficpar);  
      int i, cpt, cptcod;
     int modcovmax =1;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    int mobilavrange, mob;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    double age;
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   fprintf(ficparo,"pop_based=%d\n",popbased);                               a covariate has 2 modalities */
   fprintf(ficres,"pop_based=%d\n",popbased);      if (cptcovn<1) modcovmax=1; /* At least 1 pass */
    
   while((c=getc(ficpar))=='#' && c!= EOF){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     ungetc(c,ficpar);      if(mobilav==1) mobilavrange=5; /* default */
     fgets(line, MAXLINE, ficpar);      else mobilavrange=mobilav;
     puts(line);      for (age=bage; age<=fage; age++)
     fputs(line,ficparo);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   ungetc(c,ficpar);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
   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);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
 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);         we use a 5 terms etc. until the borders are no more concerned. 
 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);      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
 while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<=nlstate;i++){
     ungetc(c,ficpar);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     fgets(line, MAXLINE, ficpar);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     puts(line);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     fputs(line,ficparo);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   ungetc(c,ficpar);                }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   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);        }/* end age */
       }/* end mob */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    }else return -1;
     return 0;
 /*------------ gnuplot -------------*/  }/* End movingaverage */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  
    
 /*------------ free_vector  -------------*/  /************** Forecasting ******************/
  chdir(path);  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){
      /* proj1, year, month, day of starting projection 
  free_ivector(wav,1,imx);       agemin, agemax range of age
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       dateprev1 dateprev2 range of dates during which prevalence is computed
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         anproj2 year of en of projection (same day and month as proj1).
  free_ivector(num,1,n);    */
  free_vector(agedc,1,n);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    int *popage;
  fclose(ficparo);    double agec; /* generic age */
  fclose(ficres);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
 /*--------- index.htm --------*/    double ***p3mat;
     double ***mobaverage;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    char fileresf[FILENAMELENGTH];
   
      agelim=AGESUP;
   /*--------------- Prevalence limit --------------*/    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
   strcpy(filerespl,"pl");    strcpy(fileresf,"f"); 
   strcat(filerespl,fileres);    strcat(fileresf,fileres);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      printf("Problem with forecast resultfile: %s\n", fileresf);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    }
   fprintf(ficrespl,"#Prevalence limit\n");    printf("Computing forecasting: result on file '%s' \n", fileresf);
   fprintf(ficrespl,"#Age ");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
   prlim=matrix(1,nlstate,1,nlstate);    if (mobilav!=0) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      }
   k=0;    }
   agebase=ageminpar;  
   agelim=agemaxpar;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   ftolpl=1.e-10;    if (stepm<=12) stepsize=1;
   i1=cptcoveff;    if(estepm < stepm){
   if (cptcovn < 1){i1=1;}      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   for(cptcov=1;cptcov<=i1;cptcov++){    else  hstepm=estepm;   
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    hstepm=hstepm/stepm; 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
         fprintf(ficrespl,"\n#******");                                 fractional in yp1 */
         for(j=1;j<=cptcoveff;j++)    anprojmean=yp;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    yp2=modf((yp1*12),&yp);
         fprintf(ficrespl,"******\n");    mprojmean=yp;
            yp1=modf((yp2*30.5),&yp);
         for (age=agebase; age<=agelim; age++){    jprojmean=yp;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if(jprojmean==0) jprojmean=1;
           fprintf(ficrespl,"%.0f",age );    if(mprojmean==0) jprojmean=1;
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);    i1=cptcoveff;
           fprintf(ficrespl,"\n");    if (cptcovn < 1){i1=1;}
         }    
       }    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     }    
   fclose(ficrespl);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*------------- h Pij x at various ages ------------*/  /*            if (h==(int)(YEARM*yearp)){ */
      for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        k=k+1;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficresf,"\n#******");
   }        for(j=1;j<=cptcoveff;j++) {
   printf("Computing pij: result on file '%s' \n", filerespij);          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]]);
          }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficresf,"******\n");
   /*if (stepm<=24) stepsize=2;*/        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
   agelim=AGESUP;          for(i=1; i<=nlstate;i++)              
   hstepm=stepsize*YEARM; /* Every year of age */            fprintf(ficresf," p%d%d",i,j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          fprintf(ficresf," p.%d",j);
          }
   k=0;        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresf,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         for(j=1;j<=cptcoveff;j++)            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm = nhstepm/hstepm; 
         fprintf(ficrespij,"******\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    oldm=oldms;savm=savms;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (h=0; h<=nhstepm; h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if (h*hstepm/YEARM*stepm ==yearp) {
           oldm=oldms;savm=savms;                fprintf(ficresf,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"# Age");                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             for(j=1; j<=nlstate+ndeath;j++)              } 
               fprintf(ficrespij," %1d-%1d",i,j);              for(j=1; j<=nlstate+ndeath;j++) {
           fprintf(ficrespij,"\n");                ppij=0.;
           for (h=0; h<=nhstepm; h++){                for(i=1; i<=nlstate;i++) {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                  if (mobilav==1) 
             for(i=1; i<=nlstate;i++)                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
               for(j=1; j<=nlstate+ndeath;j++)                  else {
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
             fprintf(ficrespij,"\n");                  }
           }                  if (h*hstepm/YEARM*stepm== yearp) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
           fprintf(ficrespij,"\n");                  }
         }                } /* end i */
     }                if (h*hstepm/YEARM*stepm==yearp) {
   }                  fprintf(ficresf," %.3f", ppij);
                 }
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/              }/* end j */
             } /* end h */
   fclose(ficrespij);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
   /*---------- Forecasting ------------------*/      } /* end cptcod */
   if((stepm == 1) && (strcmp(model,".")==0)){    } /* end  cptcov */
     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);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    fclose(ficresf);
     free_vector(weight,1,n);}  }
   else{  
     erreur=108;  /************** Forecasting *****not tested NB*************/
     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);  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;
     int *popage;
   /*---------- Health expectancies and variances ------------*/    double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
   strcpy(filerest,"t");    double ***p3mat,***tabpop,***tabpopprev;
   strcat(filerest,fileres);    double ***mobaverage;
   if((ficrest=fopen(filerest,"w"))==NULL) {    char filerespop[FILENAMELENGTH];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   strcpy(filerese,"e");    
   strcat(filerese,fileres);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    
   }    strcpy(filerespop,"pop"); 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
  strcpy(fileresv,"v");      printf("Problem with forecast resultfile: %s\n", filerespop);
   strcat(fileresv,fileres);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    if (mobilav!=0) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       k=k+1;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       fprintf(ficrest,"\n#****** ");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       for(j=1;j<=cptcoveff;j++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
       fprintf(ficrest,"******\n");    }
   
       fprintf(ficreseij,"\n#****** ");    stepsize=(int) (stepm+YEARM-1)/YEARM;
       for(j=1;j<=cptcoveff;j++)    if (stepm<=12) stepsize=1;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    agelim=AGESUP;
     
       fprintf(ficresvij,"\n#****** ");    hstepm=1;
       for(j=1;j<=cptcoveff;j++)    hstepm=hstepm/stepm; 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvij,"******\n");    if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        printf("Problem with population file : %s\n",popfile);exit(0);
       oldm=oldms;savm=savms;        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);        } 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      popage=ivector(0,AGESUP);
       oldm=oldms;savm=savms;      popeffectif=vector(0,AGESUP);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      popcount=vector(0,AGESUP);
          
       i=1;   
        while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      imx=i;
       fprintf(ficrest,"\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         if (popbased==1) {        k=k+1;
           for(i=1; i<=nlstate;i++)        fprintf(ficrespop,"\n#******");
             prlim[i][i]=probs[(int)age][i][k];        for(j=1;j<=cptcoveff;j++) {
         }          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                }
         fprintf(ficrest," %4.0f",age);        fprintf(ficrespop,"******\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        fprintf(ficrespop,"# Age");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        if (popforecast==1)  fprintf(ficrespop," [Population]");
           }        
           epj[nlstate+1] +=epj[j];        for (cpt=0; cpt<=0;cpt++) { 
         }          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         for(i=1, vepp=0.;i <=nlstate;i++)          
           for(j=1;j <=nlstate;j++)          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             vepp += vareij[i][j][(int)age];            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));            nhstepm = nhstepm/hstepm; 
         for(j=1;j <=nlstate;j++){            
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }            oldm=oldms;savm=savms;
         fprintf(ficrest,"\n");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       }          
     }            for (h=0; h<=nhstepm; h++){
   }              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   fclose(ficreseij);              } 
   fclose(ficresvij);              for(j=1; j<=nlstate+ndeath;j++) {
   fclose(ficrest);                kk1=0.;kk2=0;
   fclose(ficpar);                for(i=1; i<=nlstate;i++) {              
   free_vector(epj,1,nlstate+1);                  if (mobilav==1) 
                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   /*------- Variance limit prevalence------*/                    else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   strcpy(fileresvpl,"vpl");                  }
   strcat(fileresvpl,fileres);                }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                if (h==(int)(calagedatem+12*cpt)){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     exit(0);                    /*fprintf(ficrespop," %.3f", kk1);
   }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                }
               }
   k=0;              for(i=1; i<=nlstate;i++){
   for(cptcov=1;cptcov<=i1;cptcov++){                kk1=0.;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  for(j=1; j<=nlstate;j++){
       k=k+1;                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
       fprintf(ficresvpl,"\n#****** ");                  }
       for(j=1;j<=cptcoveff;j++)                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
       fprintf(ficresvpl,"******\n");  
                    if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
       oldm=oldms;savm=savms;            }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }          }
  }        }
    
   fclose(ficresvpl);    /******/
   
   /*---------- End : free ----------------*/        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            nhstepm = nhstepm/hstepm; 
              
              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            oldm=oldms;savm=savms;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            for (h=0; h<=nhstepm; h++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);              if (h==(int) (calagedatem+YEARM*cpt)) {
                  fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   free_matrix(matcov,1,npar,1,npar);              } 
   free_vector(delti,1,npar);              for(j=1; j<=nlstate+ndeath;j++) {
   free_matrix(agev,1,maxwav,1,imx);                kk1=0.;kk2=0;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   if(erreur >0)                }
     printf("End of Imach with error or warning %d\n",erreur);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   else   printf("End of Imach\n");              }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* 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:    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #ifdef windows  
   /* chdir(pathcd);*/    if (popforecast==1) {
 #endif      free_ivector(popage,0,AGESUP);
  /*system("wgnuplot graph.plt");*/      free_vector(popeffectif,0,AGESUP);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      free_vector(popcount,0,AGESUP);
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  strcpy(plotcmd,GNUPLOTPROGRAM);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  strcat(plotcmd," ");    fclose(ficrespop);
  strcat(plotcmd,optionfilegnuplot);  }
  system(plotcmd);  
   /***********************************************/
 #ifdef windows  /**************** Main Program *****************/
   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: ");  int main(int argc, char *argv[])
     scanf("%s",z);  {
     if (z[0] == 'c') system("./imach");    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     else if (z[0] == 'e') system(optionfilehtm);    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     else if (z[0] == 'g') system(plotcmd);    double agedeb, agefin,hf;
     else if (z[0] == 'q') exit(0);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   }  
 #endif    double fret;
 }    double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* 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);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* 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 (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           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((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)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((int)mint[m][i]==99 || (int)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
   Youngest age at first (selected) pass %.2f, oldest age %.2f<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,agemin,agemax,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 graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#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.1.37  
changed lines
  Added in v.1.78

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