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version 1.49, 2002/06/20 14:03:39 version 1.80, 2003/06/05 15:34:14
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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
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "gnuplot"    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()
 #ifdef windows     movingaverage()
 #define DIRSEPARATOR '\\'    varevsij() 
 #else    if popbased==1 varevsij(,popbased)
 #define DIRSEPARATOR '/'    total life expectancies
 #endif    Variance of stable prevalence
    end
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";  */
 int erreur; /* Error number */  
 int nvar;  
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;   
 int nlstate=2; /* Number of live states */  #include <math.h>
 int ndeath=1; /* Number of dead states */  #include <stdio.h>
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #include <stdlib.h>
 int popbased=0;  #include <unistd.h>
   
 int *wav; /* Number of waves for this individuual 0 is possible */  #define MAXLINE 256
 int maxwav; /* Maxim number of waves */  #define GNUPLOTPROGRAM "gnuplot"
 int jmin, jmax; /* min, max spacing between 2 waves */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int mle, weightopt;  #define FILENAMELENGTH 80
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  /*#define DEBUG*/
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define windows
 double jmean; /* Mean space between 2 waves */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;  #define NINTERVMAX 8
 char filerese[FILENAMELENGTH];  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 FILE  *ficresvij;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 char fileresv[FILENAMELENGTH];  #define NCOVMAX 8 /* Maximum number of covariates */
 FILE  *ficresvpl;  #define MAXN 20000
 char fileresvpl[FILENAMELENGTH];  #define YEARM 12. /* Number of months per year */
 char title[MAXLINE];  #define AGESUP 130
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #define AGEBASE 40
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #ifdef windows
   #define DIRSEPARATOR '\\'
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  #define ODIRSEPARATOR '/'
   #else
 char filerest[FILENAMELENGTH];  #define DIRSEPARATOR '/'
 char fileregp[FILENAMELENGTH];  #define ODIRSEPARATOR '\\'
 char popfile[FILENAMELENGTH];  #endif
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  /* $Id$ */
   /* $Log$
 #define NR_END 1   * Revision 1.80  2003/06/05 15:34:14  brouard
 #define FREE_ARG char*   * Trying to add the true revision is the program and log
 #define FTOL 1.0e-10   *
   /* Revision 1.79  2003/06/05 15:17:23  brouard
 #define NRANSI  /* *** empty log message ***
 #define ITMAX 200  /* */
   /* $Revision$ */
 #define TOL 2.0e-4  /* $Date$ */
   /* $State$ */
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  int erreur; /* Error number */
   int nvar;
 #define GOLD 1.618034  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define GLIMIT 100.0  int npar=NPARMAX;
 #define TINY 1.0e-20  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 static double maxarg1,maxarg2;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int popbased=0;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
    int *wav; /* Number of waves for this individuual 0 is possible */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int maxwav; /* Maxim number of waves */
 #define rint(a) floor(a+0.5)  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 static double sqrarg;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int imx;  double jmean; /* Mean space between 2 waves */
 int stepm;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 /* Stepm, step in month: minimum step interpolation*/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int estepm;  FILE *ficlog, *ficrespow;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 int m,nb;  FILE *fichtm; /* Html File */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE *ficreseij;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  char filerese[FILENAMELENGTH];
 double **pmmij, ***probs, ***mobaverage;  FILE  *ficresvij;
 double dateintmean=0;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 double *weight;  char fileresvpl[FILENAMELENGTH];
 int **s; /* Status */  char title[MAXLINE];
 double *agedc, **covar, idx;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /**************** split *************************/  char fileregp[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char popfile[FILENAMELENGTH];
 {  
    char *s;                             /* pointer */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  
   #define NR_END 1
    l1 = strlen( path );                 /* length of path */  #define FREE_ARG char*
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FTOL 1.0e-10
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */  #define NRANSI 
 #if     defined(__bsd__)                /* get current working directory */  #define ITMAX 200 
       extern char       *getwd( );  
   #define TOL 2.0e-4 
       if ( getwd( dirc ) == NULL ) {  
 #else  #define CGOLD 0.3819660 
       extern char       *getcwd( );  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  #define GOLD 1.618034 
          return( GLOCK_ERROR_GETCWD );  #define GLIMIT 100.0 
       }  #define TINY 1.0e-20 
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  static double maxarg1,maxarg2;
       s++;                              /* after this, the filename */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       l2 = strlen( s );                 /* length of filename */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    
       strcpy( name, s );                /* save file name */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define rint(a) floor(a+0.5)
       dirc[l1-l2] = 0;                  /* add zero */  
    }  static double sqrarg;
    l1 = strlen( dirc );                 /* length of directory */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #ifdef windows  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  int imx; 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int stepm;
 #endif  /* Stepm, step in month: minimum step interpolation*/
    s = strrchr( name, '.' );            /* find last / */  
    s++;  int estepm;
    strcpy(ext,s);                       /* save extension */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    l1= strlen( name);  
    l2= strlen( s)+1;  int m,nb;
    strncpy( finame, name, l1-l2);  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    finame[l1-l2]= 0;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    return( 0 );                         /* we're done */  double **pmmij, ***probs;
 }  double dateintmean=0;
   
   double *weight;
 /******************************************/  int **s; /* Status */
   double *agedc, **covar, idx;
 void replace(char *s, char*t)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
   int i;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int lg=20;  double ftolhess; /* Tolerance for computing hessian */
   i=0;  
   lg=strlen(t);  /**************** split *************************/
   for(i=0; i<= lg; i++) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     (s[i] = t[i]);  {
     if (t[i]== '\\') s[i]='/';    char  *ss;                            /* pointer */
   }    int   l1, l2;                         /* length counters */
 }  
     l1 = strlen(path );                   /* length of path */
 int nbocc(char *s, char occ)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int i,j=0;    if ( ss == NULL ) {                   /* no directory, so use current */
   int lg=20;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   i=0;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   lg=strlen(s);      /* get current working directory */
   for(i=0; i<= lg; i++) {      /*    extern  char* getcwd ( char *buf , int len);*/
   if  (s[i] == occ ) j++;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   }        return( GLOCK_ERROR_GETCWD );
   return j;      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 void cutv(char *u,char *v, char*t, char occ)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   int i,lg,j,p=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   i=0;      strcpy( name, ss );         /* save file name */
   for(j=0; j<=strlen(t)-1; j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      dirc[l1-l2] = 0;                    /* add zero */
   }    }
     l1 = strlen( dirc );                  /* length of directory */
   lg=strlen(t);  #ifdef windows
   for(j=0; j<p; j++) {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     (u[j] = t[j]);  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
      u[p]='\0';  #endif
     ss = strrchr( name, '.' );            /* find last / */
    for(j=0; j<= lg; j++) {    ss++;
     if (j>=(p+1))(v[j-p-1] = t[j]);    strcpy(ext,ss);                       /* save extension */
   }    l1= strlen( name);
 }    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 /********************** nrerror ********************/    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 void nrerror(char error_text[])  }
 {  
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  /******************************************/
   exit(1);  
 }  void replace(char *s, char*t)
 /*********************** vector *******************/  {
 double *vector(int nl, int nh)    int i;
 {    int lg=20;
   double *v;    i=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!v) nrerror("allocation failure in vector");    for(i=0; i<= lg; i++) {
   return v-nl+NR_END;      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /************************ free vector ******************/  }
 void free_vector(double*v, int nl, int nh)  
 {  int nbocc(char *s, char occ)
   free((FREE_ARG)(v+nl-NR_END));  {
 }    int i,j=0;
     int lg=20;
 /************************ivector *******************************/    i=0;
 int *ivector(long nl,long nh)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   int *v;    if  (s[i] == occ ) j++;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    }
   if (!v) nrerror("allocation failure in ivector");    return j;
   return v-nl+NR_END;  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /******************free ivector **************************/  {
 void free_ivector(int *v, long nl, long nh)    /* cuts string t into u and v where u is ended by char occ excluding it
 {       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   free((FREE_ARG)(v+nl-NR_END));       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /******************* imatrix *******************************/    for(j=0; j<=strlen(t)-1; j++) {
 int **imatrix(long nrl, long nrh, long ncl, long nch)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    }
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    lg=strlen(t);
   int **m;    for(j=0; j<p; j++) {
        (u[j] = t[j]);
   /* allocate pointers to rows */    }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));       u[p]='\0';
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;     for(j=0; j<= lg; j++) {
   m -= nrl;      if (j>=(p+1))(v[j-p-1] = t[j]);
      }
    }
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /********************** nrerror ********************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  void nrerror(char error_text[])
   m[nrl] -= ncl;  {
      fprintf(stderr,"ERREUR ...\n");
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
   /* return pointer to array of pointers to rows */  }
   return m;  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /****************** free_imatrix *************************/    double *v;
 void free_imatrix(m,nrl,nrh,ncl,nch)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       int **m;    if (!v) nrerror("allocation failure in vector");
       long nch,ncl,nrh,nrl;    return v-nl+NR_END;
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /************************ free vector ******************/
   free((FREE_ARG) (m+nrl-NR_END));  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************* matrix *******************************/  }
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  /************************ivector *******************************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char *cvector(long nl,long nh)
   double **m;  {
     char *v;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!v) nrerror("allocation failure in cvector");
   m += NR_END;    return v-nl+NR_END;
   m -= nrl;  }
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************free ivector **************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_cvector(char *v, long nl, long nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    free((FREE_ARG)(v+nl-NR_END));
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /************************ivector *******************************/
 }  int *ivector(long nl,long nh)
   {
 /*************************free matrix ************************/    int *v;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 {    if (!v) nrerror("allocation failure in ivector");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    return v-nl+NR_END;
   free((FREE_ARG)(m+nrl-NR_END));  }
 }  
   /******************free ivector **************************/
 /******************* ma3x *******************************/  void free_ivector(int *v, long nl, long nh)
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  {
 {    free((FREE_ARG)(v+nl-NR_END));
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  }
   double ***m;  
   /******************* imatrix *******************************/
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   if (!m) nrerror("allocation failure 1 in matrix()");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m += NR_END;  { 
   m -= nrl;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* allocate pointers to rows */ 
   m[nrl] += NR_END;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   m[nrl] -= ncl;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    m -= nrl; 
     
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    /* allocate rows and set pointers to them */ 
   m[nrl][ncl] += NR_END;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m[nrl][ncl] -= nll;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (j=ncl+1; j<=nch; j++)    m[nrl] += NR_END; 
     m[nrl][j]=m[nrl][j-1]+nlay;    m[nrl] -= ncl; 
      
   for (i=nrl+1; i<=nrh; i++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    
     for (j=ncl+1; j<=nch; j++)    /* return pointer to array of pointers to rows */ 
       m[i][j]=m[i][j-1]+nlay;    return m; 
   }  } 
   return m;  
 }  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
 /*************************free ma3x ************************/        int **m;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  { 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /***************** f1dim *************************/  /******************* matrix *******************************/
 extern int ncom;  double **matrix(long nrl, long nrh, long ncl, long nch)
 extern double *pcom,*xicom;  {
 extern double (*nrfunc)(double []);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
 double f1dim(double x)  
 {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int j;    if (!m) nrerror("allocation failure 1 in matrix()");
   double f;    m += NR_END;
   double *xt;    m -= nrl;
    
   xt=vector(1,ncom);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   f=(*nrfunc)(xt);    m[nrl] += NR_END;
   free_vector(xt,1,ncom);    m[nrl] -= ncl;
   return f;  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 /*****************brent *************************/    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)     */
 {  }
   int iter;  
   double a,b,d,etemp;  /*************************free matrix ************************/
   double fu,fv,fw,fx;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double ftemp;  {
   double p,q,r,tol1,tol2,u,v,w,x,xm;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double e=0.0;    free((FREE_ARG)(m+nrl-NR_END));
    }
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  /******************* ma3x *******************************/
   x=w=v=bx;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   fw=fv=fx=(*f)(x);  {
   for (iter=1;iter<=ITMAX;iter++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     xm=0.5*(a+b);    double ***m;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     printf(".");fflush(stdout);    if (!m) nrerror("allocation failure 1 in matrix()");
 #ifdef DEBUG    m += NR_END;
     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 -= nrl;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       *xmin=x;    m[nrl] += NR_END;
       return fx;    m[nrl] -= ncl;
     }  
     ftemp=fu;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       q=(x-v)*(fx-fw);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       p=(x-v)*q-(x-w)*r;    m[nrl][ncl] += NR_END;
       q=2.0*(q-r);    m[nrl][ncl] -= nll;
       if (q > 0.0) p = -p;    for (j=ncl+1; j<=nch; j++) 
       q=fabs(q);      m[nrl][j]=m[nrl][j-1]+nlay;
       etemp=e;    
       e=d;    for (i=nrl+1; i<=nrh; i++) {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      for (j=ncl+1; j<=nch; j++) 
       else {        m[i][j]=m[i][j-1]+nlay;
         d=p/q;    }
         u=x+d;    return m; 
         if (u-a < tol2 || b-u < tol2)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
           d=SIGN(tol1,xm-x);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       }    */
     } else {  }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  /*************************free ma3x ************************/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     fu=(*f)(u);  {
     if (fu <= fx) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if (u >= x) a=x; else b=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       SHFT(v,w,x,u)    free((FREE_ARG)(m+nrl-NR_END));
         SHFT(fv,fw,fx,fu)  }
         } else {  
           if (u < x) a=u; else b=u;  /***************** f1dim *************************/
           if (fu <= fw || w == x) {  extern int ncom; 
             v=w;  extern double *pcom,*xicom;
             w=u;  extern double (*nrfunc)(double []); 
             fv=fw;   
             fw=fu;  double f1dim(double x) 
           } else if (fu <= fv || v == x || v == w) {  { 
             v=u;    int j; 
             fv=fu;    double f;
           }    double *xt; 
         }   
   }    xt=vector(1,ncom); 
   nrerror("Too many iterations in brent");    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *xmin=x;    f=(*nrfunc)(xt); 
   return fx;    free_vector(xt,1,ncom); 
 }    return f; 
   } 
 /****************** mnbrak ***********************/  
   /*****************brent *************************/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
             double (*func)(double))  { 
 {    int iter; 
   double ulim,u,r,q, dum;    double a,b,d,etemp;
   double fu;    double fu,fv,fw,fx;
      double ftemp;
   *fa=(*func)(*ax);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fb=(*func)(*bx);    double e=0.0; 
   if (*fb > *fa) {   
     SHFT(dum,*ax,*bx,dum)    a=(ax < cx ? ax : cx); 
       SHFT(dum,*fb,*fa,dum)    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
   *cx=(*bx)+GOLD*(*bx-*ax);    fw=fv=fx=(*f)(x); 
   *fc=(*func)(*cx);    for (iter=1;iter<=ITMAX;iter++) { 
   while (*fb > *fc) {      xm=0.5*(a+b); 
     r=(*bx-*ax)*(*fb-*fc);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     q=(*bx-*cx)*(*fb-*fa);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      printf(".");fflush(stdout);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      fprintf(ficlog,".");fflush(ficlog);
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #ifdef DEBUG
     if ((*bx-u)*(u-*cx) > 0.0) {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fu=(*func)(u);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     } else if ((*cx-u)*(u-ulim) > 0.0) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       fu=(*func)(u);  #endif
       if (fu < *fc) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        *xmin=x; 
           SHFT(*fb,*fc,fu,(*func)(u))        return fx; 
           }      } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      ftemp=fu;
       u=ulim;      if (fabs(e) > tol1) { 
       fu=(*func)(u);        r=(x-w)*(fx-fv); 
     } else {        q=(x-v)*(fx-fw); 
       u=(*cx)+GOLD*(*cx-*bx);        p=(x-v)*q-(x-w)*r; 
       fu=(*func)(u);        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
     SHFT(*ax,*bx,*cx,u)        q=fabs(q); 
       SHFT(*fa,*fb,*fc,fu)        etemp=e; 
       }        e=d; 
 }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 /*************** linmin ************************/        else { 
           d=p/q; 
 int ncom;          u=x+d; 
 double *pcom,*xicom;          if (u-a < tol2 || b-u < tol2) 
 double (*nrfunc)(double []);            d=SIGN(tol1,xm-x); 
          } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double brent(double ax, double bx, double cx,      } 
                double (*f)(double), double tol, double *xmin);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double f1dim(double x);      fu=(*f)(u); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      if (fu <= fx) { 
               double *fc, double (*func)(double));        if (u >= x) a=x; else b=x; 
   int j;        SHFT(v,w,x,u) 
   double xx,xmin,bx,ax;          SHFT(fv,fw,fx,fu) 
   double fx,fb,fa;          } else { 
              if (u < x) a=u; else b=u; 
   ncom=n;            if (fu <= fw || w == x) { 
   pcom=vector(1,n);              v=w; 
   xicom=vector(1,n);              w=u; 
   nrfunc=func;              fv=fw; 
   for (j=1;j<=n;j++) {              fw=fu; 
     pcom[j]=p[j];            } else if (fu <= fv || v == x || v == w) { 
     xicom[j]=xi[j];              v=u; 
   }              fv=fu; 
   ax=0.0;            } 
   xx=1.0;          } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    nrerror("Too many iterations in brent"); 
 #ifdef DEBUG    *xmin=x; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    return fx; 
 #endif  } 
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  /****************** mnbrak ***********************/
     p[j] += xi[j];  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   free_vector(xicom,1,n);              double (*func)(double)) 
   free_vector(pcom,1,n);  { 
 }    double ulim,u,r,q, dum;
     double fu; 
 /*************** powell ************************/   
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    *fa=(*func)(*ax); 
             double (*func)(double []))    *fb=(*func)(*bx); 
 {    if (*fb > *fa) { 
   void linmin(double p[], double xi[], int n, double *fret,      SHFT(dum,*ax,*bx,dum) 
               double (*func)(double []));        SHFT(dum,*fb,*fa,dum) 
   int i,ibig,j;        } 
   double del,t,*pt,*ptt,*xit;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double fp,fptt;    *fc=(*func)(*cx); 
   double *xits;    while (*fb > *fc) { 
   pt=vector(1,n);      r=(*bx-*ax)*(*fb-*fc); 
   ptt=vector(1,n);      q=(*bx-*cx)*(*fb-*fa); 
   xit=vector(1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   xits=vector(1,n);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   *fret=(*func)(p);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (j=1;j<=n;j++) pt[j]=p[j];      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (*iter=1;;++(*iter)) {        fu=(*func)(u); 
     fp=(*fret);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     ibig=0;        fu=(*func)(u); 
     del=0.0;        if (fu < *fc) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for (i=1;i<=n;i++)            SHFT(*fb,*fc,fu,(*func)(u)) 
       printf(" %d %.12f",i, p[i]);            } 
     printf("\n");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for (i=1;i<=n;i++) {        u=ulim; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        fu=(*func)(u); 
       fptt=(*fret);      } else { 
 #ifdef DEBUG        u=(*cx)+GOLD*(*cx-*bx); 
       printf("fret=%lf \n",*fret);        fu=(*func)(u); 
 #endif      } 
       printf("%d",i);fflush(stdout);      SHFT(*ax,*bx,*cx,u) 
       linmin(p,xit,n,fret,func);        SHFT(*fa,*fb,*fc,fu) 
       if (fabs(fptt-(*fret)) > del) {        } 
         del=fabs(fptt-(*fret));  } 
         ibig=i;  
       }  /*************** linmin ************************/
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  int ncom; 
       for (j=1;j<=n;j++) {  double *pcom,*xicom;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  double (*nrfunc)(double []); 
         printf(" x(%d)=%.12e",j,xit[j]);   
       }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for(j=1;j<=n;j++)  { 
         printf(" p=%.12e",p[j]);    double brent(double ax, double bx, double cx, 
       printf("\n");                 double (*f)(double), double tol, double *xmin); 
 #endif    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {                double *fc, double (*func)(double)); 
 #ifdef DEBUG    int j; 
       int k[2],l;    double xx,xmin,bx,ax; 
       k[0]=1;    double fx,fb,fa;
       k[1]=-1;   
       printf("Max: %.12e",(*func)(p));    ncom=n; 
       for (j=1;j<=n;j++)    pcom=vector(1,n); 
         printf(" %.12e",p[j]);    xicom=vector(1,n); 
       printf("\n");    nrfunc=func; 
       for(l=0;l<=1;l++) {    for (j=1;j<=n;j++) { 
         for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      xicom[j]=xi[j]; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    } 
         }    ax=0.0; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    xx=1.0; 
       }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 #endif    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       free_vector(xit,1,n);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       free_vector(xits,1,n);  #endif
       free_vector(ptt,1,n);    for (j=1;j<=n;j++) { 
       free_vector(pt,1,n);      xi[j] *= xmin; 
       return;      p[j] += xi[j]; 
     }    } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    free_vector(xicom,1,n); 
     for (j=1;j<=n;j++) {    free_vector(pcom,1,n); 
       ptt[j]=2.0*p[j]-pt[j];  } 
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     fptt=(*func)(ptt);              double (*func)(double [])) 
     if (fptt < fp) {  { 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    void linmin(double p[], double xi[], int n, double *fret, 
       if (t < 0.0) {                double (*func)(double [])); 
         linmin(p,xit,n,fret,func);    int i,ibig,j; 
         for (j=1;j<=n;j++) {    double del,t,*pt,*ptt,*xit;
           xi[j][ibig]=xi[j][n];    double fp,fptt;
           xi[j][n]=xit[j];    double *xits;
         }    pt=vector(1,n); 
 #ifdef DEBUG    ptt=vector(1,n); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    xit=vector(1,n); 
         for(j=1;j<=n;j++)    xits=vector(1,n); 
           printf(" %.12e",xit[j]);    *fret=(*func)(p); 
         printf("\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
 #endif    for (*iter=1;;++(*iter)) { 
       }      fp=(*fret); 
     }      ibig=0; 
   }      del=0.0; 
 }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 /**** Prevalence limit ****************/      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        printf(" %d %.12f",i, p[i]);
 {        fprintf(ficlog," %d %.12lf",i, p[i]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        fprintf(ficrespow," %.12lf", p[i]);
      matrix by transitions matrix until convergence is reached */      }
       printf("\n");
   int i, ii,j,k;      fprintf(ficlog,"\n");
   double min, max, maxmin, maxmax,sumnew=0.;      fprintf(ficrespow,"\n");
   double **matprod2();      for (i=1;i<=n;i++) { 
   double **out, cov[NCOVMAX], **pmij();        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double **newm;        fptt=(*fret); 
   double agefin, delaymax=50 ; /* Max number of years to converge */  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
   for (ii=1;ii<=nlstate+ndeath;ii++)        fprintf(ficlog,"fret=%lf \n",*fret);
     for (j=1;j<=nlstate+ndeath;j++){  #endif
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        printf("%d",i);fflush(stdout);
     }        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
    cov[1]=1.;        if (fabs(fptt-(*fret)) > del) { 
            del=fabs(fptt-(*fret)); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          ibig=i; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        } 
     newm=savm;  #ifdef DEBUG
     /* Covariates have to be included here again */        printf("%d %.12e",i,(*fret));
      cov[2]=agefin;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
       for (k=1; k<=cptcovn;k++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          printf(" x(%d)=%.12e",j,xit[j]);
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=1;j<=n;j++) {
       for (k=1; k<=cptcovprod;k++)          printf(" p=%.12e",p[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog," p=%.12e",p[j]);
         }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        printf("\n");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        fprintf(ficlog,"\n");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  #endif
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     savm=oldm;  #ifdef DEBUG
     oldm=newm;        int k[2],l;
     maxmax=0.;        k[0]=1;
     for(j=1;j<=nlstate;j++){        k[1]=-1;
       min=1.;        printf("Max: %.12e",(*func)(p));
       max=0.;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       for(i=1; i<=nlstate; i++) {        for (j=1;j<=n;j++) {
         sumnew=0;          printf(" %.12e",p[j]);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          fprintf(ficlog," %.12e",p[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);        }
         max=FMAX(max,prlim[i][j]);        printf("\n");
         min=FMIN(min,prlim[i][j]);        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
       maxmin=max-min;          for (j=1;j<=n;j++) {
       maxmax=FMAX(maxmax,maxmin);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if(maxmax < ftolpl){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       return prlim;          }
     }          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)));
 }        }
   #endif
 /*************** transition probabilities ***************/  
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        free_vector(xit,1,n); 
 {        free_vector(xits,1,n); 
   double s1, s2;        free_vector(ptt,1,n); 
   /*double t34;*/        free_vector(pt,1,n); 
   int i,j,j1, nc, ii, jj;        return; 
       } 
     for(i=1; i<= nlstate; i++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for(j=1; j<i;j++){      for (j=1;j<=n;j++) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        ptt[j]=2.0*p[j]-pt[j]; 
         /*s2 += param[i][j][nc]*cov[nc];*/        xit[j]=p[j]-pt[j]; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        pt[j]=p[j]; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
       }      fptt=(*func)(ptt); 
       ps[i][j]=s2;      if (fptt < fp) { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
     for(j=i+1; j<=nlstate+ndeath;j++){          linmin(p,xit,n,fret,func); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          for (j=1;j<=n;j++) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            xi[j][ibig]=xi[j][n]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/            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);
   }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     /*ps[3][2]=1;*/          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
   for(i=1; i<= nlstate; i++){            fprintf(ficlog," %.12e",xit[j]);
      s1=0;          }
     for(j=1; j<i; j++)          printf("\n");
       s1+=exp(ps[i][j]);          fprintf(ficlog,"\n");
     for(j=i+1; j<=nlstate+ndeath; j++)  #endif
       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];  } 
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /**** Prevalence limit (stable prevalence)  ****************/
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* 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++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for(jj=1; jj<= nlstate+ndeath; jj++){       matrix by transitions matrix until convergence is reached */
       ps[ii][jj]=0;  
       ps[ii][ii]=1;    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
     double **newm;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    for (ii=1;ii<=nlstate+ndeath;ii++)
    }      for (j=1;j<=nlstate+ndeath;j++){
     printf("\n ");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*     cov[1]=1.;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);   
   goto end;*/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     return ps;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
 /**************** Product of 2 matrices ******************/       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++) {
 {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          /*      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]]);*/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        }
   /* in, b, out are matrice of pointers which should have been initialized        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      before: only the contents of out is modified. The function returns        for (k=1; k<=cptcovprod;k++)
      a pointer to pointers identical to out */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for(k=ncolol; k<=ncoloh; k++)        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         out[i][k] +=in[i][j]*b[j][k];      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.;
       for(j=1;j<=nlstate;j++){
 /************* Higher Matrix Product ***************/        min=1.;
         max=0.;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        for(i=1; i<=nlstate; i++) {
 {          sumnew=0;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      duration (i.e. until          prlim[i][j]= newm[i][j]/(1-sumnew);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          max=FMAX(max,prlim[i][j]);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          min=FMIN(min,prlim[i][j]);
      (typically every 2 years instead of every month which is too big).        }
      Model is determined by parameters x and covariates have to be        maxmin=max-min;
      included manually here.        maxmax=FMAX(maxmax,maxmin);
       }
      */      if(maxmax < ftolpl){
         return prlim;
   int i, j, d, h, k;      }
   double **out, cov[NCOVMAX];    }
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  /*************** transition probabilities ***************/ 
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       oldm[i][j]=(i==j ? 1.0 : 0.0);  {
       po[i][j][0]=(i==j ? 1.0 : 0.0);    double s1, s2;
     }    /*double t34;*/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int i,j,j1, nc, ii, jj;
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){      for(i=1; i<= nlstate; i++){
       newm=savm;      for(j=1; j<i;j++){
       /* Covariates have to be included here again */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       cov[1]=1.;          /*s2 += param[i][j][nc]*cov[nc];*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
       for (k=1; k<=cptcovage;k++)        }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        ps[i][j]=s2;
       for (k=1; k<=cptcovprod;k++)        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      }
       for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        ps[i][j]=s2;
       savm=oldm;      }
       oldm=newm;    }
     }      /*ps[3][2]=1;*/
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {    for(i=1; i<= nlstate; i++){
         po[i][j][h]=newm[i][j];       s1=0;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      for(j=1; j<i; j++)
          */        s1+=exp(ps[i][j]);
       }      for(j=i+1; j<=nlstate+ndeath; j++)
   } /* end h */        s1+=exp(ps[i][j]);
   return po;      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++)
 /*************** log-likelihood *************/        ps[i][j]= exp(ps[i][j])*ps[i][i];
 double func( double *x)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {    } /* end i */
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double **out;      for(jj=1; jj<= nlstate+ndeath; jj++){
   double sw; /* Sum of weights */        ps[ii][jj]=0;
   double lli; /* Individual log likelihood */        ps[ii][ii]=1;
   long ipmx;      }
   /*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++)    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     printf(" %d\n",s[4][i]);      for(jj=1; jj<= nlstate+ndeath; jj++){
   */       printf("%lf ",ps[ii][jj]);
   cov[1]=1.;     }
       printf("\n ");
   for(k=1; k<=nlstate; k++) ll[k]=0.;      }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      printf("\n ");printf("%lf ",cov[2]);*/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*
     for(mi=1; mi<= wav[i]-1; mi++){    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for (ii=1;ii<=nlstate+ndeath;ii++)    goto end;*/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      return ps;
       for(d=0; d<dh[mi][i]; d++){  }
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /**************** Product of 2 matrices ******************/
         for (kk=1; kk<=cptcovage;kk++) {  
           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)
         }  {
            /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    /* in, b, out are matrice of pointers which should have been initialized 
         savm=oldm;       before: only the contents of out is modified. The function returns
         oldm=newm;       a pointer to pointers identical to out */
            long i, j, k;
            for(i=nrl; i<= nrh; i++)
       } /* end mult */      for(k=ncolol; k<=ncoloh; k++)
              for(j=ncl,out[i][k]=0.; j<=nch; j++)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          out[i][k] +=in[i][j]*b[j][k];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;    return out;
       sw += weight[i];  }
       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];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  {
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    /* Computes the transition matrix starting at age 'age' over 
   return -l;       'nhstepm*hstepm*stepm' months (i.e. until
 }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /*********** Maximum Likelihood Estimation ***************/       (typically every 2 years instead of every month which is too big 
        for the memory).
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       Model is determined by parameters x and covariates have to be 
 {       included manually here. 
   int i,j, iter;  
   double **xi,*delti;       */
   double fret;  
   xi=matrix(1,npar,1,npar);    int i, j, d, h, k;
   for (i=1;i<=npar;i++)    double **out, cov[NCOVMAX];
     for (j=1;j<=npar;j++)    double **newm;
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");    /* Hstepm could be zero and should return the unit matrix */
   powell(p,xi,npar,ftol,&iter,&fret,func);    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        oldm[i][j]=(i==j ? 1.0 : 0.0);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
 }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
 /**** Computes Hessian and covariance matrix ***/      for(d=1; d <=hstepm; d++){
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        newm=savm;
 {        /* Covariates have to be included here again */
   double  **a,**y,*x,pd;        cov[1]=1.;
   double **hess;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int i, j,jk;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int *indx;        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double hessii(double p[], double delta, int theta, double delti[]);        for (k=1; k<=cptcovprod;k++)
   double hessij(double p[], double delti[], int i, int j);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   hess=matrix(1,npar,1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   printf("\nCalculation of the hessian matrix. Wait...\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (i=1;i<=npar;i++){        savm=oldm;
     printf("%d",i);fflush(stdout);        oldm=newm;
     hess[i][i]=hessii(p,ftolhess,i,delti);      }
     /*printf(" %f ",p[i]);*/      for(i=1; i<=nlstate+ndeath; i++)
     /*printf(" %lf ",hess[i][i]);*/        for(j=1;j<=nlstate+ndeath;j++) {
   }          po[i][j][h]=newm[i][j];
            /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   for (i=1;i<=npar;i++) {           */
     for (j=1;j<=npar;j++)  {        }
       if (j>i) {    } /* end h */
         printf(".%d%d",i,j);fflush(stdout);    return po;
         hess[i][j]=hessij(p,delti,i,j);  }
         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;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double **out;
      double sw; /* Sum of weights */
   a=matrix(1,npar,1,npar);    double lli; /* Individual log likelihood */
   y=matrix(1,npar,1,npar);    int s1, s2;
   x=vector(1,npar);    double bbh, survp;
   indx=ivector(1,npar);    long ipmx;
   for (i=1;i<=npar;i++)    /*extern weight */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    /* We are differentiating ll according to initial status */
   ludcmp(a,npar,indx,&pd);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   for (j=1;j<=npar;j++) {      printf(" %d\n",s[4][i]);
     for (i=1;i<=npar;i++) x[i]=0;    */
     x[j]=1;    cov[1]=1.;
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       matcov[i][j]=x[i];  
     }    if(mle==1){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("\n#Hessian matrix#\n");        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=npar;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=npar;j++) {            for (j=1;j<=nlstate+ndeath;j++){
       printf("%.3e ",hess[i][j]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n");            }
   }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   /* Recompute Inverse */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (i=1;i<=npar;i++)            for (kk=1; kk<=cptcovage;kk++) {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   ludcmp(a,npar,indx,&pd);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /*  printf("\n#Hessian matrix recomputed#\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for (j=1;j<=npar;j++) {            oldm=newm;
     for (i=1;i<=npar;i++) x[i]=0;          } /* end mult */
     x[j]=1;        
     lubksb(a,npar,indx,x);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (i=1;i<=npar;i++){          /* But now since version 0.9 we anticipate for bias and large stepm.
       y[i][j]=x[i];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       printf("%.3e ",y[i][j]);           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
     printf("\n");           * 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
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   free_matrix(a,1,npar,1,npar);           * -stepm/2 to stepm/2 .
   free_matrix(y,1,npar,1,npar);           * For stepm=1 the results are the same as for previous versions of Imach.
   free_vector(x,1,npar);           * For stepm > 1 the results are less biased than in previous versions. 
   free_ivector(indx,1,npar);           */
   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
            * is higher than the multiple of stepm and negative otherwise.
 /*************** hessian matrix ****************/           */
 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]));*/
 {          if( s2 > nlstate){ 
   int i;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   int l=1, lmax=20;               to the likelihood is the probability to die between last step unit time and current 
   double k1,k2;               step unit time, which is also the differences between probability to die before dh 
   double p2[NPARMAX+1];               and probability to die before dh-stepm . 
   double res;               In version up to 0.92 likelihood was computed
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          as if date of death was unknown. Death was treated as any other
   double fx;          health state: the date of the interview describes the actual state
   int k=0,kmax=10;          and not the date of a change in health state. The former idea was
   double l1;          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   fx=func(x);          introduced the exact date of death then we should have modified
   for (i=1;i<=npar;i++) p2[i]=x[i];          the contribution of an exact death to the likelihood. This new
   for(l=0 ; l <=lmax; l++){          contribution is smaller and very dependent of the step unit
     l1=pow(10,l);          stepm. It is no more the probability to die between last interview
     delts=delt;          and month of death but the probability to survive from last
     for(k=1 ; k <kmax; k=k+1){          interview up to one month before death multiplied by the
       delt = delta*(l1*k);          probability to die within a month. Thanks to Chris
       p2[theta]=x[theta] +delt;          Jackson for correcting this bug.  Former versions increased
       k1=func(p2)-fx;          mortality artificially. The bad side is that we add another loop
       p2[theta]=x[theta]-delt;          which slows down the processing. The difference can be up to 10%
       k2=func(p2)-fx;          lower mortality.
       /*res= (k1-2.0*fx+k2)/delt/delt; */            */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            lli=log(out[s1][s2] - savm[s1][s2]);
                }else{
 #ifdef DEBUG            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       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= (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 */
 #endif          } 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*if(lli ==000.0)*/
         k=kmax;          /*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;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          sw += weight[i];
         k=kmax; l=lmax*10.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      } /* end of individual */
         delts=delt;    }  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];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   delti[theta]=delts;          for (ii=1;ii<=nlstate+ndeath;ii++)
   return res;            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++){
 {            newm=savm;
   int i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int l=1, l1, lmax=20;            for (kk=1; kk<=cptcovage;kk++) {
   double k1,k2,k3,k4,res,fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double p2[NPARMAX+1];            }
   int k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fx=func(x);            savm=oldm;
   for (k=1; k<=2; k++) {            oldm=newm;
     for (i=1;i<=npar;i++) p2[i]=x[i];          } /* end mult */
     p2[thetai]=x[thetai]+delti[thetai]/k;        
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     k1=func(p2)-fx;          /* 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 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     k2=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * probability in order to take into account the bias as a fraction of the way
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     k3=func(p2)-fx;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           */
     k4=func(p2)-fx;          s1=s[mw[mi][i]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          s2=s[mw[mi+1][i]][i];
 #ifdef DEBUG          bbh=(double)bh[mi][i]/(double)stepm; 
     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);          /* bias is positive if real duration
 #endif           * 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]));*/
           /*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 */
 /************** Inverse of matrix **************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 void ludcmp(double **a, int n, int *indx, double *d)          /*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); */
   int i,imax,j,k;          ipmx +=1;
   double big,dum,sum,temp;          sw += weight[i];
   double *vv;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   vv=vector(1,n);      } /* end of individual */
   *d=1.0;    }  else if(mle==3){  /* exponential inter-extrapolation */
   for (i=1;i<=n;i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     big=0.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (j=1;j<=n;j++)        for(mi=1; mi<= wav[i]-1; mi++){
       if ((temp=fabs(a[i][j])) > big) big=temp;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            for (j=1;j<=nlstate+ndeath;j++){
     vv[i]=1.0/big;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {            }
     for (i=1;i<j;i++) {          for(d=0; d<dh[mi][i]; d++){
       sum=a[i][j];            newm=savm;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       a[i][j]=sum;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     big=0.0;            }
     for (i=j;i<=n;i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       sum=a[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<j;k++)            savm=oldm;
         sum -= a[i][k]*a[k][j];            oldm=newm;
       a[i][j]=sum;          } /* end mult */
       if ( (dum=vv[i]*fabs(sum)) >= big) {        
         big=dum;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         imax=i;          /* 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 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (j != imax) {           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (k=1;k<=n;k++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         dum=a[imax][k];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         a[imax][k]=a[j][k];           * probability in order to take into account the bias as a fraction of the way
         a[j][k]=dum;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
       *d = -(*d);           * For stepm=1 the results are the same as for previous versions of Imach.
       vv[imax]=vv[j];           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
     indx[j]=imax;          s1=s[mw[mi][i]][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;          s2=s[mw[mi+1][i]][i];
     if (j != n) {          bbh=(double)bh[mi][i]/(double)stepm; 
       dum=1.0/(a[j][j]);          /* bias is positive if real duration
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * is higher than the multiple of stepm and negative otherwise.
     }           */
   }          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   free_vector(vv,1,n);  /* Doesn't work */          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)*/
           /*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); */
 void lubksb(double **a, int n, int *indx, double b[])          ipmx +=1;
 {          sw += weight[i];
   int i,ii=0,ip,j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double sum;        } /* end of wave */
        } /* end of individual */
   for (i=1;i<=n;i++) {    }else{  /* ml=4 no inter-extrapolation */
     ip=indx[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     sum=b[ip];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     b[ip]=b[i];        for(mi=1; mi<= wav[i]-1; mi++){
     if (ii)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            for (j=1;j<=nlstate+ndeath;j++){
     else if (sum) ii=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   for (i=n;i>=1;i--) {          for(d=0; d<dh[mi][i]; d++){
     sum=b[i];            newm=savm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     b[i]=sum/a[i][i];            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
           
 /************ Frequencies ********************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 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)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {  /* Some frequencies */            savm=oldm;
              oldm=newm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          } /* end mult */
   double ***freq; /* Frequencies */        
   double *pp;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double pos, k2, dateintsum=0,k2cpt=0;          ipmx +=1;
   FILE *ficresp;          sw += weight[i];
   char fileresp[FILENAMELENGTH];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   pp=vector(1,nlstate);      } /* end of individual */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    } /* End of if */
   strcpy(fileresp,"p");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   strcat(fileresp,fileres);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     printf("Problem with prevalence resultfile: %s\n", fileresp);    return -l;
     exit(0);  }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  /*********** Maximum Likelihood Estimation ***************/
    
   j=cptcoveff;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
      int i,j, iter;
   for(k1=1; k1<=j;k1++){    double **xi;
     for(i1=1; i1<=ncodemax[k1];i1++){    double fret;
       j1++;    char filerespow[FILENAMELENGTH];
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    xi=matrix(1,npar,1,npar);
         scanf("%d", i);*/    for (i=1;i<=npar;i++)
       for (i=-1; i<=nlstate+ndeath; i++)        for (j=1;j<=npar;j++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)          xi[i][j]=(i==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
             freq[i][jk][m]=0;    strcpy(filerespow,"pow"); 
          strcat(filerespow,fileres);
       dateintsum=0;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       k2cpt=0;      printf("Problem with resultfile: %s\n", filerespow);
       for (i=1; i<=imx; i++) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         bool=1;    }
         if  (cptcovn>0) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           for (z1=1; z1<=cptcoveff; z1++)    for (i=1;i<=nlstate;i++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for(j=1;j<=nlstate+ndeath;j++)
               bool=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         }    fprintf(ficrespow,"\n");
         if (bool==1) {    powell(p,xi,npar,ftol,&iter,&fret,func);
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);    fclose(ficrespow);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
               if(agev[m][i]==0) agev[m][i]=agemax+1;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if(agev[m][i]==1) agev[m][i]=agemax+2;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  }
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
               }  /**** Computes Hessian and covariance matrix ***/
                void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  {
                 dateintsum=dateintsum+k2;    double  **a,**y,*x,pd;
                 k2cpt++;    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);
            void lubksb(double **a, int npar, int *indx, double b[]) ;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
       if  (cptcovn>0) {    hess=matrix(1,npar,1,npar);
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    printf("\nCalculation of the hessian matrix. Wait...\n");
         fprintf(ficresp, "**********\n#");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }    for (i=1;i<=npar;i++){
       for(i=1; i<=nlstate;i++)      printf("%d",i);fflush(stdout);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      fprintf(ficlog,"%d",i);fflush(ficlog);
       fprintf(ficresp, "\n");      hess[i][i]=hessii(p,ftolhess,i,delti);
            /*printf(" %f ",p[i]);*/
       for(i=(int)agemin; i <= (int)agemax+3; i++){      /*printf(" %lf ",hess[i][i]);*/
         if(i==(int)agemax+3)    }
           printf("Total");    
         else    for (i=1;i<=npar;i++) {
           printf("Age %d", i);      for (j=1;j<=npar;j++)  {
         for(jk=1; jk <=nlstate ; jk++){        if (j>i) { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          printf(".%d%d",i,j);fflush(stdout);
             pp[jk] += freq[jk][m][i];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         }          hess[i][j]=hessij(p,delti,i,j);
         for(jk=1; jk <=nlstate ; jk++){          hess[j][i]=hess[i][j];    
           for(m=-1, pos=0; m <=0 ; m++)          /*printf(" %lf ",hess[i][j]);*/
             pos += freq[jk][m][i];        }
           if(pp[jk]>=1.e-10)      }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    }
           else    printf("\n");
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    fprintf(ficlog,"\n");
         }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(jk=1; jk <=nlstate ; jk++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    
             pp[jk] += freq[jk][m][i];    a=matrix(1,npar,1,npar);
         }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
         for(jk=1,pos=0; jk <=nlstate ; jk++)    indx=ivector(1,npar);
           pos += pp[jk];    for (i=1;i<=npar;i++)
         for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           if(pos>=1.e-5)    ludcmp(a,npar,indx,&pd);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           else    for (j=1;j<=npar;j++) {
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      for (i=1;i<=npar;i++) x[i]=0;
           if( i <= (int) agemax){      x[j]=1;
             if(pos>=1.e-5){      lubksb(a,npar,indx,x);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      for (i=1;i<=npar;i++){ 
               probs[i][jk][j1]= pp[jk]/pos;        matcov[i][j]=x[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]);*/      }
             }    }
             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 (j=1;j<=npar;j++) { 
         for(jk=-1; jk <=nlstate+ndeath; jk++)        printf("%.3e ",hess[i][j]);
           for(m=-1; m <=nlstate+ndeath; m++)        fprintf(ficlog,"%.3e ",hess[i][j]);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      }
         if(i <= (int) agemax)      printf("\n");
           fprintf(ficresp,"\n");      fprintf(ficlog,"\n");
         printf("\n");    }
       }  
     }    /* Recompute Inverse */
   }    for (i=1;i<=npar;i++)
   dateintmean=dateintsum/k2cpt;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ludcmp(a,npar,indx,&pd);
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /*  printf("\n#Hessian matrix recomputed#\n");
   free_vector(pp,1,nlstate);  
      for (j=1;j<=npar;j++) {
   /* End of Freq */      for (i=1;i<=npar;i++) x[i]=0;
 }      x[j]=1;
       lubksb(a,npar,indx,x);
 /************ Prevalence ********************/      for (i=1;i<=npar;i++){ 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        y[i][j]=x[i];
 {  /* Some frequencies */        printf("%.3e ",y[i][j]);
          fprintf(ficlog,"%.3e ",y[i][j]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      }
   double ***freq; /* Frequencies */      printf("\n");
   double *pp;      fprintf(ficlog,"\n");
   double pos, k2;    }
     */
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    free_vector(x,1,npar);
   j1=0;    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    }
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  /*************** hessian matrix ****************/
       j1++;  double hessii( double x[], double delta, int theta, double delti[])
        {
       for (i=-1; i<=nlstate+ndeath; i++)      int i;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int l=1, lmax=20;
           for(m=agemin; m <= agemax+3; m++)    double k1,k2;
             freq[i][jk][m]=0;    double p2[NPARMAX+1];
          double res;
       for (i=1; i<=imx; i++) {    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         bool=1;    double fx;
         if  (cptcovn>0) {    int k=0,kmax=10;
           for (z1=1; z1<=cptcoveff; z1++)    double l1;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
         if (bool==1) {    for(l=0 ; l <=lmax; l++){
           for(m=firstpass; m<=lastpass; m++){      l1=pow(10,l);
             k2=anint[m][i]+(mint[m][i]/12.);      delts=delt;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for(k=1 ; k <kmax; k=k+1){
               if(agev[m][i]==0) agev[m][i]=agemax+1;        delt = delta*(l1*k);
               if(agev[m][i]==1) agev[m][i]=agemax+2;        p2[theta]=x[theta] +delt;
               if (m<lastpass) {        k1=func(p2)-fx;
                 if (calagedate>0)        p2[theta]=x[theta]-delt;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        k2=func(p2)-fx;
                 else        /*res= (k1-2.0*fx+k2)/delt/delt; */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        
               }  #ifdef DEBUG
             }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }  #endif
       }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(i=(int)agemin; i <= (int)agemax+3; i++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(jk=1; jk <=nlstate ; jk++){          k=kmax;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
             pp[jk] += freq[jk][m][i];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=-1, pos=0; m <=0 ; m++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             pos += freq[jk][m][i];          delts=delt;
         }        }
              }
         for(jk=1; jk <=nlstate ; jk++){    }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    delti[theta]=delts;
             pp[jk] += freq[jk][m][i];    return res; 
         }    
          }
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
          double hessij( double x[], double delti[], int thetai,int thetaj)
         for(jk=1; jk <=nlstate ; jk++){      {
           if( i <= (int) agemax){    int i;
             if(pos>=1.e-5){    int l=1, l1, lmax=20;
               probs[i][jk][j1]= pp[jk]/pos;    double k1,k2,k3,k4,res,fx;
             }    double p2[NPARMAX+1];
           }    int k;
         }  
            fx=func(x);
       }    for (k=1; k<=2; k++) {
     }      for (i=1;i<=npar;i++) p2[i]=x[i];
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k1=func(p2)-fx;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    
   free_vector(pp,1,nlstate);      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 }  /* End of Freq */      k2=func(p2)-fx;
     
 /************* Waves Concatenation ***************/      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      k3=func(p2)-fx;
 {    
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      p2[thetai]=x[thetai]-delti[thetai]/k;
      Death is a valid wave (if date is known).      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      k4=func(p2)-fx;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      and mw[mi+1][i]. dh depends on stepm.  #ifdef DEBUG
      */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       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);
   int i, mi, m;  #endif
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    }
      double sum=0., jmean=0.;*/    return res;
   }
   int j, k=0,jk, ju, jl;  
   double sum=0.;  /************** Inverse of matrix **************/
   jmin=1e+5;  void ludcmp(double **a, int n, int *indx, double *d) 
   jmax=-1;  { 
   jmean=0.;    int i,imax,j,k; 
   for(i=1; i<=imx; i++){    double big,dum,sum,temp; 
     mi=0;    double *vv; 
     m=firstpass;   
     while(s[m][i] <= nlstate){    vv=vector(1,n); 
       if(s[m][i]>=1)    *d=1.0; 
         mw[++mi][i]=m;    for (i=1;i<=n;i++) { 
       if(m >=lastpass)      big=0.0; 
         break;      for (j=1;j<=n;j++) 
       else        if ((temp=fabs(a[i][j])) > big) big=temp; 
         m++;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }/* end while */      vv[i]=1.0/big; 
     if (s[m][i] > nlstate){    } 
       mi++;     /* Death is another wave */    for (j=1;j<=n;j++) { 
       /* if(mi==0)  never been interviewed correctly before death */      for (i=1;i<j;i++) { 
          /* Only death is a correct wave */        sum=a[i][j]; 
       mw[mi][i]=m;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
       } 
     wav[i]=mi;      big=0.0; 
     if(mi==0)      for (i=j;i<=n;i++) { 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        sum=a[i][j]; 
   }        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
   for(i=1; i<=imx; i++){        a[i][j]=sum; 
     for(mi=1; mi<wav[i];mi++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       if (stepm <=0)          big=dum; 
         dh[mi][i]=1;          imax=i; 
       else{        } 
         if (s[mw[mi+1][i]][i] > nlstate) {      } 
           if (agedc[i] < 2*AGESUP) {      if (j != imax) { 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for (k=1;k<=n;k++) { 
           if(j==0) j=1;  /* Survives at least one month after exam */          dum=a[imax][k]; 
           k=k+1;          a[imax][k]=a[j][k]; 
           if (j >= jmax) jmax=j;          a[j][k]=dum; 
           if (j <= jmin) jmin=j;        } 
           sum=sum+j;        *d = -(*d); 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        vv[imax]=vv[j]; 
           }      } 
         }      indx[j]=imax; 
         else{      if (a[j][j] == 0.0) a[j][j]=TINY; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      if (j != n) { 
           k=k+1;        dum=1.0/(a[j][j]); 
           if (j >= jmax) jmax=j;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           else if (j <= jmin)jmin=j;      } 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    } 
           sum=sum+j;    free_vector(vv,1,n);  /* Doesn't work */
         }  ;
         jk= j/stepm;  } 
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  void lubksb(double **a, int n, int *indx, double b[]) 
         if(jl <= -ju)  { 
           dh[mi][i]=jk;    int i,ii=0,ip,j; 
         else    double sum; 
           dh[mi][i]=jk+1;   
         if(dh[mi][i]==0)    for (i=1;i<=n;i++) { 
           dh[mi][i]=1; /* At least one step */      ip=indx[i]; 
       }      sum=b[ip]; 
     }      b[ip]=b[i]; 
   }      if (ii) 
   jmean=sum/k;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      else if (sum) ii=i; 
  }      b[i]=sum; 
 /*********** Tricode ****************************/    } 
 void tricode(int *Tvar, int **nbcode, int imx)    for (i=n;i>=1;i--) { 
 {      sum=b[i]; 
   int Ndum[20],ij=1, k, j, i;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   int cptcode=0;      b[i]=sum/a[i][i]; 
   cptcoveff=0;    } 
    } 
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;  /************ Frequencies ********************/
   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)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  {  /* Some frequencies */
     for (i=1; i<=imx; i++) {    
       ij=(int)(covar[Tvar[j]][i]);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       Ndum[ij]++;    int first;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    double ***freq; /* Frequencies */
       if (ij > cptcode) cptcode=ij;    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
     for (i=0; i<=cptcode; i++) {    char fileresp[FILENAMELENGTH];
       if(Ndum[i]!=0) ncodemax[j]++;    
     }    pp=vector(1,nlstate);
     ij=1;    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     for (i=1; i<=ncodemax[j]; i++) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for (k=0; k<=19; k++) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
         if (Ndum[k] != 0) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           nbcode[Tvar[j]][ij]=k;      exit(0);
              }
           ij++;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         }    j1=0;
         if (ij > ncodemax[j]) break;    
       }      j=cptcoveff;
     }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }    
     first=1;
  for (k=0; k<19; k++) Ndum[k]=0;  
     for(k1=1; k1<=j;k1++){
  for (i=1; i<=ncovmodel-2; i++) {      for(i1=1; i1<=ncodemax[k1];i1++){
       ij=Tvar[i];        j1++;
       Ndum[ij]++;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
  ij=1;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
  for (i=1; i<=10; i++) {            for(m=iagemin; m <= iagemax+3; m++)
    if((Ndum[i]!=0) && (i<=ncovcol)){              freq[i][jk][m]=0;
      Tvaraff[ij]=i;  
      ij++;      for (i=1; i<=nlstate; i++)  
    }        for(m=iagemin; m <= iagemax+3; m++)
  }          prop[i][m]=0;
          
     cptcoveff=ij-1;        dateintsum=0;
 }        k2cpt=0;
         for (i=1; i<=imx; i++) {
 /*********** Health Expectancies ****************/          bool=1;
           if  (cptcovn>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,double delti[],double **matcov )            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 {                bool=0;
   /* Health expectancies */          }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          if (bool==1){
   double age, agelim, hf;            for(m=firstpass; m<=lastpass; m++){
   double ***p3mat,***varhe;              k2=anint[m][i]+(mint[m][i]/12.);
   double **dnewm,**doldm;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   double *xp;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double **gp, **gm;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double ***gradg, ***trgradg;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   int theta;                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   xp=vector(1,npar);                }
   dnewm=matrix(1,nlstate*2,1,npar);                
   doldm=matrix(1,nlstate*2,1,nlstate*2);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                    dateintsum=dateintsum+k2;
   fprintf(ficreseij,"# Health expectancies\n");                  k2cpt++;
   fprintf(ficreseij,"# Age");                }
   for(i=1; i<=nlstate;i++)              }
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          }
   fprintf(ficreseij,"\n");        }
          
   if(estepm < stepm){        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }        if  (cptcovn>0) {
   else  hstepm=estepm;            fprintf(ficresp, "\n#********** Variable "); 
   /* We compute the life expectancy from trapezoids spaced every estepm months          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    * This is mainly to measure the difference between two models: for example          fprintf(ficresp, "**********\n#");
    * if stepm=24 months pijx are given only every 2 years and by summing them        }
    * we are calculating an estimate of the Life Expectancy assuming a linear        for(i=1; i<=nlstate;i++) 
    * progression inbetween and thus overestimating or underestimating according          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
    * to the curvature of the survival function. If, for the same date, we        fprintf(ficresp, "\n");
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        
    * to compare the new estimate of Life expectancy with the same linear        for(i=iagemin; i <= iagemax+3; i++){
    * hypothesis. A more precise result, taking into account a more precise          if(i==iagemax+3){
    * curvature will be obtained if estepm is as small as stepm. */            fprintf(ficlog,"Total");
           }else{
   /* For example we decided to compute the life expectancy with the smallest unit */            if(first==1){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              first=0;
      nhstepm is the number of hstepm from age to agelim              printf("See log file for details...\n");
      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(ficlog,"Age %d", i);
      and note for a fixed period like estepm months */          }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(jk=1; jk <=nlstate ; jk++){
      survival function given by stepm (the optimization length). Unfortunately it            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      means that if the survival funtion is printed only each two years of age and if              pp[jk] += freq[jk][m][i]; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          }
      results. So we changed our mind and took the option of the best precision.          for(jk=1; jk <=nlstate ; jk++){
   */            for(m=-1, pos=0; m <=0 ; m++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
   agelim=AGESUP;              if(first==1){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     /* nhstepm age range expressed in number of stepm */              }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            }else{
     /* if (stepm >= YEARM) hstepm=1;*/              if(first==1)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            }
     gp=matrix(0,nhstepm,1,nlstate*2);          }
     gm=matrix(0,nhstepm,1,nlstate*2);  
           for(jk=1; jk <=nlstate ; jk++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              pp[jk] += freq[jk][m][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }       
            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            posprop += prop[jk][i];
           }
     /* Computing Variances of health expectancies */          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
      for(theta=1; theta <=npar; theta++){              if(first==1)
       for(i=1; i<=npar; i++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       }            }else{
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       cptj=0;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<= nlstate; j++){            }
         for(i=1; i<=nlstate; i++){            if( i <= iagemax){
           cptj=cptj+1;              if(pos>=1.e-5){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                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]);*/
         }              }
       }              else
                      fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                  }
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(jk=-1; jk <=nlstate+ndeath; jk++)
                  for(m=-1; m <=nlstate+ndeath; m++)
       cptj=0;              if(freq[jk][m][i] !=0 ) {
       for(j=1; j<= nlstate; j++){              if(first==1)
         for(i=1;i<=nlstate;i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           cptj=cptj+1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){              }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          if(i <= iagemax)
           }            fprintf(ficresp,"\n");
         }          if(first==1)
       }            printf("Others in log...\n");
       for(j=1; j<= nlstate*2; j++)          fprintf(ficlog,"\n");
         for(h=0; h<=nhstepm-1; h++){        }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }    }
      }    dateintmean=dateintsum/k2cpt; 
       
 /* End theta */    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      for(h=0; h<=nhstepm-1; h++)    /* End of Freq */
       for(j=1; j<=nlstate*2;j++)  }
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  /************ Prevalence ********************/
        void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
      for(i=1;i<=nlstate*2;i++)    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       for(j=1;j<=nlstate*2;j++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
         varhe[i][j][(int)age] =0.;       We still use firstpass and lastpass as another selection.
     */
      printf("%d|",(int)age);fflush(stdout);   
      for(h=0;h<=nhstepm-1;h++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       for(k=0;k<=nhstepm-1;k++){    double ***freq; /* Frequencies */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    double *pp, **prop;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    double pos,posprop; 
         for(i=1;i<=nlstate*2;i++)    double  y2; /* in fractional years */
           for(j=1;j<=nlstate*2;j++)    int iagemin, iagemax;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    iagemin= (int) agemin;
     }    iagemax= (int) agemax;
     /* Computing expectancies */    /*pp=vector(1,nlstate);*/
     for(i=1; i<=nlstate;i++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       for(j=1; j<=nlstate;j++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    j1=0;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    
              j=cptcoveff;
 /* 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 (cptcovn<1) {j=1;ncodemax[1]=1;}
     
         }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficreseij,"%3.0f",age );        j1++;
     cptj=0;        
     for(i=1; i<=nlstate;i++)        for (i=1; i<=nlstate; i++)  
       for(j=1; j<=nlstate;j++){          for(m=iagemin; m <= iagemax+3; m++)
         cptj++;            prop[i][m]=0.0;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );       
       }        for (i=1; i<=imx; i++) { /* Each individual */
     fprintf(ficreseij,"\n");          bool=1;
              if  (cptcovn>0) {
     free_matrix(gm,0,nhstepm,1,nlstate*2);            for (z1=1; z1<=cptcoveff; z1++) 
     free_matrix(gp,0,nhstepm,1,nlstate*2);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);                bool=0;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (bool==1) { 
   }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   printf("\n");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   free_vector(xp,1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   free_matrix(dnewm,1,nlstate*2,1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);                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); 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
 }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
 /************ Variance ******************/                  prop[s[m][i]][iagemax+3] += weight[i]; 
 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)                } 
 {              }
   /* Variance of health expectancies */            } /* end selection of waves */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }
   double **newm;        }
   double **dnewm,**doldm;        for(i=iagemin; i <= iagemax+3; i++){  
   int i, j, nhstepm, hstepm, h, nstepm ;          
   int k, cptcode;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double *xp;            posprop += prop[jk][i]; 
   double **gp, **gm;          } 
   double ***gradg, ***trgradg;  
   double ***p3mat;          for(jk=1; jk <=nlstate ; jk++){     
   double age,agelim, hf;            if( i <=  iagemax){ 
   int theta;              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   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");            } 
   for(i=1; i<=nlstate;i++)          }/* end jk */ 
     for(j=1; j<=nlstate;j++)        }/* end i */ 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      } /* end i1 */
   fprintf(ficresvij,"\n");    } /* end k1 */
     
   xp=vector(1,npar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   dnewm=matrix(1,nlstate,1,npar);    /*free_vector(pp,1,nlstate);*/
   doldm=matrix(1,nlstate,1,nlstate);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  /* End of prevalence */
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  /************* Waves Concatenation ***************/
   }  
   else  hstepm=estepm;    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)
   /* 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.    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      nhstepm is the number of hstepm from age to agelim       Death is a valid wave (if date is known).
      nstepm is the number of stepm from age to agelin.       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      Look at hpijx to understand the reason of that which relies in memory size       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      and note for a fixed period like k years */       and mw[mi+1][i]. dh depends on stepm.
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the       */
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    int i, mi, m;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      results. So we changed our mind and took the option of the best precision.       double sum=0., jmean=0.;*/
   */    int first;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    int j, k=0,jk, ju, jl;
   agelim = AGESUP;    double sum=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    first=0;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    jmin=1e+5;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    jmax=-1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmean=0.;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    for(i=1; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);      mi=0;
     gm=matrix(0,nhstepm,1,nlstate);      m=firstpass;
       while(s[m][i] <= nlstate){
     for(theta=1; theta <=npar; theta++){        if(s[m][i]>=1)
       for(i=1; i<=npar; i++){ /* Computes gradient */          mw[++mi][i]=m;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if(m >=lastpass)
       }          break;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          else
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          m++;
       }/* end while */
       if (popbased==1) {      if (s[m][i] > nlstate){
         for(i=1; i<=nlstate;i++)        mi++;     /* Death is another wave */
           prlim[i][i]=probs[(int)age][i][ij];        /* if(mi==0)  never been interviewed correctly before death */
       }           /* Only death is a correct wave */
          mw[mi][i]=m;
       for(j=1; j<= nlstate; j++){      }
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      wav[i]=mi;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      if(mi==0){
         }        if(first==0){
       }          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if(first==1){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
        } /* end mi==0 */
       if (popbased==1) {    } /* End individuals */
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    for(i=1; i<=imx; i++){
       }      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
       for(j=1; j<= nlstate; j++){          dh[mi][i]=1;
         for(h=0; h<=nhstepm; h++){        else{
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            if (agedc[i] < 2*AGESUP) {
         }            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }            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(h=0; h<=nhstepm; h++){            if (j <= jmin) jmin=j;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            sum=sum+j;
         }            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     } /* End theta */            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             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]);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            }
           }
     for(h=0; h<=nhstepm; h++)          else{
       for(j=1; j<=nlstate;j++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         for(theta=1; theta <=npar; theta++)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           trgradg[h][j][theta]=gradg[h][theta][j];            k=k+1;
             if (j >= jmax) jmax=j;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            else if (j <= jmin)jmin=j;
     for(i=1;i<=nlstate;i++)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(j=1;j<=nlstate;j++)            /*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]);*/
         vareij[i][j][(int)age] =0.;            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]);
             sum=sum+j;
     for(h=0;h<=nhstepm;h++){          }
       for(k=0;k<=nhstepm;k++){          jk= j/stepm;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          jl= j -jk*stepm;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          ju= j -(jk+1)*stepm;
         for(i=1;i<=nlstate;i++)          if(mle <=1){ 
           for(j=1;j<=nlstate;j++)            if(jl==0){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              dh[mi][i]=jk;
       }              bh[mi][i]=0;
     }            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
     fprintf(ficresvij,"%.0f ",age );              dh[mi][i]=jk+1;
     for(i=1; i<=nlstate;i++)              bh[mi][i]=ju;
       for(j=1; j<=nlstate;j++){            }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          }else{
       }            if(jl <= -ju){
     fprintf(ficresvij,"\n");              dh[mi][i]=jk;
     free_matrix(gp,0,nhstepm,1,nlstate);              bh[mi][i]=jl;       /* bias is positive if real duration
     free_matrix(gm,0,nhstepm,1,nlstate);                                   * is higher than the multiple of stepm and negative otherwise.
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                                   */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            else{
   } /* End age */              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);            if(dh[mi][i]==0){
   free_matrix(dnewm,1,nlstate,1,nlstate);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
 }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
 /************ 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)        } /* end if mle */
 {      } /* end wave */
   /* Variance of prevalence limit */    }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    jmean=sum/k;
   double **newm;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double **dnewm,**doldm;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   int i, j, nhstepm, hstepm;   }
   int k, cptcode;  
   double *xp;  /*********** Tricode ****************************/
   double *gp, *gm;  void tricode(int *Tvar, int **nbcode, int imx)
   double **gradg, **trgradg;  {
   double age,agelim;    
   int theta;    int Ndum[20],ij=1, k, j, i, maxncov=19;
        int cptcode=0;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    cptcoveff=0; 
   fprintf(ficresvpl,"# Age");   
   for(i=1; i<=nlstate;i++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
       fprintf(ficresvpl," %1d-%1d",i,i);    for (k=1; k<=7; k++) ncodemax[k]=0;
   fprintf(ficresvpl,"\n");  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   xp=vector(1,npar);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   dnewm=matrix(1,nlstate,1,npar);                                 modality*/ 
   doldm=matrix(1,nlstate,1,nlstate);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
          Ndum[ij]++; /*store the modality */
   hstepm=1*YEARM; /* Every year of age */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   agelim = AGESUP;                                         Tvar[j]. If V=sex and male is 0 and 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                                         female is 1, then  cptcode=1.*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=0; i<=cptcode; i++) {
     gradg=matrix(1,npar,1,nlstate);        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 */
     gp=vector(1,nlstate);      }
     gm=vector(1,nlstate);  
       ij=1; 
     for(theta=1; theta <=npar; theta++){      for (i=1; i<=ncodemax[j]; i++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */        for (k=0; k<= maxncov; k++) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          if (Ndum[k] != 0) {
       }            nbcode[Tvar[j]][ij]=k; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       for(i=1;i<=nlstate;i++)            
         gp[i] = prlim[i][i];            ij++;
              }
       for(i=1; i<=npar; i++) /* Computes gradient */          if (ij > ncodemax[j]) break; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } 
       for(i=1;i<=nlstate;i++)    }  
         gm[i] = prlim[i][i];  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];   for (i=1; i<=ncovmodel-2; i++) { 
     } /* End theta */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
     trgradg =matrix(1,nlstate,1,npar);     Ndum[ij]++;
    }
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)   ij=1;
         trgradg[j][theta]=gradg[theta][j];   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
     for(i=1;i<=nlstate;i++)       Tvaraff[ij]=i; /*For printing */
       varpl[i][(int)age] =0.;       ij++;
     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 */   cptcoveff=ij-1; /*Number of simple covariates*/
   }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /*********** Health Expectancies ****************/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);  {
     free_matrix(gradg,1,npar,1,nlstate);    /* Health expectancies */
     free_matrix(trgradg,1,nlstate,1,npar);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   } /* End age */    double age, agelim, hf;
     double ***p3mat,***varhe;
   free_vector(xp,1,npar);    double **dnewm,**doldm;
   free_matrix(doldm,1,nlstate,1,npar);    double *xp;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double **gp, **gm;
     double ***gradg, ***trgradg;
 }    int theta;
   
 /************ Variance of one-step probabilities  ******************/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    xp=vector(1,npar);
 {    dnewm=matrix(1,nlstate*nlstate,1,npar);
   int i, j=0,  i1, k1, l1, t, tj;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   int k2, l2, j1,  z1;    
   int k=0,l, cptcode;    fprintf(ficreseij,"# Health expectancies\n");
   int first=1;    fprintf(ficreseij,"# Age");
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;    for(i=1; i<=nlstate;i++)
   double **dnewm,**doldm;      for(j=1; j<=nlstate;j++)
   double *xp;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   double *gp, *gm;    fprintf(ficreseij,"\n");
   double **gradg, **trgradg;  
   double **mu;    if(estepm < stepm){
   double age,agelim, cov[NCOVMAX];      printf ("Problem %d lower than %d\n",estepm, stepm);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    }
   int theta;    else  hstepm=estepm;   
   char fileresprob[FILENAMELENGTH];    /* We compute the life expectancy from trapezoids spaced every estepm months
   char fileresprobcov[FILENAMELENGTH];     * This is mainly to measure the difference between two models: for example
   char fileresprobcor[FILENAMELENGTH];     * 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 
   double ***varpij;     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   strcpy(fileresprob,"prob");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   strcat(fileresprob,fileres);     * to compare the new estimate of Life expectancy with the same linear 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {     * hypothesis. A more precise result, taking into account a more precise
     printf("Problem with resultfile: %s\n", fileresprob);     * curvature will be obtained if estepm is as small as stepm. */
   }  
   strcpy(fileresprobcov,"probcov");    /* For example we decided to compute the life expectancy with the smallest unit */
   strcat(fileresprobcov,fileres);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {       nhstepm is the number of hstepm from age to agelim 
     printf("Problem with resultfile: %s\n", fileresprobcov);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   strcpy(fileresprobcor,"probcor");       and note for a fixed period like estepm months */
   strcat(fileresprobcor,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with resultfile: %s\n", fileresprobcor);       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 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       results. So we changed our mind and took the option of the best precision.
   printf("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);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    agelim=AGESUP;
   fprintf(ficresprob,"# Age");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      /* nhstepm age range expressed in number of stepm */
   fprintf(ficresprobcov,"# Age");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficresprobcov,"# Age");      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for(i=1; i<=nlstate;i++)      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     for(j=1; j<=(nlstate+ndeath);j++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     }           in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   fprintf(ficresprob,"\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   fprintf(ficresprobcov,"\n");   
   fprintf(ficresprobcor,"\n");  
   xp=vector(1,npar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      /* Computing Variances of health expectancies */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);       for(theta=1; theta <=npar; theta++){
   first=1;        for(i=1; i<=npar; i++){ 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        }
     exit(0);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }    
   else{        cptj=0;
     fprintf(ficgp,"\n# Routine varprob");        for(j=1; j<= nlstate; j++){
   }          for(i=1; i<=nlstate; i++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            cptj=cptj+1;
     printf("Problem with html file: %s\n", optionfilehtm);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     exit(0);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   }            }
   else{          }
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");        }
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");       
     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");       
         for(i=1; i<=npar; i++) 
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
   cov[1]=1;        cptj=0;
   tj=cptcoveff;        for(j=1; j<= nlstate; j++){
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}          for(i=1;i<=nlstate;i++){
   j1=0;            cptj=cptj+1;
   for(t=1; t<=tj;t++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     for(i1=1; i1<=ncodemax[t];i1++){  
       j1++;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                  }
       if  (cptcovn>0) {          }
         fprintf(ficresprob, "\n#********** Variable ");        }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(j=1; j<= nlstate*nlstate; j++)
         fprintf(ficresprob, "**********\n#");          for(h=0; h<=nhstepm-1; h++){
         fprintf(ficresprobcov, "\n#********** Variable ");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
         fprintf(ficresprobcov, "**********\n#");       } 
             
         fprintf(ficgp, "\n#********** Variable ");  /* End theta */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
          
               for(h=0; h<=nhstepm-1; h++)
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");        for(j=1; j<=nlstate*nlstate;j++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for(theta=1; theta <=npar; theta++)
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");            trgradg[h][j][theta]=gradg[h][theta][j];
               
         fprintf(ficresprobcor, "\n#********** Variable ");      
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       for(i=1;i<=nlstate*nlstate;i++)
         fprintf(ficgp, "**********\n#");            for(j=1;j<=nlstate*nlstate;j++)
       }          varhe[i][j][(int)age] =0.;
        
       for (age=bage; age<=fage; age ++){       printf("%d|",(int)age);fflush(stdout);
         cov[2]=age;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for (k=1; k<=cptcovn;k++) {       for(h=0;h<=nhstepm-1;h++){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        for(k=0;k<=nhstepm-1;k++){
         }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         for (k=1; k<=cptcovprod;k++)          for(i=1;i<=nlstate*nlstate;i++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            for(j=1;j<=nlstate*nlstate;j++)
                      varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        }
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      }
         gp=vector(1,(nlstate)*(nlstate+ndeath));      /* Computing expectancies */
         gm=vector(1,(nlstate)*(nlstate+ndeath));      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           for(i=1; i<=npar; i++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            
            /* 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]);*/
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
                    }
           k=0;  
           for(i=1; i<= (nlstate); i++){      fprintf(ficreseij,"%3.0f",age );
             for(j=1; j<=(nlstate+ndeath);j++){      cptj=0;
               k=k+1;      for(i=1; i<=nlstate;i++)
               gp[k]=pmmij[i][j];        for(j=1; j<=nlstate;j++){
             }          cptj++;
           }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                  }
           for(i=1; i<=npar; i++)      fprintf(ficreseij,"\n");
             xp[i] = x[i] - (i==theta ?delti[theta]:0);     
          free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           k=0;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           for(i=1; i<=(nlstate); i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             for(j=1; j<=(nlstate+ndeath);j++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               k=k+1;    }
               gm[k]=pmmij[i][j];    printf("\n");
             }    fprintf(ficlog,"\n");
           }  
          free_vector(xp,1,npar);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)  /************ Variance ******************/
             trgradg[j][theta]=gradg[theta][j];  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)
          {
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    /* Variance of health expectancies */
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
            /* double **newm;*/
         pmij(pmmij,cov,ncovmodel,x,nlstate);    double **dnewm,**doldm;
            double **dnewmp,**doldmp;
         k=0;    int i, j, nhstepm, hstepm, h, nstepm ;
         for(i=1; i<=(nlstate); i++){    int k, cptcode;
           for(j=1; j<=(nlstate+ndeath);j++){    double *xp;
             k=k+1;    double **gp, **gm;  /* for var eij */
             mu[k][(int) age]=pmmij[i][j];    double ***gradg, ***trgradg; /*for var eij */
           }    double **gradgp, **trgradgp; /* for var p point j */
         }    double *gpp, *gmp; /* for var p point j */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    double ***p3mat;
             varpij[i][j][(int)age] = doldm[i][j];    double age,agelim, hf;
     double ***mobaverage;
         /*printf("\n%d ",(int)age);    int theta;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    char digit[4];
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    char digitp[25];
      }*/  
     char fileresprobmorprev[FILENAMELENGTH];
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);    if(popbased==1){
         fprintf(ficresprobcor,"\n%d ",(int)age);      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      else strcpy(digitp,"-populbased-nomobil-");
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    else 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      strcpy(digitp,"-stablbased-");
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }    if (mobilav!=0) {
         i=0;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for (k=1; k<=(nlstate);k++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           for (l=1; l<=(nlstate+ndeath);l++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             i=i++;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      }
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    }
             for (j=1; j<=i;j++){  
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    strcpy(fileresprobmorprev,"prmorprev"); 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    sprintf(digit,"%-d",ij);
             }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         }/* end of loop for state */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       } /* end of loop for age */    strcat(fileresprobmorprev,fileres);
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for (k1=1; k1<=(nlstate);k1++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         for (l1=1; l1<=(nlstate+ndeath);l1++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           if(l1==k1) continue;    }
           i=(k1-1)*(nlstate+ndeath)+l1;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           for (k2=1; k2<=(nlstate);k2++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             for (l2=1; l2<=(nlstate+ndeath);l2++){    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);
               if(l2==k2) continue;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
               j=(k2-1)*(nlstate+ndeath)+l2;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
               if(j<=i) continue;      fprintf(ficresprobmorprev," p.%-d SE",j);
               for (age=bage; age<=fage; age ++){      for(i=1; i<=nlstate;i++)
                 if ((int)age %5==0){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    }  
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(ficresprobmorprev,"\n");
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
                   mu1=mu[i][(int) age]/stepm*YEARM ;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
                   mu2=mu[j][(int) age]/stepm*YEARM;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
                   /* Computing eigen value of matrix of covariance */      exit(0);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    }
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    else{
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      fprintf(ficgp,"\n# Routine varevsij");
                   /* Eigen vectors */    }
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
                   v21=sqrt(1.-v11*v11);      printf("Problem with html file: %s\n", optionfilehtm);
                   v12=-v21;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
                   v22=v11;      exit(0);
                   /*printf(fignu*/    }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    else{
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      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");
                   if(first==1){      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                     first=0;    }
                     fprintf(ficgp,"\nset parametric;set nolabel");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    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(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>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);    fprintf(ficresvij,"# Age");
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    for(i=1; i<=nlstate;i++)
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);      for(j=1; j<=nlstate;j++)
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    fprintf(ficresvij,"\n");
                     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)) t \"%d\"",\  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    xp=vector(1,npar);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    dnewm=matrix(1,nlstate,1,npar);
                   }else{    doldm=matrix(1,nlstate,1,nlstate);
                     first=0;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  
                     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)) t \"%d\"",\    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    gpp=vector(nlstate+1,nlstate+ndeath);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    gmp=vector(nlstate+1,nlstate+ndeath);
                   }/* if first */    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                 } /* age mod 5 */    
               } /* end loop age */    if(estepm < stepm){
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);      printf ("Problem %d lower than %d\n",estepm, stepm);
               first=1;    }
             } /*l12 */    else  hstepm=estepm;   
           } /* k12 */    /* For example we decided to compute the life expectancy with the smallest unit */
         } /*l1 */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       }/* k1 */       nhstepm is the number of hstepm from age to agelim 
     } /* loop covariates */       nstepm is the number of stepm from age to agelin. 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);       Look at hpijx to understand the reason of that which relies in memory size
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       and note for a fixed period like k years */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);       survival function given by stepm (the optimization length). Unfortunately it
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       means that if the survival funtion is printed every two years of age and if
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       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.
   free_vector(xp,1,npar);    */
   fclose(ficresprob);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fclose(ficresprobcov);    agelim = AGESUP;
   fclose(ficresprobcor);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fclose(ficgp);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fclose(fichtm);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
 /******************* Printing html file ***********/      gm=matrix(0,nhstepm,1,nlstate);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
                   int lastpass, int stepm, int weightopt, char model[],\  
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      for(theta=1; theta <=npar; theta++){
                   int popforecast, int estepm ,\        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                   double jprev1, double mprev1,double anprev1, \          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   double jprev2, double mprev2,double anprev2){        }
   int jj1, k1, i1, cpt;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /*char optionfilehtm[FILENAMELENGTH];*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);        if (popbased==1) {
   }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n              prlim[i][i]=probs[(int)age][i][ij];
  - 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          }else{ /* mobilav */ 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n            for(i=1; i<=nlstate;i++)
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n              prlim[i][i]=mobaverage[(int)age][i][ij];
  - Life expectancies by age and initial health status (estepm=%2d months):          }
    <a href=\"e%s\">e%s</a> <br>\n</li>", \        }
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    
         for(j=1; j<= nlstate; j++){
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n          for(h=0; h<=nhstepm; h++){
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n          }
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        }
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        /* This for computing probability of death (h=1 means
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n           computed over hstepm matrices product = hstepm*stepm months) 
  - 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);           as a weighted average of prlim.
         */
  if(popforecast==1) fprintf(fichtm,"\n        for(j=nlstate+1;j<=nlstate+ndeath;j++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          for(i=1,gpp[j]=0.; i<= nlstate; i++)
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         <br>",fileres,fileres,fileres,fileres);        }    
  else        /* end probability of death */
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);  
 fprintf(fichtm," <li><b>Graphs</b></li><p>");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
  m=cptcoveff;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
  jj1=0;        if (popbased==1) {
  for(k1=1; k1<=m;k1++){          if(mobilav ==0){
    for(i1=1; i1<=ncodemax[k1];i1++){            for(i=1; i<=nlstate;i++)
      jj1++;              prlim[i][i]=probs[(int)age][i][ij];
      if (cptcovn > 0) {          }else{ /* mobilav */ 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            for(i=1; i<=nlstate;i++)
        for (cpt=1; cpt<=cptcoveff;cpt++)              prlim[i][i]=mobaverage[(int)age][i][ij];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }
      }  
      /* Pij */        for(j=1; j<= nlstate; j++){
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>          for(h=0; h<=nhstepm; h++){
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      /* Quasi-incidences */              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>          }
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
        /* Stable prevalence in each health state */        /* This for computing probability of death (h=1 means
        for(cpt=1; cpt<nlstate;cpt++){           computed over hstepm matrices product = hstepm*stepm months) 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>           as a weighted average of prlim.
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        */
        }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(cpt=1; cpt<=nlstate;cpt++) {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 interval) in state (%d): v%s%d%d.png <br>        }    
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          /* end probability of death */
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {        for(j=1; j<= nlstate; j++) /* vareij */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>          for(h=0; h<=nhstepm; h++){
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
      }          }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
    }        }
  }  
 fclose(fichtm);      } /* End theta */
 }  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          for(theta=1; theta <=npar; theta++)
   int ng;            trgradg[h][j][theta]=gradg[h][theta][j];
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   }        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
 #ifdef windows    
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 m=pow(2,cptcoveff);      for(i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate;j++)
  /* 1eme*/          vareij[i][j][(int)age] =0.;
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
 #ifdef windows          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          for(i=1;i<=nlstate;i++)
 #endif            for(j=1;j<=nlstate;j++)
 #ifdef unix              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      }
 #endif    
       /* pptj */
 for (i=1; i<= nlstate ; i ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          varppt[j][i]=doldmp[j][i];
     for (i=1; i<= nlstate ; i ++) {      /* end ppptj */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /*  x centered again */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);   
      for (i=1; i<= nlstate ; i ++) {      if (popbased==1) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(mobilav ==0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1; i<=nlstate;i++)
 }              prlim[i][i]=probs[(int)age][i][ij];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }else{ /* mobilav */ 
 #ifdef unix          for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            prlim[i][i]=mobaverage[(int)age][i][ij];
 #endif        }
    }      }
   }               
   /*2 eme*/      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   for (k1=1; k1<= m ; k1 ++) {         as a weighted average of prlim.
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     for (i=1; i<= nlstate+1 ; i ++) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       k=2*i;      }    
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      /* end probability of death */
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 }          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(i=1; i<=nlstate;i++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {      } 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresprobmorprev,"\n");
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        fprintf(ficresvij,"%.0f ",age );
       fprintf(ficgp,"\" t\"\" w l 0,");      for(i=1; i<=nlstate;i++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(j=1; j<=nlstate;j++){
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficresvij,"\n");
 }        free_matrix(gp,0,nhstepm,1,nlstate);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      free_matrix(gm,0,nhstepm,1,nlstate);
       else fprintf(ficgp,"\" t\"\" w l 0,");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
   /*3eme*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   for (k1=1; k1<= m ; k1 ++) {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       k=2+nlstate*(2*cpt-2);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
 */    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
       for (i=1; i< nlstate ; i ++) {    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  */
     fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
       }  
     }    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
   /* CV preval stat */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for (k1=1; k1<= m ; k1 ++) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     for (cpt=1; cpt<nlstate ; cpt ++) {    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       k=3;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fclose(ficresprobmorprev);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    fclose(ficgp);
     fclose(fichtm);
       for (i=1; i< nlstate ; i ++)  }  
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  /************ 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)
       l=3+(nlstate+ndeath)*cpt;  {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    /* Variance of prevalence limit */
       for (i=1; i< nlstate ; i ++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         l=3+(nlstate+ndeath)*cpt;    double **newm;
         fprintf(ficgp,"+$%d",l+i+1);    double **dnewm,**doldm;
       }    int i, j, nhstepm, hstepm;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int k, cptcode;
     }    double *xp;
   }      double *gp, *gm;
      double **gradg, **trgradg;
   /* proba elementaires */    double age,agelim;
    for(i=1,jk=1; i <=nlstate; i++){    int theta;
     for(k=1; k <=(nlstate+ndeath); k++){     
       if (k != i) {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         for(j=1; j <=ncovmodel; j++){    fprintf(ficresvpl,"# Age");
            for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        fprintf(ficresvpl," %1d-%1d",i,i);
           jk++;    fprintf(ficresvpl,"\n");
           fprintf(ficgp,"\n");  
         }    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
    }    
     hstepm=1*YEARM; /* Every year of age */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      for(jk=1; jk <=m; jk++) {    agelim = AGESUP;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        if (ng==2)      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      if (stepm >= YEARM) hstepm=1;
        else      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
          fprintf(ficgp,"\nset title \"Probability\"\n");      gradg=matrix(1,npar,1,nlstate);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      gp=vector(1,nlstate);
        i=1;      gm=vector(1,nlstate);
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;      for(theta=1; theta <=npar; theta++){
          for(k=1; k<=(nlstate+ndeath); k++) {        for(i=1; i<=npar; i++){ /* Computes gradient */
            if (k != k2){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              if(ng==2)        }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              else        for(i=1;i<=nlstate;i++)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          gp[i] = prlim[i][i];
              ij=1;      
              for(j=3; j <=ncovmodel; j++) {        for(i=1; i<=npar; i++) /* Computes gradient */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                  ij++;        for(i=1;i<=nlstate;i++)
                }          gm[i] = prlim[i][i];
                else  
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(i=1;i<=nlstate;i++)
              }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
              fprintf(ficgp,")/(1");      } /* End theta */
                
              for(k1=1; k1 <=nlstate; k1++){        trgradg =matrix(1,nlstate,1,npar);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
                ij=1;      for(j=1; j<=nlstate;j++)
                for(j=3; j <=ncovmodel; j++){        for(theta=1; theta <=npar; theta++)
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          trgradg[j][theta]=gradg[theta][j];
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;      for(i=1;i<=nlstate;i++)
                  }        varpl[i][(int)age] =0.;
                  else      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                }      for(i=1;i<=nlstate;i++)
                fprintf(ficgp,")");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
              }  
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      fprintf(ficresvpl,"%.0f ",age );
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      for(i=1; i<=nlstate;i++)
              i=i+ncovmodel;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
            }      fprintf(ficresvpl,"\n");
          }      free_vector(gp,1,nlstate);
        }      free_vector(gm,1,nlstate);
      }      free_matrix(gradg,1,npar,1,nlstate);
    }      free_matrix(trgradg,1,nlstate,1,npar);
    fclose(ficgp);    } /* End age */
 }  /* end gnuplot */  
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
 /*************** Moving average **************/    free_matrix(dnewm,1,nlstate,1,nlstate);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
   }
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  /************ Variance of one-step probabilities  ******************/
       for (i=1; i<=nlstate;i++)  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  {
           mobaverage[(int)agedeb][i][cptcod]=0.;    int i, j=0,  i1, k1, l1, t, tj;
        int k2, l2, j1,  z1;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    int k=0,l, cptcode;
       for (i=1; i<=nlstate;i++){    int first=1, first1;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           for (cpt=0;cpt<=4;cpt++){    double **dnewm,**doldm;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double *xp;
           }    double *gp, *gm;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    double **gradg, **trgradg;
         }    double **mu;
       }    double age,agelim, cov[NCOVMAX];
     }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        int theta;
 }    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    double ***varpij;
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    strcpy(fileresprob,"prob"); 
   int *popage;    strcat(fileresprob,fileres);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   double *popeffectif,*popcount;      printf("Problem with resultfile: %s\n", fileresprob);
   double ***p3mat;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   char fileresf[FILENAMELENGTH];    }
     strcpy(fileresprobcov,"probcov"); 
  agelim=AGESUP;    strcat(fileresprobcov,fileres);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
      strcpy(fileresprobcor,"probcor"); 
   strcpy(fileresf,"f");    strcat(fileresprobcor,fileres);
   strcat(fileresf,fileres);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if((ficresf=fopen(fileresf,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprobcor);
     printf("Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
   printf("Computing forecasting: result on file '%s' \n", fileresf);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   if (mobilav==1) {    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    
   }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   if (stepm<=12) stepsize=1;    fprintf(ficresprobcov,"# Age");
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   agelim=AGESUP;    fprintf(ficresprobcov,"# Age");
    
   hstepm=1;  
   hstepm=hstepm/stepm;    for(i=1; i<=nlstate;i++)
   yp1=modf(dateintmean,&yp);      for(j=1; j<=(nlstate+ndeath);j++){
   anprojmean=yp;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   yp2=modf((yp1*12),&yp);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   mprojmean=yp;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   yp1=modf((yp2*30.5),&yp);      }  
   jprojmean=yp;   /* fprintf(ficresprob,"\n");
   if(jprojmean==0) jprojmean=1;    fprintf(ficresprobcov,"\n");
   if(mprojmean==0) jprojmean=1;    fprintf(ficresprobcor,"\n");
     */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       k=k+1;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fprintf(ficresf,"\n#******");    first=1;
       for(j=1;j<=cptcoveff;j++) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficresf,"******\n");      exit(0);
       fprintf(ficresf,"# StartingAge FinalAge");    }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    else{
            fprintf(ficgp,"\n# Routine varprob");
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
         fprintf(ficresf,"\n");      printf("Problem with html file: %s\n", optionfilehtm);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    else{
           nhstepm = nhstepm/hstepm;      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                fprintf(fichtm,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
              fprintf(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");
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);  
             }    cov[1]=1;
             for(j=1; j<=nlstate+ndeath;j++) {    tj=cptcoveff;
               kk1=0.;kk2=0;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
               for(i=1; i<=nlstate;i++) {                  j1=0;
                 if (mobilav==1)    for(t=1; t<=tj;t++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(i1=1; i1<=ncodemax[t];i1++){ 
                 else {        j1++;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        if  (cptcovn>0) {
                 }          fprintf(ficresprob, "\n#********** Variable "); 
                          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               }          fprintf(ficresprob, "**********\n#\n");
               if (h==(int)(calagedate+12*cpt)){          fprintf(ficresprobcov, "\n#********** Variable "); 
                 fprintf(ficresf," %.3f", kk1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                                  fprintf(ficresprobcov, "**********\n#\n");
               }          
             }          fprintf(ficgp, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp, "**********\n#\n");
         }          
       }          
     }          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]]);
                  fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   fclose(ficresf);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }          fprintf(ficresprobcor, "**********\n#");    
 /************** Forecasting ******************/        }
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        
          for (age=bage; age<=fage; age ++){ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          cov[2]=age;
   int *popage;          for (k=1; k<=cptcovn;k++) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   double *popeffectif,*popcount;          }
   double ***p3mat,***tabpop,***tabpopprev;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   char filerespop[FILENAMELENGTH];          for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   agelim=AGESUP;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          gp=vector(1,(nlstate)*(nlstate+ndeath));
            gm=vector(1,(nlstate)*(nlstate+ndeath));
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      
            for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   strcpy(filerespop,"pop");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   strcat(filerespop,fileres);            
   if((ficrespop=fopen(filerespop,"w"))==NULL) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     printf("Problem with forecast resultfile: %s\n", filerespop);            
   }            k=0;
   printf("Computing forecasting: result on file '%s' \n", filerespop);            for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                k=k+1;
                 gp[k]=pmmij[i][j];
   if (mobilav==1) {              }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
     movingaverage(agedeb, fage, ageminpar, mobaverage);            
   }            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      
   if (stepm<=12) stepsize=1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              k=0;
   agelim=AGESUP;            for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
   hstepm=1;                k=k+1;
   hstepm=hstepm/stepm;                gm[k]=pmmij[i][j];
                }
   if (popforecast==1) {            }
     if((ficpop=fopen(popfile,"r"))==NULL) {       
       printf("Problem with population file : %s\n",popfile);exit(0);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     popage=ivector(0,AGESUP);          }
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                for(theta=1; theta <=npar; theta++)
     i=1;                trgradg[j][theta]=gradg[theta][j];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          
              matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     imx=i;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
       fprintf(ficrespop,"\n#******");          
       for(j=1;j<=cptcoveff;j++) {          k=0;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficrespop,"******\n");              k=k+1;
       fprintf(ficrespop,"# Age");              mu[k][(int) age]=pmmij[i][j];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            }
       if (popforecast==1)  fprintf(ficrespop," [Population]");          }
                for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       for (cpt=0; cpt<=0;cpt++) {            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                varpij[i][j][(int)age] = doldm[i][j];
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          /*printf("\n%d ",(int)age);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           nhstepm = nhstepm/hstepm;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                      fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           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(ficresprob,"\n%d ",(int)age);
                  fprintf(ficresprobcov,"\n%d ",(int)age);
           for (h=0; h<=nhstepm; h++){          fprintf(ficresprobcor,"\n%d ",(int)age);
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          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(j=1; j<=nlstate+ndeath;j++) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               kk1=0.;kk2=0;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
               for(i=1; i<=nlstate;i++) {                          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                 if (mobilav==1)          }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          i=0;
                 else {          for (k=1; k<=(nlstate);k++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            for (l=1; l<=(nlstate+ndeath);l++){ 
                 }              i=i++;
               }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               if (h==(int)(calagedate+12*cpt)){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              for (j=1; j<=i;j++){
                   /*fprintf(ficrespop," %.3f", kk1);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }              }
             }            }
             for(i=1; i<=nlstate;i++){          }/* end of loop for state */
               kk1=0.;        } /* end of loop for age */
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        /* Confidence intervalle of pij  */
                 }        /*
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          fprintf(ficgp,"\nset noparametric;unset label");
             }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         }        */
       }  
          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   /******/        first1=1;
         for (k2=1; k2<=(nlstate);k2++){
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              if(l2==k2) continue;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            j=(k2-1)*(nlstate+ndeath)+l2;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for (k1=1; k1<=(nlstate);k1++){
           nhstepm = nhstepm/hstepm;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                          if(l1==k1) continue;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                i=(k1-1)*(nlstate+ndeath)+l1;
           oldm=oldms;savm=savms;                if(i<=j) continue;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  for (age=bage; age<=fage; age ++){ 
           for (h=0; h<=nhstepm; h++){                  if ((int)age %5==0){
             if (h==(int) (calagedate+YEARM*cpt)) {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
             }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
             for(j=1; j<=nlstate+ndeath;j++) {                    mu1=mu[i][(int) age]/stepm*YEARM ;
               kk1=0.;kk2=0;                    mu2=mu[j][(int) age]/stepm*YEARM;
               for(i=1; i<=nlstate;i++) {                                  c12=cv12/sqrt(v1*v2);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                        /* Computing eigen value of matrix of covariance */
               }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             }                    /* Eigen vectors */
           }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    /*v21=sqrt(1.-v11*v11); *//* error */
         }                    v21=(lc1-v1)/cv12*v11;
       }                    v12=-v21;
    }                    v22=v11;
   }                    tnalp=v21/v11;
                      if(first1==1){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      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);
   if (popforecast==1) {                    }
     free_ivector(popage,0,AGESUP);                    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);
     free_vector(popeffectif,0,AGESUP);                    /*printf(fignu*/
     free_vector(popcount,0,AGESUP);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    if(first==1){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      first=0;
   fclose(ficrespop);                      fprintf(ficgp,"\nset parametric;unset label");
 }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 /***********************************************/                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
 /**************** Main Program *****************/                      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);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
 int main(int argc, char *argv[])                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       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",\
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double agedeb, agefin,hf;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                    }else{
                       first=0;
   double fret;                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   double **xi,tmp,delta;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double dum; /* Dummy variable */                      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",\
   double ***p3mat;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   int *indx;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   char line[MAXLINE], linepar[MAXLINE];                    }/* if first */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                  } /* age mod 5 */
   int firstobs=1, lastobs=10;                } /* end loop age */
   int sdeb, sfin; /* Status at beginning and end */                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   int c,  h , cpt,l;                first=1;
   int ju,jl, mi;              } /*l12 */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            } /* k12 */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          } /*l1 */
   int mobilav=0,popforecast=0;        }/* k1 */
   int hstepm, nhstepm;      } /* loop covariates */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   double bage, fage, age, agelim, agebase;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   double ftolpl=FTOL;    free_vector(xp,1,npar);
   double **prlim;    fclose(ficresprob);
   double *severity;    fclose(ficresprobcov);
   double ***param; /* Matrix of parameters */    fclose(ficresprobcor);
   double  *p;    fclose(ficgp);
   double **matcov; /* Matrix of covariance */    fclose(fichtm);
   double ***delti3; /* Scale */  }
   double *delti; /* Scale */  
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  /******************* Printing html file ***********/
   double *epj, vepp;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   double kk1, kk2;                    int lastpass, int stepm, int weightopt, char model[],\
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                      int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   char *alph[]={"a","a","b","c","d","e"}, str[4];                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   char z[1]="c", occ;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
 #include <sys/time.h>      printf("Problem with %s \n",optionfilehtm), exit(0);
 #include <time.h>      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    }
    
   /* long total_usecs;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   struct timeval start_time, end_time;   - 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
     - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   getcwd(pathcd, size);   - Life expectancies by age and initial health status (estepm=%2d months): 
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
   printf("\n%s",version);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     scanf("%s",pathtot);  
   }   m=cptcoveff;
   else{   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     strcpy(pathtot,argv[1]);  
   }   jj1=0;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/   for(k1=1; k1<=m;k1++){
   /*cygwin_split_path(pathtot,path,optionfile);     for(i1=1; i1<=ncodemax[k1];i1++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       jj1++;
   /* cutv(path,optionfile,pathtot,'\\');*/       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);         for (cpt=1; cpt<=cptcoveff;cpt++) 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   chdir(path);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   replace(pathc,path);       }
        /* Pij */
 /*-------- arguments in the command line --------*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   strcpy(fileres,"r");       /* Quasi-incidences */
   strcat(fileres, optionfilefiname);       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>
   strcat(fileres,".txt");    /* Other files have txt extension */  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
   /*---------arguments file --------*/         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     printf("Problem with optionfile %s\n",optionfile);         }
     goto end;       for(cpt=1; cpt<=nlstate;cpt++) {
   }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   strcpy(filereso,"o");       }
   strcat(filereso,fileres);       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   if((ficparo=fopen(filereso,"w"))==NULL) {  health expectancies in states (1) and (2): e%s%d.png<br>
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   }     } /* end i1 */
    }/* End k1 */
   /* Reads comments: lines beginning with '#' */   fprintf(fichtm,"</ul>");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     puts(line);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     fputs(line,ficparo);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   }   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   ungetc(c,ficpar);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   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);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);   - 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);
   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){  /*  if(popforecast==1) fprintf(fichtm,"\n */
     ungetc(c,ficpar);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     fgets(line, MAXLINE, ficpar);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     puts(line);  /*      <br>",fileres,fileres,fileres,fileres); */
     fputs(line,ficparo);  /*  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); */
   ungetc(c,ficpar);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    
       m=cptcoveff;
   covar=matrix(0,NCOVMAX,1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;   jj1=0;
    for(k1=1; k1<=m;k1++){
   ncovmodel=2+cptcovn;     for(i1=1; i1<=ncodemax[k1];i1++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */       jj1++;
         if (cptcovn > 0) {
   /* Read guess parameters */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /* Reads comments: lines beginning with '#' */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   while((c=getc(ficpar))=='#' && c!= EOF){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     fgets(line, MAXLINE, ficpar);       }
     puts(line);       for(cpt=1; cpt<=nlstate;cpt++) {
     fputs(line,ficparo);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   }  interval) in state (%d): v%s%d%d.png <br>
   ungetc(c,ficpar);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
         }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     } /* end i1 */
     for(i=1; i <=nlstate; i++)   }/* End k1 */
     for(j=1; j <=nlstate+ndeath-1; j++){   fprintf(fichtm,"</ul>");
       fscanf(ficpar,"%1d%1d",&i1,&j1);  fclose(fichtm);
       fprintf(ficparo,"%1d%1d",i1,j1);  }
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){  /******************* Gnuplot file **************/
         fscanf(ficpar," %lf",&param[i][j][k]);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       }    int ng;
       fscanf(ficpar,"\n");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("\n");      printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficparo,"\n");      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }    }
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
   p=param[1][1];      /*#endif */
    m=pow(2,cptcoveff);
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){   /* 1eme*/
     ungetc(c,ficpar);    for (cpt=1; cpt<= nlstate ; cpt ++) {
     fgets(line, MAXLINE, ficpar);     for (k1=1; k1<= m ; k1 ++) {
     puts(line);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     fputs(line,ficparo);       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);
   }  
   ungetc(c,ficpar);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       }
   for(i=1; i <=nlstate; i++){       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
     for(j=1; j <=nlstate+ndeath-1; j++){       for (i=1; i<= nlstate ; i ++) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       printf("%1d%1d",i,j);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficparo,"%1d%1d",i1,j1);       } 
       for(k=1; k<=ncovmodel;k++){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
         fscanf(ficpar,"%le",&delti3[i][j][k]);       for (i=1; i<= nlstate ; i ++) {
         printf(" %le",delti3[i][j][k]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficparo," %le",delti3[i][j][k]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       }  
       fscanf(ficpar,"\n");       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       printf("\n");     }
       fprintf(ficparo,"\n");    }
     }    /*2 eme*/
   }    
   delti=delti3[1][1];    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   /* Reads comments: lines beginning with '#' */      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);      for (i=1; i<= nlstate+1 ; i ++) {
     fgets(line, MAXLINE, ficpar);        k=2*i;
     puts(line);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     fputs(line,ficparo);        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   ungetc(c,ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
   matcov=matrix(1,npar,1,npar);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   for(i=1; i <=npar; i++){        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     fscanf(ficpar,"%s",&str);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
     printf("%s",str);        for (j=1; j<= nlstate+1 ; j ++) {
     fprintf(ficparo,"%s",str);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     for(j=1; j <=i; j++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fscanf(ficpar," %le",&matcov[i][j]);        }   
       printf(" %.5le",matcov[i][j]);        fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficparo," %.5le",matcov[i][j]);        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 ++) {
     fscanf(ficpar,"\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     printf("\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fprintf(ficparo,"\n");        }   
   }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   for(i=1; i <=npar; i++)        else fprintf(ficgp,"\" t\"\" w l 0,");
     for(j=i+1;j<=npar;j++)      }
       matcov[i][j]=matcov[j][i];    }
        
   printf("\n");    /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
     /*-------- Rewriting paramater file ----------*/      for (cpt=1; cpt<= nlstate ; cpt ++) {
      strcpy(rfileres,"r");    /* "Rparameterfile */        k=2+nlstate*(2*cpt-2);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
      strcat(rfileres,".");    /* */        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);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     if((ficres =fopen(rfileres,"w"))==NULL) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     fprintf(ficres,"#%s\n",version);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     /*-------- data file ----------*/          
     if((fic=fopen(datafile,"r"))==NULL)    {        */
       printf("Problem with datafile: %s\n", datafile);goto end;        for (i=1; i< nlstate ; i ++) {
     }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
     n= lastobs;        } 
     severity = vector(1,maxwav);      }
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    
     moisnais=vector(1,n);    /* CV preval stable (period) */
     annais=vector(1,n);    for (k1=1; k1<= m ; k1 ++) { 
     moisdc=vector(1,n);      for (cpt=1; cpt<=nlstate ; cpt ++) {
     andc=vector(1,n);        k=3;
     agedc=vector(1,n);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     cod=ivector(1,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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     weight=vector(1,n);        
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for (i=1; i<= nlstate ; i ++)
     mint=matrix(1,maxwav,1,n);          fprintf(ficgp,"+$%d",k+i+1);
     anint=matrix(1,maxwav,1,n);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     s=imatrix(1,maxwav+1,1,n);        
     adl=imatrix(1,maxwav+1,1,n);            l=3+(nlstate+ndeath)*cpt;
     tab=ivector(1,NCOVMAX);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     ncodemax=ivector(1,8);        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
     i=1;          fprintf(ficgp,"+$%d",l+i+1);
     while (fgets(line, MAXLINE, fic) != NULL)    {        }
       if ((i >= firstobs) && (i <=lastobs)) {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
              } 
         for (j=maxwav;j>=1;j--){    }  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    
           strcpy(line,stra);    /* proba elementaires */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1,jk=1; i <=nlstate; i++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(k=1; k <=(nlstate+ndeath); k++){
         }        if (k != i) {
                  for(j=1; j <=ncovmodel; j++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            jk++; 
             fprintf(ficgp,"\n");
         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);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         }       for(jk=1; jk <=m; jk++) {
         num[i]=atol(stra);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
                 if (ng==2)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
         i=i+1;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
       }         i=1;
     }         for(k2=1; k2<=nlstate; k2++) {
     /* printf("ii=%d", ij);           k3=i;
        scanf("%d",i);*/           for(k=1; k<=(nlstate+ndeath); k++) {
   imx=i-1; /* Number of individuals */             if (k != k2){
                if(ng==2)
   /* for (i=1; i<=imx; i++){                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;               else
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;               ij=1;
     }*/               for(j=3; j <=ncovmodel; j++) {
    /*  for (i=1; i<=imx; i++){                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
      if (s[4][i]==9)  s[4][i]=-1;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
      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++;
                   }
                   else
   /* Calculation of the number of parameter from char model*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   Tvar=ivector(1,15);               }
   Tprod=ivector(1,15);               fprintf(ficgp,")/(1");
   Tvaraff=ivector(1,15);               
   Tvard=imatrix(1,15,1,2);               for(k1=1; k1 <=nlstate; k1++){   
   Tage=ivector(1,15);                       fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                     ij=1;
   if (strlen(model) >1){                 for(j=3; j <=ncovmodel; j++){
     j=0, j1=0, k1=1, k2=1;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     j=nbocc(model,'+');                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     j1=nbocc(model,'*');                     ij++;
     cptcovn=j+1;                   }
     cptcovprod=j1;                   else
                         fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     strcpy(modelsav,model);                 }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                 fprintf(ficgp,")");
       printf("Error. Non available option model=%s ",model);               }
       goto end;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   i=i+ncovmodel;
     for(i=(j+1); i>=1;i--){             }
       cutv(stra,strb,modelsav,'+');           } /* end k */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);         } /* end k2 */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/       } /* end jk */
       /*scanf("%d",i);*/     } /* end ng */
       if (strchr(strb,'*')) {     fclose(ficgp); 
         cutv(strd,strc,strb,'*');  }  /* end gnuplot */
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  /*************** Moving average **************/
           Tvar[i]=atoi(stre);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           cptcovage++;  
             Tage[cptcovage]=i;    int i, cpt, cptcod;
             /*printf("stre=%s ", stre);*/    int modcovmax =1;
         }    int mobilavrange, mob;
         else if (strcmp(strd,"age")==0) {    double age;
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           Tvar[i]=atoi(stre);                             a covariate has 2 modalities */
           cptcovage++;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           Tage[cptcovage]=i;  
         }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         else {      if(mobilav==1) mobilavrange=5; /* default */
           cutv(strb,stre,strc,'V');      else mobilavrange=mobilav;
           Tvar[i]=ncovcol+k1;      for (age=bage; age<=fage; age++)
           cutv(strb,strc,strd,'V');        for (i=1; i<=nlstate;i++)
           Tprod[k1]=i;          for (cptcod=1;cptcod<=modcovmax;cptcod++)
           Tvard[k1][1]=atoi(strc);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
           Tvard[k1][2]=atoi(stre);      /* We keep the original values on the extreme ages bage, fage and for 
           Tvar[cptcovn+k2]=Tvard[k1][1];         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           Tvar[cptcovn+k2+1]=Tvard[k1][2];         we use a 5 terms etc. until the borders are no more concerned. 
           for (k=1; k<=lastobs;k++)      */ 
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for (mob=3;mob <=mobilavrange;mob=mob+2){
           k1++;        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           k2=k2+2;          for (i=1; i<=nlstate;i++){
         }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
       else {                for (cpt=1;cpt<=(mob-1)/2;cpt++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
        /*  scanf("%d",i);*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
       cutv(strd,strc,strb,'V');                }
       Tvar[i]=atoi(strc);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
       }            }
       strcpy(modelsav,stra);            }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        }/* end age */
         scanf("%d",i);*/      }/* end mob */
     }    }else return -1;
 }    return 0;
    }/* End movingaverage */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/  /************** Forecasting ******************/
     fclose(fic);  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 
     /*  if(mle==1){*/       agemin, agemax range of age
     if (weightopt != 1) { /* Maximisation without weights*/       dateprev1 dateprev2 range of dates during which prevalence is computed
       for(i=1;i<=n;i++) weight[i]=1.0;       anproj2 year of en of projection (same day and month as proj1).
     }    */
     /*-calculation of age at interview from date of interview and age at death -*/    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     agev=matrix(1,maxwav,1,imx);    int *popage;
     double agec; /* generic age */
     for (i=1; i<=imx; i++) {    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       for(m=2; (m<= maxwav); m++) {    double *popeffectif,*popcount;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double ***p3mat;
          anint[m][i]=9999;    double ***mobaverage;
          s[m][i]=-1;    char fileresf[FILENAMELENGTH];
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    agelim=AGESUP;
       }    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     }   
     strcpy(fileresf,"f"); 
     for (i=1; i<=imx; i++)  {    strcat(fileresf,fileres);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    if((ficresf=fopen(fileresf,"w"))==NULL) {
       for(m=1; (m<= maxwav); m++){      printf("Problem with forecast resultfile: %s\n", fileresf);
         if(s[m][i] >0){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           if (s[m][i] >= nlstate+1) {    }
             if(agedc[i]>0)    printf("Computing forecasting: result on file '%s' \n", fileresf);
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
            else {  
               if (andc[i]!=9999){    if (mobilav!=0) {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               agev[m][i]=-1;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
               }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           }      }
           else if(s[m][i] !=9){ /* Should no more exist */    }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    stepsize=(int) (stepm+YEARM-1)/YEARM;
               agev[m][i]=1;    if (stepm<=12) stepsize=1;
             else if(agev[m][i] <agemin){    if(estepm < stepm){
               agemin=agev[m][i];      printf ("Problem %d lower than %d\n",estepm, stepm);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    }
             }    else  hstepm=estepm;   
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    hstepm=hstepm/stepm; 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
             }                                 fractional in yp1 */
             /*agev[m][i]=anint[m][i]-annais[i];*/    anprojmean=yp;
             /*   agev[m][i] = age[i]+2*m;*/    yp2=modf((yp1*12),&yp);
           }    mprojmean=yp;
           else { /* =9 */    yp1=modf((yp2*30.5),&yp);
             agev[m][i]=1;    jprojmean=yp;
             s[m][i]=-1;    if(jprojmean==0) jprojmean=1;
           }    if(mprojmean==0) jprojmean=1;
         }  
         else /*= 0 Unknown */    i1=cptcoveff;
           agev[m][i]=1;    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); 
     }    
     for (i=1; i<=imx; i++)  {    fprintf(ficresf,"#****** Routine prevforecast **\n");
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {  /*            if (h==(int)(YEARM*yearp)){ */
           printf("Error: Wrong value in nlstate or ndeath\n");      for(cptcov=1, k=0;cptcov<=i1;cptcov++){
           goto end;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         }        k=k+1;
       }        fprintf(ficresf,"\n#******");
     }        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
         fprintf(ficresf,"******\n");
     free_vector(severity,1,maxwav);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
     free_imatrix(outcome,1,maxwav+1,1,n);        for(j=1; j<=nlstate+ndeath;j++){ 
     free_vector(moisnais,1,n);          for(i=1; i<=nlstate;i++)              
     free_vector(annais,1,n);            fprintf(ficresf," p%d%d",i,j);
     /* free_matrix(mint,1,maxwav,1,n);          fprintf(ficresf," p.%d",j);
        free_matrix(anint,1,maxwav,1,n);*/        }
     free_vector(moisdc,1,n);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     free_vector(andc,1,n);          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
      
     wav=ivector(1,imx);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            nhstepm = nhstepm/hstepm; 
                p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* Concatenates waves */            oldm=oldms;savm=savms;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
       Tcode=ivector(1,100);              if (h*hstepm/YEARM*stepm ==yearp) {
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                fprintf(ficresf,"\n");
       ncodemax[1]=1;                for(j=1;j<=cptcoveff;j++) 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                      fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
    codtab=imatrix(1,100,1,10);              } 
    h=0;              for(j=1; j<=nlstate+ndeath;j++) {
    m=pow(2,cptcoveff);                ppij=0.;
                  for(i=1; i<=nlstate;i++) {
    for(k=1;k<=cptcoveff; k++){                  if (mobilav==1) 
      for(i=1; i <=(m/pow(2,k));i++){                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
        for(j=1; j <= ncodemax[k]; j++){                  else {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
            h++;                  }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                  if (h*hstepm/YEARM*stepm== yearp) {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
          }                  }
        }                } /* end i */
      }                if (h*hstepm/YEARM*stepm==yearp) {
    }                  fprintf(ficresf," %.3f", ppij);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                }
       codtab[1][2]=1;codtab[2][2]=2; */              }/* end j */
    /* for(i=1; i <=m ;i++){            } /* end h */
       for(k=1; k <=cptcovn; k++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          } /* end agec */
       }        } /* end yearp */
       printf("\n");      } /* end cptcod */
       }    } /* end  cptcov */
       scanf("%d",i);*/         
        if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */    fclose(ficresf);
   }
      
      /************** Forecasting *****not tested NB*************/
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int *popage;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double calagedatem, agelim, kk1, kk2;
          double *popeffectif,*popcount;
     /* For Powell, parameters are in a vector p[] starting at p[1]    double ***p3mat,***tabpop,***tabpopprev;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    double ***mobaverage;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    char filerespop[FILENAMELENGTH];
   
     if(mle==1){    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    agelim=AGESUP;
        calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     /*--------- 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);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
      
     
    jk=1;    strcpy(filerespop,"pop"); 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    strcat(filerespop,fileres);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
    for(i=1,jk=1; i <=nlstate; i++){      printf("Problem with forecast resultfile: %s\n", filerespop);
      for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
        if (k != i)    }
          {    printf("Computing forecasting: result on file '%s' \n", filerespop);
            printf("%d%d ",i,k);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);    if (mobilav!=0) {
              jk++;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
            printf("\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            fprintf(ficres,"\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }      }
      }    }
    }  
  if(mle==1){    stepsize=(int) (stepm+YEARM-1)/YEARM;
     /* Computing hessian and covariance matrix */    if (stepm<=12) stepsize=1;
     ftolhess=ftol; /* Usually correct */    
     hesscov(matcov, p, npar, delti, ftolhess, func);    agelim=AGESUP;
  }    
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    hstepm=1;
     printf("# Scales (for hessian or gradient estimation)\n");    hstepm=hstepm/stepm; 
      for(i=1,jk=1; i <=nlstate; i++){    
       for(j=1; j <=nlstate+ndeath; j++){    if (popforecast==1) {
         if (j!=i) {      if((ficpop=fopen(popfile,"r"))==NULL) {
           fprintf(ficres,"%1d%1d",i,j);        printf("Problem with population file : %s\n",popfile);exit(0);
           printf("%1d%1d",i,j);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
           for(k=1; k<=ncovmodel;k++){      } 
             printf(" %.5e",delti[jk]);      popage=ivector(0,AGESUP);
             fprintf(ficres," %.5e",delti[jk]);      popeffectif=vector(0,AGESUP);
             jk++;      popcount=vector(0,AGESUP);
           }      
           printf("\n");      i=1;   
           fprintf(ficres,"\n");      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
         }     
       }      imx=i;
      }      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
        }
     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(cptcov=1,k=0;cptcov<=i2;cptcov++){
     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(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     for(i=1;i<=npar;i++){        k=k+1;
       /*  if (k>nlstate) k=1;        fprintf(ficrespop,"\n#******");
       i1=(i-1)/(ncovmodel*nlstate)+1;        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       printf("%s%d%d",alph[k],i1,tab[i]);*/        }
       fprintf(ficres,"%3d",i);        fprintf(ficrespop,"******\n");
       printf("%3d",i);        fprintf(ficrespop,"# Age");
       for(j=1; j<=i;j++){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         fprintf(ficres," %.5e",matcov[i][j]);        if (popforecast==1)  fprintf(ficrespop," [Population]");
         printf(" %.5e",matcov[i][j]);        
       }        for (cpt=0; cpt<=0;cpt++) { 
       fprintf(ficres,"\n");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       printf("\n");          
       k++;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                nhstepm = nhstepm/hstepm; 
     while((c=getc(ficpar))=='#' && c!= EOF){            
       ungetc(c,ficpar);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fgets(line, MAXLINE, ficpar);            oldm=oldms;savm=savms;
       puts(line);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       fputs(line,ficparo);          
     }            for (h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);              if (h==(int) (calagedatem+YEARM*cpt)) {
     estepm=0;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     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;              for(j=1; j<=nlstate+ndeath;j++) {
     if (fage <= 2) {                kk1=0.;kk2=0;
       bage = ageminpar;                for(i=1; i<=nlstate;i++) {              
       fage = agemaxpar;                  if (mobilav==1) 
     }                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                      else {
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     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);                }
                  if (h==(int)(calagedatem+12*cpt)){
     while((c=getc(ficpar))=='#' && c!= EOF){                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     ungetc(c,ficpar);                    /*fprintf(ficrespop," %.3f", kk1);
     fgets(line, MAXLINE, ficpar);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     puts(line);                }
     fputs(line,ficparo);              }
   }              for(i=1; i<=nlstate;i++){
   ungetc(c,ficpar);                kk1=0.;
                    for(j=1; j<=nlstate;j++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                  }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
                    }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
     fgets(line, MAXLINE, ficpar);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     puts(line);            }
     fputs(line,ficparo);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          }
   ungetc(c,ficpar);        }
     
     /******/
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   fscanf(ficpar,"pop_based=%d\n",&popbased);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   fprintf(ficparo,"pop_based=%d\n",popbased);              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fprintf(ficres,"pop_based=%d\n",popbased);              nhstepm = nhstepm/hstepm; 
              
   while((c=getc(ficpar))=='#' && c!= EOF){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);            oldm=oldms;savm=savms;
     fgets(line, MAXLINE, ficpar);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     puts(line);            for (h=0; h<=nhstepm; h++){
     fputs(line,ficparo);              if (h==(int) (calagedatem+YEARM*cpt)) {
   }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   ungetc(c,ficpar);              } 
               for(j=1; j<=nlstate+ndeath;j++) {
   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);                kk1=0.;kk2=0;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                for(i=1; i<=nlstate;i++) {              
 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);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
 while((c=getc(ficpar))=='#' && c!= EOF){              }
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);          }
     fputs(line,ficparo);        }
   }     } 
   ungetc(c,ficpar);    }
    
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
 /*------------ gnuplot -------------*/    }
   strcpy(optionfilegnuplot,optionfilefiname);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(optionfilegnuplot,".gp");    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    fclose(ficrespop);
     printf("Problem with file %s",optionfilegnuplot);  }
   }  
   fclose(ficgp);  /***********************************************/
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  /**************** Main Program *****************/
 /*--------- index.htm --------*/  /***********************************************/
   
   strcpy(optionfilehtm,optionfile);  int main(int argc, char *argv[])
   strcat(optionfilehtm,".htm");  {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     printf("Problem with %s \n",optionfilehtm), exit(0);    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   }    double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   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    double fret;
 \n    double **xi,tmp,delta;
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    double dum; /* Dummy variable */
 <hr  size=\"2\" color=\"#EC5E5E\">    double ***p3mat;
  <ul><li><h4>Parameter files</h4>\n    double ***mobaverage;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    int *indx;
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    char line[MAXLINE], linepar[MAXLINE];
   fclose(fichtm);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    int sdeb, sfin; /* Status at beginning and end */
      int c,  h , cpt,l;
 /*------------ free_vector  -------------*/    int ju,jl, mi;
  chdir(path);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
      int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
  free_ivector(wav,1,imx);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int mobilav=0,popforecast=0;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      int hstepm, nhstepm;
  free_ivector(num,1,n);    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
  free_vector(agedc,1,n);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);    double bage, fage, age, agelim, agebase;
  fclose(ficres);    double ftolpl=FTOL;
     double **prlim;
     double *severity;
   /*--------------- Prevalence limit --------------*/    double ***param; /* Matrix of parameters */
      double  *p;
   strcpy(filerespl,"pl");    double **matcov; /* Matrix of covariance */
   strcat(filerespl,fileres);    double ***delti3; /* Scale */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double *delti; /* Scale */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double ***eij, ***vareij;
   }    double **varpl; /* Variances of prevalence limits by age */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double *epj, vepp;
   fprintf(ficrespl,"#Prevalence limit\n");    double kk1, kk2;
   fprintf(ficrespl,"#Age ");    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");    char *alph[]={"a","a","b","c","d","e"}, str[4];
    
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char z[1]="c", occ;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  #include <sys/time.h>
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  #include <time.h>
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   
   k=0;    /* long total_usecs;
   agebase=ageminpar;       struct timeval start_time, end_time;
   agelim=agemaxpar;    
   ftolpl=1.e-10;       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   i1=cptcoveff;    getcwd(pathcd, size);
   if (cptcovn < 1){i1=1;}  
     printf("\n%s",version);
   for(cptcov=1;cptcov<=i1;cptcov++){    if(argc <=1){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf("\nEnter the parameter file name: ");
         k=k+1;      scanf("%s",pathtot);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    else{
         for(j=1;j<=cptcoveff;j++)      strcpy(pathtot,argv[1]);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespl,"******\n");    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
            /*cygwin_split_path(pathtot,path,optionfile);
         for (age=agebase; age<=agelim; age++){      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* cutv(path,optionfile,pathtot,'\\');*/
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
           fprintf(ficrespl," %.5f", prlim[i][i]);    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
           fprintf(ficrespl,"\n");    chdir(path);
         }    replace(pathc,path);
       }  
     }    /*-------- arguments in the command line --------*/
   fclose(ficrespl);  
     /* Log file */
   /*------------- h Pij x at various ages ------------*/    strcat(filelog, optionfilefiname);
      strcat(filelog,".log");    /* */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    if((ficlog=fopen(filelog,"w"))==NULL)    {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      printf("Problem with logfile %s\n",filelog);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      goto end;
   }    }
   printf("Computing pij: result on file '%s' \n", filerespij);    fprintf(ficlog,"Log filename:%s\n",filelog);
      fprintf(ficlog,"\n%s",version);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficlog,"\nEnter the parameter file name: ");
   /*if (stepm<=24) stepsize=2;*/    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    /* */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
   /* hstepm=1;   aff par mois*/    strcat(fileres,".txt");    /* Other files have txt extension */
   
   k=0;    /*---------arguments file --------*/
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       k=k+1;      printf("Problem with optionfile %s\n",optionfile);
         fprintf(ficrespij,"\n#****** ");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
         for(j=1;j<=cptcoveff;j++)      goto end;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespij,"******\n");  
            strcpy(filereso,"o");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    strcat(filereso,fileres);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if((ficparo=fopen(filereso,"w"))==NULL) {
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/      goto end;
     }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    /* Reads comments: lines beginning with '#' */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      while((c=getc(ficpar))=='#' && c!= EOF){
           fprintf(ficrespij,"# Age");      ungetc(c,ficpar);
           for(i=1; i<=nlstate;i++)      fgets(line, MAXLINE, ficpar);
             for(j=1; j<=nlstate+ndeath;j++)      puts(line);
               fprintf(ficrespij," %1d-%1d",i,j);      fputs(line,ficparo);
           fprintf(ficrespij,"\n");    }
            for (h=0; h<=nhstepm; h++){    ungetc(c,ficpar);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
               for(j=1; j<=nlstate+ndeath;j++)    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
             fprintf(ficrespij,"\n");    while((c=getc(ficpar))=='#' && c!= EOF){
              }      ungetc(c,ficpar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fgets(line, MAXLINE, ficpar);
           fprintf(ficrespij,"\n");      puts(line);
         }      fputs(line,ficparo);
     }    }
   }    ungetc(c,ficpar);
     
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);     
     covar=matrix(0,NCOVMAX,1,n); 
   fclose(ficrespij);    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
   /*---------- Forecasting ------------------*/    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   if((stepm == 1) && (strcmp(model,".")==0)){    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     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);    /* Read guess parameters */
   }    /* Reads comments: lines beginning with '#' */
   else{    while((c=getc(ficpar))=='#' && c!= EOF){
     erreur=108;      ungetc(c,ficpar);
     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);      fgets(line, MAXLINE, ficpar);
   }      puts(line);
        fputs(line,ficparo);
     }
   /*---------- Health expectancies and variances ------------*/    ungetc(c,ficpar);
     
   strcpy(filerest,"t");    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   strcat(filerest,fileres);    for(i=1; i <=nlstate; i++)
   if((ficrest=fopen(filerest,"w"))==NULL) {      for(j=1; j <=nlstate+ndeath-1; j++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        fscanf(ficpar,"%1d%1d",&i1,&j1);
   }        fprintf(ficparo,"%1d%1d",i1,j1);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
   strcpy(filerese,"e");        for(k=1; k<=ncovmodel;k++){
   strcat(filerese,fileres);          fscanf(ficpar," %lf",&param[i][j][k]);
   if((ficreseij=fopen(filerese,"w"))==NULL) {          if(mle==1){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            printf(" %lf",param[i][j][k]);
   }            fprintf(ficlog," %lf",param[i][j][k]);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          }
           else
  strcpy(fileresv,"v");            fprintf(ficlog," %lf",param[i][j][k]);
   strcat(fileresv,fileres);          fprintf(ficparo," %lf",param[i][j][k]);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fscanf(ficpar,"\n");
   }        if(mle==1)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          printf("\n");
   calagedate=-1;        fprintf(ficlog,"\n");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        fprintf(ficparo,"\n");
       }
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    p=param[1][1];
       fprintf(ficrest,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    /* Reads comments: lines beginning with '#' */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficrest,"******\n");      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       fprintf(ficreseij,"\n#****** ");      puts(line);
       for(j=1;j<=cptcoveff;j++)      fputs(line,ficparo);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficreseij,"******\n");    ungetc(c,ficpar);
   
       fprintf(ficresvij,"\n#****** ");    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(j=1;j<=cptcoveff;j++)    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i <=nlstate; i++){
       fprintf(ficresvij,"******\n");      for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        printf("%1d%1d",i,j);
       oldm=oldms;savm=savms;        fprintf(ficparo,"%1d%1d",i1,j1);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar,"%le",&delti3[i][j][k]);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          printf(" %le",delti3[i][j][k]);
       oldm=oldms;savm=savms;          fprintf(ficparo," %le",delti3[i][j][k]);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        }
            fscanf(ficpar,"\n");
         printf("\n");
          fprintf(ficparo,"\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");    delti=delti3[1][1];
   
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    
         if (popbased==1) {    /* Reads comments: lines beginning with '#' */
           for(i=1; i<=nlstate;i++)    while((c=getc(ficpar))=='#' && c!= EOF){
             prlim[i][i]=probs[(int)age][i][k];      ungetc(c,ficpar);
         }      fgets(line, MAXLINE, ficpar);
              puts(line);
         fprintf(ficrest," %4.0f",age);      fputs(line,ficparo);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    ungetc(c,ficpar);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    matcov=matrix(1,npar,1,npar);
           }    for(i=1; i <=npar; i++){
           epj[nlstate+1] +=epj[j];      fscanf(ficpar,"%s",&str);
         }      if(mle==1)
         printf("%s",str);
         for(i=1, vepp=0.;i <=nlstate;i++)      fprintf(ficlog,"%s",str);
           for(j=1;j <=nlstate;j++)      fprintf(ficparo,"%s",str);
             vepp += vareij[i][j][(int)age];      for(j=1; j <=i; j++){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));        fscanf(ficpar," %le",&matcov[i][j]);
         for(j=1;j <=nlstate;j++){        if(mle==1){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          printf(" %.5le",matcov[i][j]);
         }          fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficrest,"\n");        }
       }        else
     }          fprintf(ficlog," %.5le",matcov[i][j]);
   }        fprintf(ficparo," %.5le",matcov[i][j]);
 free_matrix(mint,1,maxwav,1,n);      }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      fscanf(ficpar,"\n");
     free_vector(weight,1,n);      if(mle==1)
   fclose(ficreseij);        printf("\n");
   fclose(ficresvij);      fprintf(ficlog,"\n");
   fclose(ficrest);      fprintf(ficparo,"\n");
   fclose(ficpar);    }
   free_vector(epj,1,nlstate+1);    for(i=1; i <=npar; i++)
        for(j=i+1;j<=npar;j++)
   /*------- Variance limit prevalence------*/          matcov[i][j]=matcov[j][i];
      
   strcpy(fileresvpl,"vpl");    if(mle==1)
   strcat(fileresvpl,fileres);      printf("\n");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);  
   }    /*-------- Rewriting paramater file ----------*/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
   k=0;    strcat(rfileres,".");    /* */
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(rfileres,optionfilext);    /* Other files have txt extension */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if((ficres =fopen(rfileres,"w"))==NULL) {
       k=k+1;      printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficresvpl,"\n#****** ");      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficres,"#%s\n",version);
       fprintf(ficresvpl,"******\n");      
          /*-------- data file ----------*/
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    if((fic=fopen(datafile,"r"))==NULL)    {
       oldm=oldms;savm=savms;      printf("Problem with datafile: %s\n", datafile);goto end;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }    }
  }  
     n= lastobs;
   fclose(ficresvpl);    severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
   /*---------- End : free ----------------*/    num=ivector(1,n);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    moisnais=vector(1,n);
      annais=vector(1,n);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    moisdc=vector(1,n);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    andc=vector(1,n);
      agedc=vector(1,n);
      cod=ivector(1,n);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    weight=vector(1,n);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    mint=matrix(1,maxwav,1,n);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    anint=matrix(1,maxwav,1,n);
      s=imatrix(1,maxwav+1,1,n);
   free_matrix(matcov,1,npar,1,npar);    tab=ivector(1,NCOVMAX);
   free_vector(delti,1,npar);    ncodemax=ivector(1,8);
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
   fprintf(fichtm,"\n</body>");      if ((i >= firstobs) && (i <=lastobs)) {
   fclose(fichtm);          
   fclose(ficgp);        for (j=maxwav;j>=1;j--){
            cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
   if(erreur >0)          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
     printf("End of Imach with error or warning %d\n",erreur);          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   else   printf("End of Imach\n");        }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          
          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
   /* 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);*/        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
  end:        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
 #ifdef windows        for (j=ncovcol;j>=1;j--){
   /* chdir(pathcd);*/          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 #endif        } 
  /*system("wgnuplot graph.plt");*/        num[i]=atol(stra);
  /*system("../gp37mgw/wgnuplot graph.plt");*/          
  /*system("cd ../gp37mgw");*/        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          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;}*/
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");        i=i+1;
  strcat(plotcmd,optionfilegnuplot);      }
  system(plotcmd);    }
     /* printf("ii=%d", ij);
 #ifdef windows       scanf("%d",i);*/
   while (z[0] != 'q') {    imx=i-1; /* Number of individuals */
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    /* for (i=1; i<=imx; i++){
     scanf("%s",z);      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
     if (z[0] == 'c') system("./imach");      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     else if (z[0] == 'e') system(optionfilehtm);      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
     else if (z[0] == 'g') system(plotcmd);      }*/
     else if (z[0] == 'q') exit(0);     /*  for (i=1; i<=imx; i++){
   }       if (s[4][i]==9)  s[4][i]=-1; 
 #endif       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.1.49  
changed lines
  Added in v.1.80

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