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version 1.41.2.2, 2003/06/13 07:45:28 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 "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
     print results files
 /*#define windows*/    if mle==1 
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */       computes hessian
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    open gnuplot file
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open html file
     stable prevalence
 #define NINTERVMAX 8     for age prevalim()
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    h Pij x
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    variance of p varprob
 #define NCOVMAX 8 /* Maximum number of covariates */    forecasting if prevfcast==1 prevforecast call prevalence()
 #define MAXN 20000    health expectancies
 #define YEARM 12. /* Number of months per year */    Variance-covariance of DFLE
 #define AGESUP 130    prevalence()
 #define AGEBASE 40     movingaverage()
     varevsij() 
     if popbased==1 varevsij(,popbased)
 int erreur; /* Error number */    total life expectancies
 int nvar;    Variance of stable prevalence
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;   end
 int npar=NPARMAX;  */
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;   
   #include <math.h>
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <stdio.h>
 int maxwav; /* Maxim number of waves */  #include <stdlib.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <unistd.h>
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define MAXLINE 256
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GNUPLOTPROGRAM "gnuplot"
 double jmean; /* Mean space between 2 waves */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define FILENAMELENGTH 80
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  /*#define DEBUG*/
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #define windows
 FILE *ficgp,*ficresprob,*ficpop;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 FILE *ficreseij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   char fileresv[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NR_END 1  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FREE_ARG char*  #define NCOVMAX 8 /* Maximum number of covariates */
 #define FTOL 1.0e-10  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 #define NRANSI  #define AGESUP 130
 #define ITMAX 200  #define AGEBASE 40
   #ifdef windows
 #define TOL 2.0e-4  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #define CGOLD 0.3819660  #else
 #define ZEPS 1.0e-10  #define DIRSEPARATOR '/'
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define ODIRSEPARATOR '\\'
   #endif
 #define GOLD 1.618034  
 #define GLIMIT 100.0  /* $Id$ */
 #define TINY 1.0e-20  /* $Log$
    * Revision 1.80  2003/06/05 15:34:14  brouard
 static double maxarg1,maxarg2;   * Trying to add the true revision is the program and log
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   *
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  /* Revision 1.79  2003/06/05 15:17:23  brouard
    /* *** empty log message ***
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  /* */
 #define rint(a) floor(a+0.5)  /* $Revision$ */
   /* $Date$ */
 static double sqrarg;  /* $State$ */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
   int erreur; /* Error number */
 int imx;  int nvar;
 int stepm;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 /* Stepm, step in month: minimum step interpolation*/  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 int estepm;  int ndeath=1; /* Number of dead states */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int *wav; /* Number of waves for this individuual 0 is possible */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int maxwav; /* Maxim number of waves */
 double **pmmij, ***probs, ***mobaverage;  int jmin, jmax; /* min, max spacing between 2 waves */
 double dateintmean=0;  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double *weight;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int **s; /* Status */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double *agedc, **covar, idx;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double ftolhess; /* Tolerance for computing hessian */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 /**************** split *************************/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  FILE *ficresprobmorprev;
 {  FILE *fichtm; /* Html File */
    char *s;                             /* pointer */  FILE *ficreseij;
    int  l1, l2;                         /* length counters */  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
    l1 = strlen( path );                 /* length of path */  char fileresv[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE  *ficresvpl;
 #ifdef windows  char fileresvpl[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  char title[MAXLINE];
 #else  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    s = strrchr( path, '/' );            /* find last / */  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  char filelog[FILENAMELENGTH]; /* Log file */
       extern char       *getwd( );  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
       if ( getwd( dirc ) == NULL ) {  char popfile[FILENAMELENGTH];
 #else  
       extern char       *getcwd( );  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define NR_END 1
 #endif  #define FREE_ARG char*
          return( GLOCK_ERROR_GETCWD );  #define FTOL 1.0e-10
       }  
       strcpy( name, path );             /* we've got it */  #define NRANSI 
    } else {                             /* strip direcotry from path */  #define ITMAX 200 
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  #define TOL 2.0e-4 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  #define CGOLD 0.3819660 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define ZEPS 1.0e-10 
       dirc[l1-l2] = 0;                  /* add zero */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    }  
    l1 = strlen( dirc );                 /* length of directory */  #define GOLD 1.618034 
 #ifdef windows  #define GLIMIT 100.0 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define TINY 1.0e-20 
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  static double maxarg1,maxarg2;
 #endif  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    s = strrchr( name, '.' );            /* find last / */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    s++;    
    strcpy(ext,s);                       /* save extension */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    l1= strlen( name);  #define rint(a) floor(a+0.5)
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  static double sqrarg;
    finame[l1-l2]= 0;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    return( 0 );                         /* we're done */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  
   int imx; 
   int stepm;
 /******************************************/  /* Stepm, step in month: minimum step interpolation*/
   
 void replace(char *s, char*t)  int estepm;
 {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   int i;  
   int lg=20;  int m,nb;
   i=0;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   lg=strlen(t);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   for(i=0; i<= lg; i++) {  double **pmmij, ***probs;
     (s[i] = t[i]);  double dateintmean=0;
     if (t[i]== '\\') s[i]='/';  
   }  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 int nbocc(char *s, char occ)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
   int i,j=0;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int lg=20;  double ftolhess; /* Tolerance for computing hessian */
   i=0;  
   lg=strlen(s);  /**************** split *************************/
   for(i=0; i<= lg; i++) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   if  (s[i] == occ ) j++;  {
   }    char  *ss;                            /* pointer */
   return j;    int   l1, l2;                         /* length counters */
 }  
     l1 = strlen(path );                   /* length of path */
 void cutv(char *u,char *v, char*t, char occ)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int i,lg,j,p=0;    if ( ss == NULL ) {                   /* no directory, so use current */
   i=0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for(j=0; j<=strlen(t)-1; j++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      /* get current working directory */
   }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   lg=strlen(t);        return( GLOCK_ERROR_GETCWD );
   for(j=0; j<p; j++) {      }
     (u[j] = t[j]);      strcpy( name, path );               /* we've got it */
   }    } else {                              /* strip direcotry from path */
      u[p]='\0';      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
    for(j=0; j<= lg; j++) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (j>=(p+1))(v[j-p-1] = t[j]);      strcpy( name, ss );         /* save file name */
   }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
     }
 /********************** nrerror ********************/    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
 void nrerror(char error_text[])    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   fprintf(stderr,"ERREUR ...\n");    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   fprintf(stderr,"%s\n",error_text);  #endif
   exit(1);    ss = strrchr( name, '.' );            /* find last / */
 }    ss++;
 /*********************** vector *******************/    strcpy(ext,ss);                       /* save extension */
 double *vector(int nl, int nh)    l1= strlen( name);
 {    l2= strlen(ss)+1;
   double *v;    strncpy( finame, name, l1-l2);
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    finame[l1-l2]= 0;
   if (!v) nrerror("allocation failure in vector");    return( 0 );                          /* we're done */
   return v-nl+NR_END;  }
 }  
   
 /************************ free vector ******************/  /******************************************/
 void free_vector(double*v, int nl, int nh)  
 {  void replace(char *s, char*t)
   free((FREE_ARG)(v+nl-NR_END));  {
 }    int i;
     int lg=20;
 /************************ivector *******************************/    i=0;
 int *ivector(long nl,long nh)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   int *v;      (s[i] = t[i]);
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));      if (t[i]== '\\') s[i]='/';
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;  }
 }  
   int nbocc(char *s, char occ)
 /******************free ivector **************************/  {
 void free_ivector(int *v, long nl, long nh)    int i,j=0;
 {    int lg=20;
   free((FREE_ARG)(v+nl-NR_END));    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /******************* imatrix *******************************/    if  (s[i] == occ ) j++;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    return j;
 {  }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  void cutv(char *u,char *v, char*t, char occ)
    {
   /* allocate pointers to rows */    /* cuts string t into u and v where u is ended by char occ excluding it
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   if (!m) nrerror("allocation failure 1 in matrix()");       gives u="abcedf" and v="ghi2j" */
   m += NR_END;    int i,lg,j,p=0;
   m -= nrl;    i=0;
      for(j=0; j<=strlen(t)-1; j++) {
        if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   /* allocate rows and set pointers to them */    }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    lg=strlen(t);
   m[nrl] += NR_END;    for(j=0; j<p; j++) {
   m[nrl] -= ncl;      (u[j] = t[j]);
      }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;       u[p]='\0';
    
   /* return pointer to array of pointers to rows */     for(j=0; j<= lg; j++) {
   return m;      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  /********************** nrerror ********************/
       int **m;  
       long nch,ncl,nrh,nrl;  void nrerror(char error_text[])
      /* free an int matrix allocated by imatrix() */  {
 {    fprintf(stderr,"ERREUR ...\n");
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    fprintf(stderr,"%s\n",error_text);
   free((FREE_ARG) (m+nrl-NR_END));    exit(EXIT_FAILURE);
 }  }
   /*********************** vector *******************/
 /******************* matrix *******************************/  double *vector(int nl, int nh)
 double **matrix(long nrl, long nrh, long ncl, long nch)  {
 {    double *v;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double **m;    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /************************ free vector ******************/
   m -= nrl;  void free_vector(double*v, int nl, int nh)
   {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /************************ivector *******************************/
   char *cvector(long nl,long nh)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
   return m;    char *v;
 }    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
     if (!v) nrerror("allocation failure in cvector");
 /*************************free matrix ************************/    return v-nl+NR_END;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /******************free ivector **************************/
   free((FREE_ARG)(m+nrl-NR_END));  void free_cvector(char *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /************************ivector *******************************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int *ivector(long nl,long nh)
   double ***m;  {
     int *v;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m += NR_END;    return v-nl+NR_END;
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************free ivector **************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void free_ivector(int *v, long nl, long nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    free((FREE_ARG)(v+nl-NR_END));
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /******************* imatrix *******************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m[nrl][ncl] += NR_END;  { 
   m[nrl][ncl] -= nll;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (j=ncl+1; j<=nch; j++)    int **m; 
     m[nrl][j]=m[nrl][j-1]+nlay;    
      /* allocate pointers to rows */ 
   for (i=nrl+1; i<=nrh; i++) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for (j=ncl+1; j<=nch; j++)    m += NR_END; 
       m[i][j]=m[i][j-1]+nlay;    m -= nrl; 
   }    
   return m;    
 }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 /*************************free ma3x ************************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m[nrl] += NR_END; 
 {    m[nrl] -= ncl; 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /***************** f1dim *************************/  } 
 extern int ncom;  
 extern double *pcom,*xicom;  /****************** free_imatrix *************************/
 extern double (*nrfunc)(double []);  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
 double f1dim(double x)        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   int j;  { 
   double f;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double *xt;    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /******************* matrix *******************************/
   f=(*nrfunc)(xt);  double **matrix(long nrl, long nrh, long ncl, long nch)
   free_vector(xt,1,ncom);  {
   return f;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /*****************brent *************************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   int iter;    m -= nrl;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double ftemp;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m[nrl] += NR_END;
   double e=0.0;    m[nrl] -= ncl;
    
   a=(ax < cx ? ax : cx);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   b=(ax > cx ? ax : cx);    return m;
   x=w=v=bx;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   fw=fv=fx=(*f)(x);     */
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /*************************free matrix ************************/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     printf(".");fflush(stdout);  {
 #ifdef DEBUG    free((FREE_ARG)(m[nrl]+ncl-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);    free((FREE_ARG)(m+nrl-NR_END));
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /******************* ma3x *******************************/
       *xmin=x;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       return fx;  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     ftemp=fu;    double ***m;
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       q=(x-v)*(fx-fw);    if (!m) nrerror("allocation failure 1 in matrix()");
       p=(x-v)*q-(x-w)*r;    m += NR_END;
       q=2.0*(q-r);    m -= nrl;
       if (q > 0.0) p = -p;  
       q=fabs(q);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       etemp=e;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       e=d;    m[nrl] += NR_END;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl] -= ncl;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         d=p/q;  
         u=x+d;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         if (u-a < tol2 || b-u < tol2)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           d=SIGN(tol1,xm-x);    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
     } else {    for (j=ncl+1; j<=nch; j++) 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    for (i=nrl+1; i<=nrh; i++) {
     fu=(*f)(u);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if (fu <= fx) {      for (j=ncl+1; j<=nch; j++) 
       if (u >= x) a=x; else b=x;        m[i][j]=m[i][j-1]+nlay;
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)    return m; 
         } else {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
           if (u < x) a=u; else b=u;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           if (fu <= fw || w == x) {    */
             v=w;  }
             w=u;  
             fv=fw;  /*************************free ma3x ************************/
             fw=fu;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
           } else if (fu <= fv || v == x || v == w) {  {
             v=u;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
             fv=fu;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           }    free((FREE_ARG)(m+nrl-NR_END));
         }  }
   }  
   nrerror("Too many iterations in brent");  /***************** f1dim *************************/
   *xmin=x;  extern int ncom; 
   return fx;  extern double *pcom,*xicom;
 }  extern double (*nrfunc)(double []); 
    
 /****************** mnbrak ***********************/  double f1dim(double x) 
   { 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int j; 
             double (*func)(double))    double f;
 {    double *xt; 
   double ulim,u,r,q, dum;   
   double fu;    xt=vector(1,ncom); 
      for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *fa=(*func)(*ax);    f=(*nrfunc)(xt); 
   *fb=(*func)(*bx);    free_vector(xt,1,ncom); 
   if (*fb > *fa) {    return f; 
     SHFT(dum,*ax,*bx,dum)  } 
       SHFT(dum,*fb,*fa,dum)  
       }  /*****************brent *************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *fc=(*func)(*cx);  { 
   while (*fb > *fc) {    int iter; 
     r=(*bx-*ax)*(*fb-*fc);    double a,b,d,etemp;
     q=(*bx-*cx)*(*fb-*fa);    double fu,fv,fw,fx;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    double ftemp;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double e=0.0; 
     if ((*bx-u)*(u-*cx) > 0.0) {   
       fu=(*func)(u);    a=(ax < cx ? ax : cx); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    b=(ax > cx ? ax : cx); 
       fu=(*func)(u);    x=w=v=bx; 
       if (fu < *fc) {    fw=fv=fx=(*f)(x); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    for (iter=1;iter<=ITMAX;iter++) { 
           SHFT(*fb,*fc,fu,(*func)(u))      xm=0.5*(a+b); 
           }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       u=ulim;      printf(".");fflush(stdout);
       fu=(*func)(u);      fprintf(ficlog,".");fflush(ficlog);
     } else {  #ifdef DEBUG
       u=(*cx)+GOLD*(*cx-*bx);      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);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     SHFT(*ax,*bx,*cx,u)  #endif
       SHFT(*fa,*fb,*fc,fu)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
 }        return fx; 
       } 
 /*************** linmin ************************/      ftemp=fu;
       if (fabs(e) > tol1) { 
 int ncom;        r=(x-w)*(fx-fv); 
 double *pcom,*xicom;        q=(x-v)*(fx-fw); 
 double (*nrfunc)(double []);        p=(x-v)*q-(x-w)*r; 
          q=2.0*(q-r); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        if (q > 0.0) p = -p; 
 {        q=fabs(q); 
   double brent(double ax, double bx, double cx,        etemp=e; 
                double (*f)(double), double tol, double *xmin);        e=d; 
   double f1dim(double x);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
               double *fc, double (*func)(double));        else { 
   int j;          d=p/q; 
   double xx,xmin,bx,ax;          u=x+d; 
   double fx,fb,fa;          if (u-a < tol2 || b-u < tol2) 
              d=SIGN(tol1,xm-x); 
   ncom=n;        } 
   pcom=vector(1,n);      } else { 
   xicom=vector(1,n);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   nrfunc=func;      } 
   for (j=1;j<=n;j++) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     pcom[j]=p[j];      fu=(*f)(u); 
     xicom[j]=xi[j];      if (fu <= fx) { 
   }        if (u >= x) a=x; else b=x; 
   ax=0.0;        SHFT(v,w,x,u) 
   xx=1.0;          SHFT(fv,fw,fx,fu) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);          } else { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);            if (u < x) a=u; else b=u; 
 #ifdef DEBUG            if (fu <= fw || w == x) { 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);              v=w; 
 #endif              w=u; 
   for (j=1;j<=n;j++) {              fv=fw; 
     xi[j] *= xmin;              fw=fu; 
     p[j] += xi[j];            } else if (fu <= fv || v == x || v == w) { 
   }              v=u; 
   free_vector(xicom,1,n);              fv=fu; 
   free_vector(pcom,1,n);            } 
 }          } 
     } 
 /*************** powell ************************/    nrerror("Too many iterations in brent"); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    *xmin=x; 
             double (*func)(double []))    return fx; 
 {  } 
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  /****************** mnbrak ***********************/
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double fp,fptt;              double (*func)(double)) 
   double *xits;  { 
   pt=vector(1,n);    double ulim,u,r,q, dum;
   ptt=vector(1,n);    double fu; 
   xit=vector(1,n);   
   xits=vector(1,n);    *fa=(*func)(*ax); 
   *fret=(*func)(p);    *fb=(*func)(*bx); 
   for (j=1;j<=n;j++) pt[j]=p[j];    if (*fb > *fa) { 
   for (*iter=1;;++(*iter)) {      SHFT(dum,*ax,*bx,dum) 
     fp=(*fret);        SHFT(dum,*fb,*fa,dum) 
     ibig=0;        } 
     del=0.0;    *cx=(*bx)+GOLD*(*bx-*ax); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    *fc=(*func)(*cx); 
     for (i=1;i<=n;i++)    while (*fb > *fc) { 
       printf(" %d %.12f",i, p[i]);      r=(*bx-*ax)*(*fb-*fc); 
     printf("\n");      q=(*bx-*cx)*(*fb-*fa); 
     for (i=1;i<=n;i++) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       fptt=(*fret);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 #ifdef DEBUG      if ((*bx-u)*(u-*cx) > 0.0) { 
       printf("fret=%lf \n",*fret);        fu=(*func)(u); 
 #endif      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       printf("%d",i);fflush(stdout);        fu=(*func)(u); 
       linmin(p,xit,n,fret,func);        if (fu < *fc) { 
       if (fabs(fptt-(*fret)) > del) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         del=fabs(fptt-(*fret));            SHFT(*fb,*fc,fu,(*func)(u)) 
         ibig=i;            } 
       }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 #ifdef DEBUG        u=ulim; 
       printf("%d %.12e",i,(*fret));        fu=(*func)(u); 
       for (j=1;j<=n;j++) {      } else { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        u=(*cx)+GOLD*(*cx-*bx); 
         printf(" x(%d)=%.12e",j,xit[j]);        fu=(*func)(u); 
       }      } 
       for(j=1;j<=n;j++)      SHFT(*ax,*bx,*cx,u) 
         printf(" p=%.12e",p[j]);        SHFT(*fa,*fb,*fc,fu) 
       printf("\n");        } 
 #endif  } 
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /*************** linmin ************************/
 #ifdef DEBUG  
       int k[2],l;  int ncom; 
       k[0]=1;  double *pcom,*xicom;
       k[1]=-1;  double (*nrfunc)(double []); 
       printf("Max: %.12e",(*func)(p));   
       for (j=1;j<=n;j++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         printf(" %.12e",p[j]);  { 
       printf("\n");    double brent(double ax, double bx, double cx, 
       for(l=0;l<=1;l++) {                 double (*f)(double), double tol, double *xmin); 
         for (j=1;j<=n;j++) {    double f1dim(double x); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);                double *fc, double (*func)(double)); 
         }    int j; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double xx,xmin,bx,ax; 
       }    double fx,fb,fa;
 #endif   
     ncom=n; 
     pcom=vector(1,n); 
       free_vector(xit,1,n);    xicom=vector(1,n); 
       free_vector(xits,1,n);    nrfunc=func; 
       free_vector(ptt,1,n);    for (j=1;j<=n;j++) { 
       free_vector(pt,1,n);      pcom[j]=p[j]; 
       return;      xicom[j]=xi[j]; 
     }    } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    ax=0.0; 
     for (j=1;j<=n;j++) {    xx=1.0; 
       ptt[j]=2.0*p[j]-pt[j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       xit[j]=p[j]-pt[j];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       pt[j]=p[j];  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fptt=(*func)(ptt);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (fptt < fp) {  #endif
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    for (j=1;j<=n;j++) { 
       if (t < 0.0) {      xi[j] *= xmin; 
         linmin(p,xit,n,fret,func);      p[j] += xi[j]; 
         for (j=1;j<=n;j++) {    } 
           xi[j][ibig]=xi[j][n];    free_vector(xicom,1,n); 
           xi[j][n]=xit[j];    free_vector(pcom,1,n); 
         }  } 
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /*************** powell ************************/
         for(j=1;j<=n;j++)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           printf(" %.12e",xit[j]);              double (*func)(double [])) 
         printf("\n");  { 
 #endif    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
     }    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
 }    double fp,fptt;
     double *xits;
 /**** Prevalence limit ****************/    pt=vector(1,n); 
     ptt=vector(1,n); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    xit=vector(1,n); 
 {    xits=vector(1,n); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    *fret=(*func)(p); 
      matrix by transitions matrix until convergence is reached */    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   int i, ii,j,k;      fp=(*fret); 
   double min, max, maxmin, maxmax,sumnew=0.;      ibig=0; 
   double **matprod2();      del=0.0; 
   double **out, cov[NCOVMAX], **pmij();      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   double **newm;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   double agefin, delaymax=50 ; /* Max number of years to converge */      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
   for (ii=1;ii<=nlstate+ndeath;ii++)        printf(" %d %.12f",i, p[i]);
     for (j=1;j<=nlstate+ndeath;j++){        fprintf(ficlog," %d %.12lf",i, p[i]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fprintf(ficrespow," %.12lf", p[i]);
     }      }
       printf("\n");
    cov[1]=1.;      fprintf(ficlog,"\n");
        fprintf(ficrespow,"\n");
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for (i=1;i<=n;i++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     newm=savm;        fptt=(*fret); 
     /* Covariates have to be included here again */  #ifdef DEBUG
      cov[2]=agefin;        printf("fret=%lf \n",*fret);
          fprintf(ficlog,"fret=%lf \n",*fret);
       for (k=1; k<=cptcovn;k++) {  #endif
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        printf("%d",i);fflush(stdout);
         /*      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,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        if (fabs(fptt-(*fret)) > del) { 
       for (k=1; k<=cptcovprod;k++)          del=fabs(fptt-(*fret)); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          ibig=i; 
         } 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #ifdef DEBUG
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        printf("%d %.12e",i,(*fret));
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        fprintf(ficlog,"%d %.12e",i,(*fret));
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     savm=oldm;          printf(" x(%d)=%.12e",j,xit[j]);
     oldm=newm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){        for(j=1;j<=n;j++) {
       min=1.;          printf(" p=%.12e",p[j]);
       max=0.;          fprintf(ficlog," p=%.12e",p[j]);
       for(i=1; i<=nlstate; i++) {        }
         sumnew=0;        printf("\n");
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        fprintf(ficlog,"\n");
         prlim[i][j]= newm[i][j]/(1-sumnew);  #endif
         max=FMAX(max,prlim[i][j]);      } 
         min=FMIN(min,prlim[i][j]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       }  #ifdef DEBUG
       maxmin=max-min;        int k[2],l;
       maxmax=FMAX(maxmax,maxmin);        k[0]=1;
     }        k[1]=-1;
     if(maxmax < ftolpl){        printf("Max: %.12e",(*func)(p));
       return prlim;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
 /*************** transition probabilities ***************/        printf("\n");
         fprintf(ficlog,"\n");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   double s1, s2;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   /*double t34;*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i,j,j1, nc, ii, jj;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
     for(i=1; i<= nlstate; i++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=1; j<i;j++){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        }
         /*s2 += param[i][j][nc]*cov[nc];*/  #endif
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }        free_vector(xit,1,n); 
       ps[i][j]=s2;        free_vector(xits,1,n); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
     for(j=i+1; j<=nlstate+ndeath;j++){        return; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      for (j=1;j<=n;j++) { 
       }        ptt[j]=2.0*p[j]-pt[j]; 
       ps[i][j]=s2;        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
   }      } 
     /*ps[3][2]=1;*/      fptt=(*func)(ptt); 
       if (fptt < fp) { 
   for(i=1; i<= nlstate; i++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
      s1=0;        if (t < 0.0) { 
     for(j=1; j<i; j++)          linmin(p,xit,n,fret,func); 
       s1+=exp(ps[i][j]);          for (j=1;j<=n;j++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)            xi[j][ibig]=xi[j][n]; 
       s1+=exp(ps[i][j]);            xi[j][n]=xit[j]; 
     ps[i][i]=1./(s1+1.);          }
     for(j=1; j<i; j++)  #ifdef DEBUG
       ps[i][j]= exp(ps[i][j])*ps[i][i];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=i+1; j<=nlstate+ndeath; j++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          for(j=1;j<=n;j++){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */            printf(" %.12e",xit[j]);
   } /* end i */            fprintf(ficlog," %.12e",xit[j]);
           }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          printf("\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){          fprintf(ficlog,"\n");
       ps[ii][jj]=0;  #endif
       ps[ii][ii]=1;        }
     }      } 
   }    } 
   } 
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  /**** Prevalence limit (stable prevalence)  ****************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    }  {
     printf("\n ");    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*    int i, ii,j,k;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    double min, max, maxmin, maxmax,sumnew=0.;
   goto end;*/    double **matprod2();
     return ps;    double **out, cov[NCOVMAX], **pmij();
 }    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
 /**************** Product of 2 matrices ******************/  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      for (j=1;j<=nlstate+ndeath;j++){
 {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized     cov[1]=1.;
      before: only the contents of out is modified. The function returns   
      a pointer to pointers identical to out */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   long i, j, k;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(i=nrl; i<= nrh; i++)      newm=savm;
     for(k=ncolol; k<=ncoloh; k++)      /* Covariates have to be included here again */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)       cov[2]=agefin;
         out[i][k] +=in[i][j]*b[j][k];    
         for (k=1; k<=cptcovn;k++) {
   return out;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 /************* Higher Matrix Product ***************/        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]]];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      duration (i.e. until        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).      savm=oldm;
      Model is determined by parameters x and covariates have to be      oldm=newm;
      included manually here.      maxmax=0.;
       for(j=1;j<=nlstate;j++){
      */        min=1.;
         max=0.;
   int i, j, d, h, k;        for(i=1; i<=nlstate; i++) {
   double **out, cov[NCOVMAX];          sumnew=0;
   double **newm;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   /* Hstepm could be zero and should return the unit matrix */          max=FMAX(max,prlim[i][j]);
   for (i=1;i<=nlstate+ndeath;i++)          min=FMIN(min,prlim[i][j]);
     for (j=1;j<=nlstate+ndeath;j++){        }
       oldm[i][j]=(i==j ? 1.0 : 0.0);        maxmin=max-min;
       po[i][j][0]=(i==j ? 1.0 : 0.0);        maxmax=FMAX(maxmax,maxmin);
     }      }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if(maxmax < ftolpl){
   for(h=1; h <=nhstepm; h++){        return prlim;
     for(d=1; d <=hstepm; d++){      }
       newm=savm;    }
       /* Covariates have to be included here again */  }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*************** transition probabilities ***************/ 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    double s1, s2;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      for(i=1; i<= nlstate; i++){
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for(j=1; j<i;j++){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          /*s2 += param[i][j][nc]*cov[nc];*/
       savm=oldm;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       oldm=newm;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     }        }
     for(i=1; i<=nlstate+ndeath; i++)        ps[i][j]=s2;
       for(j=1;j<=nlstate+ndeath;j++) {        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
         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(j=i+1; j<=nlstate+ndeath;j++){
          */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       }          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   } /* end h */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   return po;        }
 }        ps[i][j]=s2;
       }
     }
 /*************** log-likelihood *************/      /*ps[3][2]=1;*/
 double func( double *x)  
 {    for(i=1; i<= nlstate; i++){
   int i, ii, j, k, mi, d, kk;       s1=0;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(j=1; j<i; j++)
   double **out;        s1+=exp(ps[i][j]);
   double sw; /* Sum of weights */      for(j=i+1; j<=nlstate+ndeath; j++)
   double lli; /* Individual log likelihood */        s1+=exp(ps[i][j]);
   int s1, s2;      ps[i][i]=1./(s1+1.);
   long ipmx;      for(j=1; j<i; j++)
   /*extern weight */        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* We are differentiating ll according to initial status */      for(j=i+1; j<=nlstate+ndeath; j++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /*for(i=1;i<imx;i++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     printf(" %d\n",s[4][i]);    } /* end i */
   */  
   cov[1]=1.;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   for(k=1; k<=nlstate; k++) ll[k]=0.;        ps[ii][jj]=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        ps[ii][ii]=1;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      }
     for(mi=1; mi<= wav[i]-1; mi++){    }
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++){  
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
           savm[ii][j]=(ii==j ? 1.0 : 0.0);      for(jj=1; jj<= nlstate+ndeath; jj++){
         }       printf("%lf ",ps[ii][jj]);
       for(d=0; d<dh[mi][i]; d++){     }
         newm=savm;      printf("\n ");
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      }
         for (kk=1; kk<=cptcovage;kk++) {      printf("\n ");printf("%lf ",cov[2]);*/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*
         }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
            goto end;*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      return ps;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  }
         savm=oldm;  
         oldm=newm;  /**************** Product of 2 matrices ******************/
          
          double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       } /* end mult */  {
          /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       s1=s[mw[mi][i]][i];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       s2=s[mw[mi+1][i]][i];    /* in, b, out are matrice of pointers which should have been initialized 
       if( s2 > nlstate){       before: only the contents of out is modified. The function returns
         /* i.e. if s2 is a death state and if the date of death is known then the contribution       a pointer to pointers identical to out */
            to the likelihood is the probability to die between last step unit time and current    long i, j, k;
            step unit time, which is also the differences between probability to die before dh    for(i=nrl; i<= nrh; i++)
            and probability to die before dh-stepm .      for(k=ncolol; k<=ncoloh; k++)
            In version up to 0.92 likelihood was computed        for(j=ncl,out[i][k]=0.; j<=nch; j++)
            as if date of death was unknown. Death was treated as any other          out[i][k] +=in[i][j]*b[j][k];
            health state: the date of the interview describes the actual state  
            and not the date of a change in health state. The former idea was    return out;
            to consider that at each interview the state was recorded  }
            (healthy, disable or death) and IMaCh was corrected; but when we  
            introduced the exact date of death then we should have modified  
            the contribution of an exact death to the likelihood. This new  /************* Higher Matrix Product ***************/
            contribution is smaller and very dependent of the step unit  
            stepm. It is no more the probability to die between last interview  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
            and month of death but the probability to survive from last  {
            interview up to one month before death multiplied by the    /* Computes the transition matrix starting at age 'age' over 
            probability to die within a month. Thanks to Chris       'nhstepm*hstepm*stepm' months (i.e. until
            Jackson for correcting this bug.  Former versions increased       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            mortality artificially. The bad side is that we add another loop       nhstepm*hstepm matrices. 
            which slows down the processing. The difference can be up to 10%       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
            lower mortality.       (typically every 2 years instead of every month which is too big 
         */       for the memory).
         lli=log(out[s1][s2] - savm[s1][s2]);       Model is determined by parameters x and covariates have to be 
       }else{       included manually here. 
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */  
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/       */
       }  
       ipmx +=1;    int i, j, d, h, k;
       sw += weight[i];    double **out, cov[NCOVMAX];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double **newm;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/  
     } /* end of wave */    /* Hstepm could be zero and should return the unit matrix */
   } /* end of individual */    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        oldm[i][j]=(i==j ? 1.0 : 0.0);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      }
   /*exit(0);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return -l;    for(h=1; h <=nhstepm; h++){
 }      for(d=1; d <=hstepm; d++){
         newm=savm;
         /* Covariates have to be included here again */
 /*********** Maximum Likelihood Estimation ***************/        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {        for (k=1; k<=cptcovage;k++)
   int i,j, iter;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double **xi,*delti;        for (k=1; k<=cptcovprod;k++)
   double fret;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       xi[i][j]=(i==j ? 1.0 : 0.0);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   printf("Powell\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   powell(p,xi,npar,ftol,&iter,&fret,func);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        oldm=newm;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      }
       for(i=1; i<=nlstate+ndeath; i++)
 }        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
 /**** Computes Hessian and covariance matrix ***/          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))           */
 {        }
   double  **a,**y,*x,pd;    } /* end h */
   double **hess;    return po;
   int i, j,jk;  }
   int *indx;  
   
   double hessii(double p[], double delta, int theta, double delti[]);  /*************** log-likelihood *************/
   double hessij(double p[], double delti[], int i, int j);  double func( double *x)
   void lubksb(double **a, int npar, int *indx, double b[]) ;  {
   void ludcmp(double **a, int npar, int *indx, double *d) ;    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
   hess=matrix(1,npar,1,npar);    double **out;
     double sw; /* Sum of weights */
   printf("\nCalculation of the hessian matrix. Wait...\n");    double lli; /* Individual log likelihood */
   for (i=1;i<=npar;i++){    int s1, s2;
     printf("%d",i);fflush(stdout);    double bbh, survp;
     hess[i][i]=hessii(p,ftolhess,i,delti);    long ipmx;
     /*printf(" %f ",p[i]);*/    /*extern weight */
     /*printf(" %lf ",hess[i][i]);*/    /* 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 (i=1;i<=npar;i++) {      printf(" %d\n",s[4][i]);
     for (j=1;j<=npar;j++)  {    */
       if (j>i) {    cov[1]=1.;
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);    for(k=1; k<=nlstate; k++) ll[k]=0.;
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/    if(mle==1){
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   a=matrix(1,npar,1,npar);            }
   y=matrix(1,npar,1,npar);          for(d=0; d<dh[mi][i]; d++){
   x=vector(1,npar);            newm=savm;
   indx=ivector(1,npar);            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]=hess[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,
   for (j=1;j<=npar;j++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1;i<=npar;i++) x[i]=0;            savm=oldm;
     x[j]=1;            oldm=newm;
     lubksb(a,npar,indx,x);          } /* end mult */
     for (i=1;i<=npar;i++){        
       matcov[i][j]=x[i];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     }          /* But now since version 0.9 we anticipate for bias and large stepm.
   }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
   printf("\n#Hessian matrix#\n");           * the nearest (and in case of equal distance, to the lowest) interval but now
   for (i=1;i<=npar;i++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (j=1;j<=npar;j++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       printf("%.3e ",hess[i][j]);           * 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
     printf("\n");           * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   /* Recompute Inverse */           */
   for (i=1;i<=npar;i++)          s1=s[mw[mi][i]][i];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          s2=s[mw[mi+1][i]][i];
   ludcmp(a,npar,indx,&pd);          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
   /*  printf("\n#Hessian matrix recomputed#\n");           * is higher than the multiple of stepm and negative otherwise.
            */
   for (j=1;j<=npar;j++) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for (i=1;i<=npar;i++) x[i]=0;          if( s2 > nlstate){ 
     x[j]=1;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     lubksb(a,npar,indx,x);               to the likelihood is the probability to die between last step unit time and current 
     for (i=1;i<=npar;i++){               step unit time, which is also the differences between probability to die before dh 
       y[i][j]=x[i];               and probability to die before dh-stepm . 
       printf("%.3e ",y[i][j]);               In version up to 0.92 likelihood was computed
     }          as if date of death was unknown. Death was treated as any other
     printf("\n");          health state: the date of the interview describes the actual state
   }          and not the date of a change in health state. The former idea was
   */          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   free_matrix(a,1,npar,1,npar);          introduced the exact date of death then we should have modified
   free_matrix(y,1,npar,1,npar);          the contribution of an exact death to the likelihood. This new
   free_vector(x,1,npar);          contribution is smaller and very dependent of the step unit
   free_ivector(indx,1,npar);          stepm. It is no more the probability to die between last interview
   free_matrix(hess,1,npar,1,npar);          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
 }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
 /*************** hessian matrix ****************/          which slows down the processing. The difference can be up to 10%
 double hessii( double x[], double delta, int theta, double delti[])          lower mortality.
 {            */
   int i;            lli=log(out[s1][s2] - savm[s1][s2]);
   int l=1, lmax=20;          }else{
   double k1,k2;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double p2[NPARMAX+1];            /*  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 */
   double res;          } 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double fx;          /*if(lli ==000.0)*/
   int k=0,kmax=10;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   double l1;          ipmx +=1;
           sw += weight[i];
   fx=func(x);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (i=1;i<=npar;i++) p2[i]=x[i];        } /* end of wave */
   for(l=0 ; l <=lmax; l++){      } /* end of individual */
     l1=pow(10,l);    }  else if(mle==2){
     delts=delt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(k=1 ; k <kmax; k=k+1){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       delt = delta*(l1*k);        for(mi=1; mi<= wav[i]-1; mi++){
       p2[theta]=x[theta] +delt;          for (ii=1;ii<=nlstate+ndeath;ii++)
       k1=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
       p2[theta]=x[theta]-delt;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       k2=func(p2)-fx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*res= (k1-2.0*fx+k2)/delt/delt; */            }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          for(d=0; d<=dh[mi][i]; d++){
                  newm=savm;
 #ifdef DEBUG            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            for (kk=1; kk<=cptcovage;kk++) {
 #endif              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         k=kmax;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            oldm=newm;
         k=kmax; l=lmax*10.;          } /* end mult */
       }        
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         delts=delt;          /* 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 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
   delti[theta]=delts;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   return res;           * (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
            * -stepm/2 to stepm/2 .
 double hessij( double x[], double delti[], int thetai,int thetaj)           * For stepm=1 the results are the same as for previous versions of Imach.
 {           * For stepm > 1 the results are less biased than in previous versions. 
   int i;           */
   int l=1, l1, lmax=20;          s1=s[mw[mi][i]][i];
   double k1,k2,k3,k4,res,fx;          s2=s[mw[mi+1][i]][i];
   double p2[NPARMAX+1];          bbh=(double)bh[mi][i]/(double)stepm; 
   int k;          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   fx=func(x);           */
   for (k=1; k<=2; k++) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for (i=1;i<=npar;i++) p2[i]=x[i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     k1=func(p2)-fx;          /*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); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          ipmx +=1;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          sw += weight[i];
     k2=func(p2)-fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
     p2[thetai]=x[thetai]-delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }  else if(mle==3){  /* exponential inter-extrapolation */
     k3=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k4=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            }
 #endif          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   return res;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************** Inverse of matrix **************/            }
 void ludcmp(double **a, int n, int *indx, double *d)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i,imax,j,k;            savm=oldm;
   double big,dum,sum,temp;            oldm=newm;
   double *vv;          } /* end mult */
          
   vv=vector(1,n);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   *d=1.0;          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (i=1;i<=n;i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     big=0.0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=n;j++)           * the nearest (and in case of equal distance, to the lowest) interval but now
       if ((temp=fabs(a[i][j])) > big) big=temp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     vv[i]=1.0/big;           * 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
   for (j=1;j<=n;j++) {           * -stepm/2 to stepm/2 .
     for (i=1;i<j;i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
       sum=a[i][j];           * For stepm > 1 the results are less biased than in previous versions. 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     big=0.0;          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=j;i<=n;i++) {          /* bias is positive if real duration
       sum=a[i][j];           * is higher than the multiple of stepm and negative otherwise.
       for (k=1;k<j;k++)           */
         sum -= a[i][k]*a[k][j];          /* 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 */
       a[i][j]=sum;          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 */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         big=dum;          /*if(lli ==000.0)*/
         imax=i;          /*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;
     }          sw += weight[i];
     if (j != imax) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (k=1;k<=n;k++) {        } /* end of wave */
         dum=a[imax][k];      } /* end of individual */
         a[imax][k]=a[j][k];    }else{  /* ml=4 no inter-extrapolation */
         a[j][k]=dum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       *d = -(*d);        for(mi=1; mi<= wav[i]-1; mi++){
       vv[imax]=vv[j];          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     indx[j]=imax;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (a[j][j] == 0.0) a[j][j]=TINY;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != n) {            }
       dum=1.0/(a[j][j]);          for(d=0; d<dh[mi][i]; d++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   free_vector(vv,1,n);  /* Doesn't work */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 ;            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void lubksb(double **a, int n, int *indx, double b[])                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   int i,ii=0,ip,j;            oldm=newm;
   double sum;          } /* end mult */
          
   for (i=1;i<=n;i++) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     ip=indx[i];          ipmx +=1;
     sum=b[ip];          sw += weight[i];
     b[ip]=b[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (ii)        } /* end of wave */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      } /* end of individual */
     else if (sum) ii=i;    } /* End of if */
     b[i]=sum;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (i=n;i>=1;i--) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     sum=b[i];    return -l;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  }
     b[i]=sum/a[i][i];  
   }  
 }  /*********** Maximum Likelihood Estimation ***************/
   
 /************ Frequencies ********************/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  {
 {  /* Some frequencies */    int i,j, iter;
      double **xi;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    double fret;
   double ***freq; /* Frequencies */    char filerespow[FILENAMELENGTH];
   double *pp;    xi=matrix(1,npar,1,npar);
   double pos, k2, dateintsum=0,k2cpt=0;    for (i=1;i<=npar;i++)
   FILE *ficresp;      for (j=1;j<=npar;j++)
   char fileresp[FILENAMELENGTH];        xi[i][j]=(i==j ? 1.0 : 0.0);
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
   pp=vector(1,nlstate);    strcpy(filerespow,"pow"); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(filerespow,fileres);
   strcpy(fileresp,"p");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   strcat(fileresp,fileres);      printf("Problem with resultfile: %s\n", filerespow);
   if((ficresp=fopen(fileresp,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    }
     exit(0);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   }    for (i=1;i<=nlstate;i++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for(j=1;j<=nlstate+ndeath;j++)
   j1=0;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   j=cptcoveff;    powell(p,xi,npar,ftol,&iter,&fret,func);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
      fclose(ficrespow);
   for(k1=1; k1<=j;k1++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       j1++;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
         scanf("%d", i);*/  }
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /**** Computes Hessian and covariance matrix ***/
           for(m=agemin; m <= agemax+3; m++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
             freq[i][jk][m]=0;  {
          double  **a,**y,*x,pd;
       dateintsum=0;    double **hess;
       k2cpt=0;    int i, j,jk;
       for (i=1; i<=imx; i++) {    int *indx;
         bool=1;  
         if  (cptcovn>0) {    double hessii(double p[], double delta, int theta, double delti[]);
           for (z1=1; z1<=cptcoveff; z1++)    double hessij(double p[], double delti[], int i, int j);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    void lubksb(double **a, int npar, int *indx, double b[]) ;
               bool=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
         }  
         if (bool==1) {    hess=matrix(1,npar,1,npar);
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);    printf("\nCalculation of the hessian matrix. Wait...\n");
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;    for (i=1;i<=npar;i++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;      printf("%d",i);fflush(stdout);
               if (m<lastpass) {      fprintf(ficlog,"%d",i);fflush(ficlog);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      hess[i][i]=hessii(p,ftolhess,i,delti);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      /*printf(" %f ",p[i]);*/
               }      /*printf(" %lf ",hess[i][i]);*/
                  }
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    
                 dateintsum=dateintsum+k2;    for (i=1;i<=npar;i++) {
                 k2cpt++;      for (j=1;j<=npar;j++)  {
               }        if (j>i) { 
             }          printf(".%d%d",i,j);fflush(stdout);
           }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         }          hess[i][j]=hessij(p,delti,i,j);
       }          hess[j][i]=hess[i][j];    
                  /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
       }
       if  (cptcovn>0) {    }
         fprintf(ficresp, "\n#********** Variable ");    printf("\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n");
         fprintf(ficresp, "**********\n#");  
       }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    
       fprintf(ficresp, "\n");    a=matrix(1,npar,1,npar);
          y=matrix(1,npar,1,npar);
       for(i=(int)agemin; i <= (int)agemax+3; i++){    x=vector(1,npar);
         if(i==(int)agemax+3)    indx=ivector(1,npar);
           printf("Total");    for (i=1;i<=npar;i++)
         else      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           printf("Age %d", i);    ludcmp(a,npar,indx,&pd);
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (j=1;j<=npar;j++) {
             pp[jk] += freq[jk][m][i];      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
         for(jk=1; jk <=nlstate ; jk++){      lubksb(a,npar,indx,x);
           for(m=-1, pos=0; m <=0 ; m++)      for (i=1;i<=npar;i++){ 
             pos += freq[jk][m][i];        matcov[i][j]=x[i];
           if(pp[jk]>=1.e-10)      }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    }
           else  
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
         for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++) { 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        printf("%.3e ",hess[i][j]);
             pp[jk] += freq[jk][m][i];        fprintf(ficlog,"%.3e ",hess[i][j]);
         }      }
       printf("\n");
         for(jk=1,pos=0; jk <=nlstate ; jk++)      fprintf(ficlog,"\n");
           pos += pp[jk];    }
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5)    /* Recompute Inverse */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for (i=1;i<=npar;i++)
           else      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    ludcmp(a,npar,indx,&pd);
           if( i <= (int) agemax){  
             if(pos>=1.e-5){    /*  printf("\n#Hessian matrix recomputed#\n");
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;    for (j=1;j<=npar;j++) {
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      for (i=1;i<=npar;i++) x[i]=0;
             }      x[j]=1;
             else      lubksb(a,npar,indx,x);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      for (i=1;i<=npar;i++){ 
           }        y[i][j]=x[i];
         }        printf("%.3e ",y[i][j]);
                fprintf(ficlog,"%.3e ",y[i][j]);
         for(jk=-1; jk <=nlstate+ndeath; jk++)      }
           for(m=-1; m <=nlstate+ndeath; m++)      printf("\n");
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      fprintf(ficlog,"\n");
         if(i <= (int) agemax)    }
           fprintf(ficresp,"\n");    */
         printf("\n");  
       }    free_matrix(a,1,npar,1,npar);
     }    free_matrix(y,1,npar,1,npar);
   }    free_vector(x,1,npar);
   dateintmean=dateintsum/k2cpt;    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  }
    
   /* End of Freq */  /*************** hessian matrix ****************/
 }  double hessii( double x[], double delta, int theta, double delti[])
   {
 /************ Prevalence ********************/    int 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)    int l=1, lmax=20;
 {  /* Some frequencies */    double k1,k2;
      double p2[NPARMAX+1];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double res;
   double ***freq; /* Frequencies */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double *pp;    double fx;
   double pos, k2;    int k=0,kmax=10;
     double l1;
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    fx=func(x);
      for (i=1;i<=npar;i++) p2[i]=x[i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for(l=0 ; l <=lmax; l++){
   j1=0;      l1=pow(10,l);
        delts=delt;
   j=cptcoveff;      for(k=1 ; k <kmax; k=k+1){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
  for(k1=1; k1<=j;k1++){        k1=func(p2)-fx;
     for(i1=1; i1<=ncodemax[k1];i1++){        p2[theta]=x[theta]-delt;
       j1++;        k2=func(p2)-fx;
          /*res= (k1-2.0*fx+k2)/delt/delt; */
       for (i=-1; i<=nlstate+ndeath; i++)          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          
           for(m=agemin; m <= agemax+3; m++)  #ifdef DEBUG
             freq[i][jk][m]=0;        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);
       for (i=1; i<=imx; i++) {  #endif
         bool=1;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if  (cptcovn>0) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           for (z1=1; z1<=cptcoveff; z1++)          k=kmax;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         if (bool==1) {        }
           for(m=firstpass; m<=lastpass; m++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             k2=anint[m][i]+(mint[m][i]/12.);          delts=delt;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    }
               if (m<lastpass)    delti[theta]=delts;
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    return res; 
               else    
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  }
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  
             }  double hessij( double x[], double delti[], int thetai,int thetaj)
           }  {
         }    int i;
       }    int l=1, l1, lmax=20;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    double k1,k2,k3,k4,res,fx;
           for(jk=1; jk <=nlstate ; jk++){    double p2[NPARMAX+1];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int k;
               pp[jk] += freq[jk][m][i];  
           }    fx=func(x);
           for(jk=1; jk <=nlstate ; jk++){    for (k=1; k<=2; k++) {
             for(m=-1, pos=0; m <=0 ; m++)      for (i=1;i<=npar;i++) p2[i]=x[i];
             pos += freq[jk][m][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
              k1=func(p2)-fx;
          for(jk=1; jk <=nlstate ; jk++){    
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      p2[thetai]=x[thetai]+delti[thetai]/k;
              pp[jk] += freq[jk][m][i];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          }      k2=func(p2)-fx;
              
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          for(jk=1; jk <=nlstate ; jk++){                k3=func(p2)-fx;
            if( i <= (int) agemax){    
              if(pos>=1.e-5){      p2[thetai]=x[thetai]-delti[thetai]/k;
                probs[i][jk][j1]= pp[jk]/pos;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
              }      k4=func(p2)-fx;
            }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
          }  #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);
     }  #endif
   }    }
     return res;
    }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
 }  /* End of Freq */  { 
     int i,imax,j,k; 
 /************* Waves Concatenation ***************/    double big,dum,sum,temp; 
     double *vv; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)   
 {    vv=vector(1,n); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    *d=1.0; 
      Death is a valid wave (if date is known).    for (i=1;i<=n;i++) { 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      big=0.0; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (j=1;j<=n;j++) 
      and mw[mi+1][i]. dh depends on stepm.        if ((temp=fabs(a[i][j])) > big) big=temp; 
      */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   int i, mi, m;    } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    for (j=1;j<=n;j++) { 
      double sum=0., jmean=0.;*/      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   int j, k=0,jk, ju, jl;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double sum=0.;        a[i][j]=sum; 
   jmin=1e+5;      } 
   jmax=-1;      big=0.0; 
   jmean=0.;      for (i=j;i<=n;i++) { 
   for(i=1; i<=imx; i++){        sum=a[i][j]; 
     mi=0;        for (k=1;k<j;k++) 
     m=firstpass;          sum -= a[i][k]*a[k][j]; 
     while(s[m][i] <= nlstate){        a[i][j]=sum; 
       if(s[m][i]>=1)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         mw[++mi][i]=m;          big=dum; 
       if(m >=lastpass)          imax=i; 
         break;        } 
       else      } 
         m++;      if (j != imax) { 
     }/* end while */        for (k=1;k<=n;k++) { 
     if (s[m][i] > nlstate){          dum=a[imax][k]; 
       mi++;     /* Death is another wave */          a[imax][k]=a[j][k]; 
       /* if(mi==0)  never been interviewed correctly before death */          a[j][k]=dum; 
          /* Only death is a correct wave */        } 
       mw[mi][i]=m;        *d = -(*d); 
     }        vv[imax]=vv[j]; 
       } 
     wav[i]=mi;      indx[j]=imax; 
     if(mi==0)      if (a[j][j] == 0.0) a[j][j]=TINY; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for(i=1; i<=imx; i++){      } 
     for(mi=1; mi<wav[i];mi++){    } 
       if (stepm <=0)    free_vector(vv,1,n);  /* Doesn't work */
         dh[mi][i]=1;  ;
       else{  } 
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  void lubksb(double **a, int n, int *indx, double b[]) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  { 
           if(j==0) j=1;  /* Survives at least one month after exam */    int i,ii=0,ip,j; 
           k=k+1;    double sum; 
           if (j >= jmax) jmax=j;   
           if (j <= jmin) jmin=j;    for (i=1;i<=n;i++) { 
           sum=sum+j;      ip=indx[i]; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      sum=b[ip]; 
           }      b[ip]=b[i]; 
         }      if (ii) 
         else{        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      else if (sum) ii=i; 
           k=k+1;      b[i]=sum; 
           if (j >= jmax) jmax=j;    } 
           else if (j <= jmin)jmin=j;    for (i=n;i>=1;i--) { 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      sum=b[i]; 
           sum=sum+j;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         }      b[i]=sum/a[i][i]; 
         jk= j/stepm;    } 
         jl= j -jk*stepm;  } 
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)  /************ Frequencies ********************/
           dh[mi][i]=jk;  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)
         else  {  /* Some frequencies */
           dh[mi][i]=jk+1;    
         if(dh[mi][i]==0)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           dh[mi][i]=1; /* At least one step */    int first;
       }    double ***freq; /* Frequencies */
     }    double *pp, **prop;
   }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   jmean=sum/k;    FILE *ficresp;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    char fileresp[FILENAMELENGTH];
  }    
 /*********** Tricode ****************************/    pp=vector(1,nlstate);
 void tricode(int *Tvar, int **nbcode, int imx)    prop=matrix(1,nlstate,iagemin,iagemax+3);
 {    strcpy(fileresp,"p");
   int Ndum[20],ij=1, k, j, i;    strcat(fileresp,fileres);
   int cptcode=0;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   cptcoveff=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   for (k=0; k<19; k++) Ndum[k]=0;      exit(0);
   for (k=1; k<=7; k++) ncodemax[k]=0;    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    j1=0;
     for (i=1; i<=imx; i++) {    
       ij=(int)(covar[Tvar[j]][i]);    j=cptcoveff;
       Ndum[ij]++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;    first=1;
     }  
     for(k1=1; k1<=j;k1++){
     for (i=0; i<=cptcode; i++) {      for(i1=1; i1<=ncodemax[k1];i1++){
       if(Ndum[i]!=0) ncodemax[j]++;        j1++;
     }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     ij=1;          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     for (i=1; i<=ncodemax[j]; i++) {            for(m=iagemin; m <= iagemax+3; m++)
       for (k=0; k<=19; k++) {              freq[i][jk][m]=0;
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;      for (i=1; i<=nlstate; i++)  
                  for(m=iagemin; m <= iagemax+3; m++)
           ij++;          prop[i][m]=0;
         }        
         if (ij > ncodemax[j]) break;        dateintsum=0;
       }          k2cpt=0;
     }        for (i=1; i<=imx; i++) {
   }            bool=1;
           if  (cptcovn>0) {
  for (k=0; k<19; k++) Ndum[k]=0;            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  for (i=1; i<=ncovmodel-2; i++) {                bool=0;
       ij=Tvar[i];          }
       Ndum[ij]++;          if (bool==1){
     }            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
  ij=1;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
  for (i=1; i<=10; i++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    if((Ndum[i]!=0) && (i<=ncovcol)){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
      Tvaraff[ij]=i;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      ij++;                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]][iagemax+3] += weight[i];
                  }
     cptcoveff=ij-1;                
 }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
 /*********** Health Expectancies ****************/                  k2cpt++;
                 }
 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 )              }
             }
 {          }
   /* Health expectancies */        }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;         
   double age, agelim, hf;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;        if  (cptcovn>0) {
   double *xp;          fprintf(ficresp, "\n#********** Variable "); 
   double **gp, **gm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double ***gradg, ***trgradg;          fprintf(ficresp, "**********\n#");
   int theta;        }
         for(i=1; i<=nlstate;i++) 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   xp=vector(1,npar);        fprintf(ficresp, "\n");
   dnewm=matrix(1,nlstate*2,1,npar);        
   doldm=matrix(1,nlstate*2,1,nlstate*2);        for(i=iagemin; i <= iagemax+3; i++){
            if(i==iagemax+3){
   fprintf(ficreseij,"# Health expectancies\n");            fprintf(ficlog,"Total");
   fprintf(ficreseij,"# Age");          }else{
   for(i=1; i<=nlstate;i++)            if(first==1){
     for(j=1; j<=nlstate;j++)              first=0;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);              printf("See log file for details...\n");
   fprintf(ficreseij,"\n");            }
             fprintf(ficlog,"Age %d", i);
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   else  hstepm=estepm;                pp[jk] += freq[jk][m][i]; 
   /* We compute the life expectancy from trapezoids spaced every estepm months          }
    * This is mainly to measure the difference between two models: for example          for(jk=1; jk <=nlstate ; jk++){
    * if stepm=24 months pijx are given only every 2 years and by summing them            for(m=-1, pos=0; m <=0 ; m++)
    * we are calculating an estimate of the Life Expectancy assuming a linear              pos += freq[jk][m][i];
    * progression inbetween and thus overestimating or underestimating according            if(pp[jk]>=1.e-10){
    * to the curvature of the survival function. If, for the same date, we              if(first==1){
    * estimate the model with stepm=1 month, we can keep estepm to 24 months              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    * to compare the new estimate of Life expectancy with the same linear              }
    * hypothesis. A more precise result, taking into account a more precise              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    * curvature will be obtained if estepm is as small as stepm. */            }else{
               if(first==1)
   /* For example we decided to compute the life expectancy with the smallest unit */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      nhstepm is the number of hstepm from age to agelim            }
      nstepm is the number of stepm from age to agelin.          }
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */          for(jk=1; jk <=nlstate ; jk++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
      survival function given by stepm (the optimization length). Unfortunately it              pp[jk] += freq[jk][m][i];
      means that if the survival funtion is printed only each two years of age and if          }       
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
      results. So we changed our mind and took the option of the best precision.            pos += pp[jk];
   */            posprop += prop[jk][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }
           for(jk=1; jk <=nlstate ; jk++){
   agelim=AGESUP;            if(pos>=1.e-5){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(first==1)
     /* nhstepm age range expressed in number of stepm */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     /* 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 prev[%d]=NaNQ%%",jk,pp[jk],jk);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            }
     gp=matrix(0,nhstepm,1,nlstate*2);            if( i <= iagemax){
     gm=matrix(0,nhstepm,1,nlstate*2);              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                probs[i][jk][j1]= pp[jk]/pos;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                }
                else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            }
           }
     /* Computing Variances of health expectancies */          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
      for(theta=1; theta <=npar; theta++){            for(m=-1; m <=nlstate+ndeath; m++)
       for(i=1; i<=npar; i++){              if(freq[jk][m][i] !=0 ) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              if(first==1)
       }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
       cptj=0;          if(i <= iagemax)
       for(j=1; j<= nlstate; j++){            fprintf(ficresp,"\n");
         for(i=1; i<=nlstate; i++){          if(first==1)
           cptj=cptj+1;            printf("Others in log...\n");
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          fprintf(ficlog,"\n");
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        }
           }      }
         }    }
       }    dateintmean=dateintsum/k2cpt; 
         
          fclose(ficresp);
       for(i=1; i<=npar; i++)    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    free_vector(pp,1,nlstate);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      free_matrix(prop,1,nlstate,iagemin, iagemax+3);
          /* End of Freq */
       cptj=0;  }
       for(j=1; j<= nlstate; j++){  
         for(i=1;i<=nlstate;i++){  /************ Prevalence ********************/
           cptj=cptj+1;  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(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  {  
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
           }       in each health status at the date of interview (if between dateprev1 and dateprev2).
         }       We still use firstpass and lastpass as another selection.
       }    */
         
        int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
       for(j=1; j<= nlstate*2; j++)    double *pp, **prop;
         for(h=0; h<=nhstepm-1; h++){    double pos,posprop; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double  y2; /* in fractional years */
         }    int iagemin, iagemax;
   
      }    iagemin= (int) agemin;
        iagemax= (int) agemax;
 /* End theta */    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
      for(h=0; h<=nhstepm-1; h++)    
       for(j=1; j<=nlstate*2;j++)    j=cptcoveff;
         for(theta=1; theta <=npar; theta++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         trgradg[h][j][theta]=gradg[h][theta][j];    
     for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
      for(i=1;i<=nlstate*2;i++)        j1++;
       for(j=1;j<=nlstate*2;j++)        
         varhe[i][j][(int)age] =0.;        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
     for(h=0;h<=nhstepm-1;h++){            prop[i][m]=0.0;
       for(k=0;k<=nhstepm-1;k++){       
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        for (i=1; i<=imx; i++) { /* Each individual */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          bool=1;
         for(i=1;i<=nlstate*2;i++)          if  (cptcovn>0) {
           for(j=1;j<=nlstate*2;j++)            for (z1=1; z1<=cptcoveff; z1++) 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
     }          } 
           if (bool==1) { 
                  for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     /* Computing expectancies */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for(i=1; i<=nlstate;i++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(j=1; j<=nlstate;j++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;                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); 
                          if (s[m][i]>0 && s[m][i]<=nlstate) { 
 /* 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(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
     fprintf(ficreseij,"%3.0f",age );              }
     cptj=0;            } /* end selection of waves */
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){        }
         cptj++;        for(i=iagemin; i <= iagemax+3; i++){  
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          
       }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficreseij,"\n");            posprop += prop[jk][i]; 
              } 
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);          for(jk=1; jk <=nlstate ; jk++){     
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);            if( i <=  iagemax){ 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);              if(posprop>=1.e-5){ 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                probs[i][jk][j1]= prop[jk][i]/posprop;
   }              } 
   free_vector(xp,1,npar);            } 
   free_matrix(dnewm,1,nlstate*2,1,npar);          }/* end jk */ 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        }/* end i */ 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      } /* end i1 */
 }    } /* end k1 */
     
 /************ Variance ******************/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 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)    /*free_vector(pp,1,nlstate);*/
 {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   /* Variance of health expectancies */  }  /* End of prevalence */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /************* Waves Concatenation ***************/
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h, nstepm ;  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)
   int k, cptcode;  {
   double *xp;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   double **gp, **gm;       Death is a valid wave (if date is known).
   double ***gradg, ***trgradg;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   double ***p3mat;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double age,agelim, hf;       and mw[mi+1][i]. dh depends on stepm.
   int theta;       */
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    int i, mi, m;
   fprintf(ficresvij,"# Age");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   for(i=1; i<=nlstate;i++)       double sum=0., jmean=0.;*/
     for(j=1; j<=nlstate;j++)    int first;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int j, k=0,jk, ju, jl;
   fprintf(ficresvij,"\n");    double sum=0.;
     first=0;
   xp=vector(1,npar);    jmin=1e+5;
   dnewm=matrix(1,nlstate,1,npar);    jmax=-1;
   doldm=matrix(1,nlstate,1,nlstate);    jmean=0.;
      for(i=1; i<=imx; i++){
   if(estepm < stepm){      mi=0;
     printf ("Problem %d lower than %d\n",estepm, stepm);      m=firstpass;
   }      while(s[m][i] <= nlstate){
   else  hstepm=estepm;          if(s[m][i]>=1)
   /* For example we decided to compute the life expectancy with the smallest unit */          mw[++mi][i]=m;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        if(m >=lastpass)
      nhstepm is the number of hstepm from age to agelim          break;
      nstepm is the number of stepm from age to agelin.        else
      Look at hpijx to understand the reason of that which relies in memory size          m++;
      and note for a fixed period like k years */      }/* end while */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      if (s[m][i] > nlstate){
      survival function given by stepm (the optimization length). Unfortunately it        mi++;     /* Death is another wave */
      means that if the survival funtion is printed only each two years of age and if        /* if(mi==0)  never been interviewed correctly before death */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same           /* Only death is a correct wave */
      results. So we changed our mind and took the option of the best precision.        mw[mi][i]=m;
   */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
   agelim = AGESUP;      wav[i]=mi;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      if(mi==0){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if(first==0){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          first=1;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        }
     gp=matrix(0,nhstepm,1,nlstate);        if(first==1){
     gm=matrix(0,nhstepm,1,nlstate);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         }
     for(theta=1; theta <=npar; theta++){      } /* end mi==0 */
       for(i=1; i<=npar; i++){ /* Computes gradient */    } /* End individuals */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    for(i=1; i<=imx; i++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(mi=1; mi<wav[i];mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if (stepm <=0)
           dh[mi][i]=1;
       if (popbased==1) {        else{
         for(i=1; i<=nlstate;i++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           prlim[i][i]=probs[(int)age][i][ij];            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 */
       for(j=1; j<= nlstate; j++){            k=k+1;
         for(h=0; h<=nhstepm; h++){            if (j >= jmax) jmax=j;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            if (j <= jmin) jmin=j;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            sum=sum+j;
         }            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       }            /*      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]);
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            else{
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
              /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       if (popbased==1) {            k=k+1;
         for(i=1; i<=nlstate;i++)            if (j >= jmax) jmax=j;
           prlim[i][i]=probs[(int)age][i][ij];            else if (j <= jmin)jmin=j;
       }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       for(j=1; j<= nlstate; j++){            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]);
         for(h=0; h<=nhstepm; h++){            sum=sum+j;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          jk= j/stepm;
         }          jl= j -jk*stepm;
       }          ju= j -(jk+1)*stepm;
           if(mle <=1){ 
       for(j=1; j<= nlstate; j++)            if(jl==0){
         for(h=0; h<=nhstepm; h++){              dh[mi][i]=jk;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              bh[mi][i]=0;
         }            }else{ /* We want a negative bias in order to only have interpolation ie
     } /* End theta */                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              bh[mi][i]=ju;
             }
     for(h=0; h<=nhstepm; h++)          }else{
       for(j=1; j<=nlstate;j++)            if(jl <= -ju){
         for(theta=1; theta <=npar; theta++)              dh[mi][i]=jk;
           trgradg[h][j][theta]=gradg[h][theta][j];              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                                   */
     for(i=1;i<=nlstate;i++)            }
       for(j=1;j<=nlstate;j++)            else{
         vareij[i][j][(int)age] =0.;              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
     for(h=0;h<=nhstepm;h++){            }
       for(k=0;k<=nhstepm;k++){            if(dh[mi][i]==0){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              dh[mi][i]=1; /* At least one step */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);              bh[mi][i]=ju; /* At least one step */
         for(i=1;i<=nlstate;i++)              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           for(j=1;j<=nlstate;j++)            }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          }
       }        } /* end if mle */
     }      } /* end wave */
     }
     fprintf(ficresvij,"%.0f ",age );    jmean=sum/k;
     for(i=1; i<=nlstate;i++)    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);   }
       }  
     fprintf(ficresvij,"\n");  /*********** Tricode ****************************/
     free_matrix(gp,0,nhstepm,1,nlstate);  void tricode(int *Tvar, int **nbcode, int imx)
     free_matrix(gm,0,nhstepm,1,nlstate);  {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    int Ndum[20],ij=1, k, j, i, maxncov=19;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int cptcode=0;
   } /* End age */    cptcoveff=0; 
     
   free_vector(xp,1,npar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   free_matrix(doldm,1,nlstate,1,npar);    for (k=1; k<=7; k++) ncodemax[k]=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
 /************ Variance of prevlim ******************/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 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)        Ndum[ij]++; /*store the modality */
 {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   /* Variance of prevalence limit */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                                         Tvar[j]. If V=sex and male is 0 and 
   double **newm;                                         female is 1, then  cptcode=1.*/
   double **dnewm,**doldm;      }
   int i, j, nhstepm, hstepm;  
   int k, cptcode;      for (i=0; i<=cptcode; i++) {
   double *xp;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   double *gp, *gm;      }
   double **gradg, **trgradg;  
   double age,agelim;      ij=1; 
   int theta;      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          if (Ndum[k] != 0) {
   fprintf(ficresvpl,"# Age");            nbcode[Tvar[j]][ij]=k; 
   for(i=1; i<=nlstate;i++)            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       fprintf(ficresvpl," %1d-%1d",i,i);            
   fprintf(ficresvpl,"\n");            ij++;
           }
   xp=vector(1,npar);          if (ij > ncodemax[j]) break; 
   dnewm=matrix(1,nlstate,1,npar);        }  
   doldm=matrix(1,nlstate,1,nlstate);      } 
      }  
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */   for (k=0; k< maxncov; k++) Ndum[k]=0;
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   for (i=1; i<=ncovmodel-2; i++) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     if (stepm >= YEARM) hstepm=1;     ij=Tvar[i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */     Ndum[ij]++;
     gradg=matrix(1,npar,1,nlstate);   }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);   ij=1;
    for (i=1; i<= maxncov; i++) {
     for(theta=1; theta <=npar; theta++){     if((Ndum[i]!=0) && (i<=ncovcol)){
       for(i=1; i<=npar; i++){ /* Computes gradient */       Tvaraff[ij]=i; /*For printing */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       ij++;
       }     }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   }
       for(i=1;i<=nlstate;i++)   
         gp[i] = prlim[i][i];   cptcoveff=ij-1; /*Number of simple covariates*/
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*********** Health Expectancies ****************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
         gm[i] = prlim[i][i];  
   {
       for(i=1;i<=nlstate;i++)    /* Health expectancies */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     } /* End theta */    double age, agelim, hf;
     double ***p3mat,***varhe;
     trgradg =matrix(1,nlstate,1,npar);    double **dnewm,**doldm;
     double *xp;
     for(j=1; j<=nlstate;j++)    double **gp, **gm;
       for(theta=1; theta <=npar; theta++)    double ***gradg, ***trgradg;
         trgradg[j][theta]=gradg[theta][j];    int theta;
   
     for(i=1;i<=nlstate;i++)    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       varpl[i][(int)age] =0.;    xp=vector(1,npar);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     for(i=1;i<=nlstate;i++)    
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     fprintf(ficresvpl,"%.0f ",age );    for(i=1; i<=nlstate;i++)
     for(i=1; i<=nlstate;i++)      for(j=1; j<=nlstate;j++)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficresvpl,"\n");    fprintf(ficreseij,"\n");
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    if(estepm < stepm){
     free_matrix(gradg,1,npar,1,nlstate);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_matrix(trgradg,1,nlstate,1,npar);    }
   } /* End age */    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   free_vector(xp,1,npar);     * This is mainly to measure the difference between two models: for example
   free_matrix(doldm,1,nlstate,1,npar);     * if stepm=24 months pijx are given only every 2 years and by summing them
   free_matrix(dnewm,1,nlstate,1,nlstate);     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
 }     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
 /************ Variance of one-step probabilities  ******************/     * to compare the new estimate of Life expectancy with the same linear 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)     * hypothesis. A more precise result, taking into account a more precise
 {     * curvature will be obtained if estepm is as small as stepm. */
   int i, j, i1, k1, j1, z1;  
   int k=0, cptcode;    /* For example we decided to compute the life expectancy with the smallest unit */
   double **dnewm,**doldm;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double *xp;       nhstepm is the number of hstepm from age to agelim 
   double *gp, *gm;       nstepm is the number of stepm from age to agelin. 
   double **gradg, **trgradg;       Look at hpijx to understand the reason of that which relies in memory size
   double age,agelim, cov[NCOVMAX];       and note for a fixed period like estepm months */
   int theta;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   char fileresprob[FILENAMELENGTH];       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
   strcpy(fileresprob,"prob");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   strcat(fileresprob,fileres);       results. So we changed our mind and took the option of the best precision.
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    */
     printf("Problem with resultfile: %s\n", fileresprob);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    agelim=AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");      /* nhstepm age range expressed in number of stepm */
   fprintf(ficresprob,"# Age");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   for(i=1; i<=nlstate;i++)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     for(j=1; j<=(nlstate+ndeath);j++)      /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      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*nlstate);
   fprintf(ficresprob,"\n");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   xp=vector(1,npar);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     
   cov[1]=1;  
   j=cptcoveff;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   j1=0;      /* Computing Variances of health expectancies */
   for(k1=1; k1<=1;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){       for(theta=1; theta <=npar; theta++){
     j1++;        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     if  (cptcovn>0) {        }
       fprintf(ficresprob, "\n#********** Variable ");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
       fprintf(ficresprob, "**********\n#");        cptj=0;
     }        for(j=1; j<= nlstate; j++){
              for(i=1; i<=nlstate; i++){
       for (age=bage; age<=fage; age ++){            cptj=cptj+1;
         cov[2]=age;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         for (k=1; k<=cptcovn;k++) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            }
                    }
         }        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       
         for (k=1; k<=cptcovprod;k++)       
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for(i=1; i<=npar; i++) 
                  xp[i] = x[i] - (i==theta ?delti[theta]:0);
         gradg=matrix(1,npar,1,9);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         trgradg=matrix(1,9,1,npar);        
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        cptj=0;
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for(j=1; j<= nlstate; j++){
              for(i=1;i<=nlstate;i++){
         for(theta=1; theta <=npar; theta++){            cptj=cptj+1;
           for(i=1; i<=npar; i++)            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                        gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            }
                    }
           k=0;        }
           for(i=1; i<= (nlstate+ndeath); i++){        for(j=1; j<= nlstate*nlstate; j++)
             for(j=1; j<=(nlstate+ndeath);j++){          for(h=0; h<=nhstepm-1; h++){
               k=k+1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               gp[k]=pmmij[i][j];          }
             }       } 
           }     
            /* End theta */
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       for(h=0; h<=nhstepm-1; h++)
           k=0;        for(j=1; j<=nlstate*nlstate;j++)
           for(i=1; i<=(nlstate+ndeath); i++){          for(theta=1; theta <=npar; theta++)
             for(j=1; j<=(nlstate+ndeath);j++){            trgradg[h][j][theta]=gradg[h][theta][j];
               k=k+1;       
               gm[k]=pmmij[i][j];  
             }       for(i=1;i<=nlstate*nlstate;i++)
           }        for(j=1;j<=nlstate*nlstate;j++)
                varhe[i][j][(int)age] =0.;
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];         printf("%d|",(int)age);fflush(stdout);
         }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        for(k=0;k<=nhstepm-1;k++){
           for(theta=1; theta <=npar; theta++)          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             trgradg[j][theta]=gradg[theta][j];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                  for(i=1;i<=nlstate*nlstate;i++)
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            for(j=1;j<=nlstate*nlstate;j++)
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                }
         pmij(pmmij,cov,ncovmodel,x,nlstate);      }
              /* Computing expectancies */
         k=0;      for(i=1; i<=nlstate;i++)
         for(i=1; i<=(nlstate+ndeath); i++){        for(j=1; j<=nlstate;j++)
           for(j=1; j<=(nlstate+ndeath);j++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             k=k+1;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             gm[k]=pmmij[i][j];            
           }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         }  
                }
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      fprintf(ficreseij,"%3.0f",age );
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      cptj=0;
      }*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
         fprintf(ficresprob,"\n%d ",(int)age);          cptj++;
           fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)        }
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));      fprintf(ficreseij,"\n");
       
       }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
   }    printf("\n");
   free_vector(xp,1,npar);    fprintf(ficlog,"\n");
   fclose(ficresprob);  
      free_vector(xp,1,npar);
 }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 /******************* Printing html file ***********/    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 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 optionfile[], \  /************ Variance ******************/
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\  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)
  char version[], int popforecast, int estepm ){  {
   int jj1, k1, i1, cpt;    /* Variance of health expectancies */
   FILE *fichtm;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /*char optionfilehtm[FILENAMELENGTH];*/    /* double **newm;*/
     double **dnewm,**doldm;
   strcpy(optionfilehtm,optionfile);    double **dnewmp,**doldmp;
   strcat(optionfilehtm,".htm");    int i, j, nhstepm, hstepm, h, nstepm ;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    int k, cptcode;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double *xp;
   }    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    double **gradgp, **trgradgp; /* for var p point j */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    double *gpp, *gmp; /* for var p point j */
 \n    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 Total number of observations=%d <br>\n    double ***p3mat;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    double age,agelim, hf;
 <hr  size=\"2\" color=\"#EC5E5E\">    double ***mobaverage;
  <ul><li>Outputs files<br>\n    int theta;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    char digit[4];
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    char digitp[25];
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    char fileresprobmorprev[FILENAMELENGTH];
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n  
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    if(popbased==1){
       if(mobilav!=0)
  fprintf(fichtm,"\n        strcpy(digitp,"-populbased-mobilav-");
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      else strcpy(digitp,"-populbased-nomobil-");
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    }
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    else 
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      strcpy(digitp,"-stablbased-");
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
     if (mobilav!=0) {
  if(popforecast==1) fprintf(fichtm,"\n      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         <br>",fileres,fileres,fileres,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  else      }
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    }
 fprintf(fichtm," <li>Graphs</li><p>");  
     strcpy(fileresprobmorprev,"prmorprev"); 
  m=cptcoveff;    sprintf(digit,"%-d",ij);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
  jj1=0;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  for(k1=1; k1<=m;k1++){    strcat(fileresprobmorprev,fileres);
    for(i1=1; i1<=ncodemax[k1];i1++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        jj1++;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        if (cptcovn > 0) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    }
          for (cpt=1; cpt<=cptcoveff;cpt++)    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    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);
        }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          fprintf(ficresprobmorprev," p.%-d SE",j);
        for(cpt=1; cpt<nlstate;cpt++){      for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }  
        }    fprintf(ficresprobmorprev,"\n");
     for(cpt=1; cpt<=nlstate;cpt++) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 interval) in state (%d): v%s%d%d.gif <br>      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        exit(0);
      }    }
      for(cpt=1; cpt<=nlstate;cpt++) {    else{
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      fprintf(ficgp,"\n# Routine varevsij");
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }
      }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      printf("Problem with html file: %s\n", optionfilehtm);
 health expectancies in states (1) and (2): e%s%d.gif<br>      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      exit(0);
 fprintf(fichtm,"\n</body>");    }
    }    else{
    }      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");
 fclose(fichtm);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 }    }
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    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");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   strcpy(optionfilegnuplot,optionfilefiname);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   strcat(optionfilegnuplot,".gp.txt");    fprintf(ficresvij,"\n");
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
 #ifdef windows    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficgp,"cd \"%s\" \n",pathc);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 #endif  
 m=pow(2,cptcoveff);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
  /* 1eme*/    gmp=vector(nlstate+1,nlstate+ndeath);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    for (k1=1; k1<= m ; k1 ++) {    
     if(estepm < stepm){
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
 for (i=1; i<= nlstate ; i ++) {    else  hstepm=estepm;   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* For example we decided to compute the life expectancy with the smallest unit */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 }       nhstepm is the number of hstepm from age to agelim 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       nstepm is the number of stepm from age to agelin. 
     for (i=1; i<= nlstate ; i ++) {       Look at hpijx to understand the reason of that which relies in memory size
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       and note for a fixed period like k years */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* 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
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       means that if the survival funtion is printed every two years of age and if
      for (i=1; i<= nlstate ; i ++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       results. So we changed our mind and took the option of the best precision.
   else fprintf(ficgp," \%%*lf (\%%*lf)");    */
 }      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*2 eme*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {      gm=matrix(0,nhstepm,1,nlstate);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  
      
     for (i=1; i<= nlstate+1 ; i ++) {      for(theta=1; theta <=npar; theta++){
       k=2*i;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if (popbased==1) {
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          if(mobilav ==0){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(i=1; i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {              prlim[i][i]=probs[(int)age][i][ij];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }else{ /* mobilav */ 
         else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=nlstate;i++)
 }                prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficgp,"\" t\"\" w l 0,");          }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<= nlstate; j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(h=0; h<=nhstepm; h++){
 }              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       else fprintf(ficgp,"\" t\"\" w l 0,");          }
     }        }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   /*3eme*/        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for (k1=1; k1<= m ; k1 ++) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       k=2+nlstate*(2*cpt-2);        }    
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        /* end probability of death */
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);   
         if (popbased==1) {
 */          if(mobilav ==0){
       for (i=1; i< nlstate ; i ++) {            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);              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
       }            for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              prlim[i][i]=mobaverage[(int)age][i][ij];
     }          }
     }        }
    
   /* CV preval stat */        for(j=1; j<= nlstate; j++){
     for (k1=1; k1<= m ; k1 ++) {          for(h=0; h<=nhstepm; h++){
     for (cpt=1; cpt<nlstate ; cpt ++) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       k=3;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          }
         }
       for (i=1; i< nlstate ; i ++)        /* This for computing probability of death (h=1 means
         fprintf(ficgp,"+$%d",k+i+1);           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);           as a weighted average of prlim.
              */
       l=3+(nlstate+ndeath)*cpt;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       for (i=1; i< nlstate ; i ++) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         l=3+(nlstate+ndeath)*cpt;        }    
         fprintf(ficgp,"+$%d",l+i+1);        /* end probability of death */
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for(j=1; j<= nlstate; j++) /* vareij */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(h=0; h<=nhstepm; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }            }
    
   /* proba elementaires */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    for(i=1,jk=1; i <=nlstate; i++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     for(k=1; k <=(nlstate+ndeath); k++){        }
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){      } /* End theta */
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           jk++;  
           fprintf(ficgp,"\n");      for(h=0; h<=nhstepm; h++) /* veij */
         }        for(j=1; j<=nlstate;j++)
       }          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
     }  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for(jk=1; jk <=m; jk++) {        for(theta=1; theta <=npar; theta++)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          trgradgp[j][theta]=gradgp[theta][j];
    i=1;    
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(k=1; k<=(nlstate+ndeath); k++) {      for(i=1;i<=nlstate;i++)
        if (k != k2){        for(j=1;j<=nlstate;j++)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          vareij[i][j][(int)age] =0.;
 ij=1;  
         for(j=3; j <=ncovmodel; j++) {      for(h=0;h<=nhstepm;h++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(k=0;k<=nhstepm;k++){
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
             ij++;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           }          for(i=1;i<=nlstate;i++)
           else            for(j=1;j<=nlstate;j++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }        }
           fprintf(ficgp,")/(1");      }
            
         for(k1=1; k1 <=nlstate; k1++){        /* pptj */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 ij=1;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           for(j=3; j <=ncovmodel; j++){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          varppt[j][i]=doldmp[j][i];
             ij++;      /* end ppptj */
           }      /*  x centered again */
           else      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           }   
           fprintf(ficgp,")");      if (popbased==1) {
         }        if(mobilav ==0){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          for(i=1; i<=nlstate;i++)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            prlim[i][i]=probs[(int)age][i][ij];
         i=i+ncovmodel;        }else{ /* mobilav */ 
        }          for(i=1; i<=nlstate;i++)
      }            prlim[i][i]=mobaverage[(int)age][i][ij];
    }        }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      }
    }               
          /* This for computing probability of death (h=1 means
   fclose(ficgp);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
 }  /* end gnuplot */         as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
 /*************** Moving average **************/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
   int i, cpt, cptcod;      /* end probability of death */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           mobaverage[(int)agedeb][i][cptcod]=0.;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
            for(i=1; i<=nlstate;i++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       for (i=1; i<=nlstate;i++){        }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      } 
           for (cpt=0;cpt<=4;cpt++){      fprintf(ficresprobmorprev,"\n");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }      fprintf(ficresvij,"%.0f ",age );
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
       }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     }        }
          fprintf(ficresvij,"\n");
 }      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 /************** Forecasting ******************/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 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){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   int *popage;    free_vector(gmp,nlstate+1,nlstate+ndeath);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   double *popeffectif,*popcount;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   double ***p3mat;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   char fileresf[FILENAMELENGTH];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
  agelim=AGESUP;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   strcpy(fileresf,"f");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   strcat(fileresf,fileres);    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);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /*  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);
     printf("Problem with forecast resultfile: %s\n", fileresf);  */
   }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
     free_vector(xp,1,npar);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
   if (mobilav==1) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fclose(ficgp);
   if (stepm<=12) stepsize=1;    fclose(fichtm);
    }  
   agelim=AGESUP;  
    /************ Variance of prevlim ******************/
   hstepm=1;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   hstepm=hstepm/stepm;  {
   yp1=modf(dateintmean,&yp);    /* Variance of prevalence limit */
   anprojmean=yp;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   yp2=modf((yp1*12),&yp);    double **newm;
   mprojmean=yp;    double **dnewm,**doldm;
   yp1=modf((yp2*30.5),&yp);    int i, j, nhstepm, hstepm;
   jprojmean=yp;    int k, cptcode;
   if(jprojmean==0) jprojmean=1;    double *xp;
   if(mprojmean==0) jprojmean=1;    double *gp, *gm;
      double **gradg, **trgradg;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    double age,agelim;
      int theta;
   for(cptcov=1;cptcov<=i2;cptcov++){     
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       k=k+1;    fprintf(ficresvpl,"# Age");
       fprintf(ficresf,"\n#******");    for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvpl,"\n");
       }  
       fprintf(ficresf,"******\n");    xp=vector(1,npar);
       fprintf(ficresf,"# StartingAge FinalAge");    dnewm=matrix(1,nlstate,1,npar);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    doldm=matrix(1,nlstate,1,nlstate);
          
          hstepm=1*YEARM; /* Every year of age */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         fprintf(ficresf,"\n");    agelim = AGESUP;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      if (stepm >= YEARM) hstepm=1;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           nhstepm = nhstepm/hstepm;      gradg=matrix(1,npar,1,nlstate);
                gp=vector(1,nlstate);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gm=vector(1,nlstate);
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++){ /* Computes gradient */
           for (h=0; h<=nhstepm; h++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }        for(i=1;i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {          gp[i] = prlim[i][i];
               kk1=0.;kk2=0;      
               for(i=1; i<=nlstate;i++) {                      for(i=1; i<=npar; i++) /* Computes gradient */
                 if (mobilav==1)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 else {        for(i=1;i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          gm[i] = prlim[i][i];
                 }  
                        for(i=1;i<=nlstate;i++)
               }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               if (h==(int)(calagedate+12*cpt)){      } /* End theta */
                 fprintf(ficresf," %.3f", kk1);  
                              trgradg =matrix(1,nlstate,1,npar);
               }  
             }      for(j=1; j<=nlstate;j++)
           }        for(theta=1; theta <=npar; theta++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          trgradg[j][theta]=gradg[theta][j];
         }  
       }      for(i=1;i<=nlstate;i++)
     }        varpl[i][(int)age] =0.;
   }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
              matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   fclose(ficresf);  
 }      fprintf(ficresvpl,"%.0f ",age );
 /************** Forecasting ******************/      for(i=1; i<=nlstate;i++)
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      free_vector(gp,1,nlstate);
   int *popage;      free_vector(gm,1,nlstate);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      free_matrix(gradg,1,npar,1,nlstate);
   double *popeffectif,*popcount;      free_matrix(trgradg,1,nlstate,1,npar);
   double ***p3mat,***tabpop,***tabpopprev;    } /* End age */
   char filerespop[FILENAMELENGTH];  
     free_vector(xp,1,npar);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(doldm,1,nlstate,1,npar);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewm,1,nlstate,1,nlstate);
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  }
    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /************ Variance of one-step probabilities  ******************/
    void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
    {
   strcpy(filerespop,"pop");    int i, j=0,  i1, k1, l1, t, tj;
   strcat(filerespop,fileres);    int k2, l2, j1,  z1;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    int k=0,l, cptcode;
     printf("Problem with forecast resultfile: %s\n", filerespop);    int first=1, first1;
   }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    double **dnewm,**doldm;
     double *xp;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double *gp, *gm;
     double **gradg, **trgradg;
   if (mobilav==1) {    double **mu;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age,agelim, cov[NCOVMAX];
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   }    int theta;
     char fileresprob[FILENAMELENGTH];
   stepsize=(int) (stepm+YEARM-1)/YEARM;    char fileresprobcov[FILENAMELENGTH];
   if (stepm<=12) stepsize=1;    char fileresprobcor[FILENAMELENGTH];
    
   agelim=AGESUP;    double ***varpij;
    
   hstepm=1;    strcpy(fileresprob,"prob"); 
   hstepm=hstepm/stepm;    strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if (popforecast==1) {      printf("Problem with resultfile: %s\n", fileresprob);
     if((ficpop=fopen(popfile,"r"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       printf("Problem with population file : %s\n",popfile);exit(0);    }
     }    strcpy(fileresprobcov,"probcov"); 
     popage=ivector(0,AGESUP);    strcat(fileresprobcov,fileres);
     popeffectif=vector(0,AGESUP);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     popcount=vector(0,AGESUP);      printf("Problem with resultfile: %s\n", fileresprobcov);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     i=1;      }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    strcpy(fileresprobcor,"probcor"); 
        strcat(fileresprobcor,fileres);
     imx=i;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      printf("Problem with resultfile: %s\n", fileresprobcor);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   for(cptcov=1;cptcov<=i2;cptcov++){    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       k=k+1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficrespop,"\n#******");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       for(j=1;j<=cptcoveff;j++) {    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       }    
       fprintf(ficrespop,"******\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fprintf(ficrespop,"# Age");    fprintf(ficresprob,"# Age");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       if (popforecast==1)  fprintf(ficrespop," [Population]");    fprintf(ficresprobcov,"# Age");
          fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       for (cpt=0; cpt<=0;cpt++) {    fprintf(ficresprobcov,"# Age");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for(i=1; i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(j=1; j<=(nlstate+ndeath);j++){
           nhstepm = nhstepm/hstepm;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                  fprintf(ficresprobcov," p%1d-%1d ",i,j);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           oldm=oldms;savm=savms;      }  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     /* fprintf(ficresprob,"\n");
            fprintf(ficresprobcov,"\n");
           for (h=0; h<=nhstepm; h++){    fprintf(ficresprobcor,"\n");
             if (h==(int) (calagedate+YEARM*cpt)) {   */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);   xp=vector(1,npar);
             }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             for(j=1; j<=nlstate+ndeath;j++) {    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               kk1=0.;kk2=0;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               for(i=1; i<=nlstate;i++) {                  varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                 if (mobilav==1)    first=1;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
                 else {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
                 }      exit(0);
               }    }
               if (h==(int)(calagedate+12*cpt)){    else{
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      fprintf(ficgp,"\n# Routine varprob");
                   /*fprintf(ficrespop," %.3f", kk1);    }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
               }      printf("Problem with html file: %s\n", optionfilehtm);
             }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
             for(i=1; i<=nlstate;i++){      exit(0);
               kk1=0.;    }
                 for(j=1; j<=nlstate;j++){    else{
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                 }      fprintf(fichtm,"\n");
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    cov[1]=1;
       }    tj=cptcoveff;
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   /******/    j1=0;
     for(t=1; t<=tj;t++){
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      for(i1=1; i1<=ncodemax[t];i1++){ 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          j1++;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        if  (cptcovn>0) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          fprintf(ficresprob, "\n#********** Variable "); 
           nhstepm = nhstepm/hstepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                    fprintf(ficresprob, "**********\n#\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobcov, "\n#********** Variable "); 
           oldm=oldms;savm=savms;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresprobcov, "**********\n#\n");
           for (h=0; h<=nhstepm; h++){          
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(ficgp, "\n#********** Variable "); 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             }          fprintf(ficgp, "**********\n#\n");
             for(j=1; j<=nlstate+ndeath;j++) {          
               kk1=0.;kk2=0;          
               for(i=1; i<=nlstate;i++) {                        fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              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 (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          
             }          fprintf(ficresprobcor, "\n#********** Variable ");    
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobcor, "**********\n#");    
         }        }
       }        
    }        for (age=bage; age<=fage; age ++){ 
   }          cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
   if (popforecast==1) {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_ivector(popage,0,AGESUP);          for (k=1; k<=cptcovprod;k++)
     free_vector(popeffectif,0,AGESUP);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     free_vector(popcount,0,AGESUP);          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   fclose(ficrespop);          gm=vector(1,(nlstate)*(nlstate+ndeath));
 }      
           for(theta=1; theta <=npar; theta++){
 /***********************************************/            for(i=1; i<=npar; i++)
 /**************** Main Program *****************/              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
 /***********************************************/            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
 int main(int argc, char *argv[])            
 {            k=0;
             for(i=1; i<= (nlstate); i++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              for(j=1; j<=(nlstate+ndeath);j++){
   double agedeb, agefin,hf;                k=k+1;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                gp[k]=pmmij[i][j];
               }
   double fret;            }
   double **xi,tmp,delta;            
             for(i=1; i<=npar; i++)
   double dum; /* Dummy variable */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   double ***p3mat;      
   int *indx;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   char line[MAXLINE], linepar[MAXLINE];            k=0;
   char title[MAXLINE];            for(i=1; i<=(nlstate); i++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              for(j=1; j<=(nlstate+ndeath);j++){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                k=k+1;
                  gm[k]=pmmij[i][j];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];              }
             }
   char filerest[FILENAMELENGTH];       
   char fileregp[FILENAMELENGTH];            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   char popfile[FILENAMELENGTH];              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          }
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   int c,  h , cpt,l;            for(theta=1; theta <=npar; theta++)
   int ju,jl, mi;              trgradg[j][theta]=gradg[theta][j];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   int mobilav=0,popforecast=0;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   int hstepm, nhstepm;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double bage, fage, age, agelim, agebase;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   double ftolpl=FTOL;  
   double **prlim;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   double *severity;          
   double ***param; /* Matrix of parameters */          k=0;
   double  *p;          for(i=1; i<=(nlstate); i++){
   double **matcov; /* Matrix of covariance */            for(j=1; j<=(nlstate+ndeath);j++){
   double ***delti3; /* Scale */              k=k+1;
   double *delti; /* Scale */              mu[k][(int) age]=pmmij[i][j];
   double ***eij, ***vareij;            }
   double **varpl; /* Variances of prevalence limits by age */          }
   double *epj, vepp;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   double kk1, kk2;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;              varpij[i][j][(int)age] = doldm[i][j];
    
           /*printf("\n%d ",(int)age);
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   char *alph[]={"a","a","b","c","d","e"}, str[4];            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]));
             }*/
   char z[1]="c", occ;  
 #include <sys/time.h>          fprintf(ficresprob,"\n%d ",(int)age);
 #include <time.h>          fprintf(ficresprobcov,"\n%d ",(int)age);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          fprintf(ficresprobcor,"\n%d ",(int)age);
    
   /* long total_usecs;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   struct timeval start_time, end_time;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   getcwd(pathcd, size);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   printf("\n%s",version);          i=0;
   if(argc <=1){          for (k=1; k<=(nlstate);k++){
     printf("\nEnter the parameter file name: ");            for (l=1; l<=(nlstate+ndeath);l++){ 
     scanf("%s",pathtot);              i=i++;
   }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   else{              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     strcpy(pathtot,argv[1]);              for (j=1; j<=i;j++){
   }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   /*cygwin_split_path(pathtot,path,optionfile);              }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            }
   /* cutv(path,optionfile,pathtot,'\\');*/          }/* end of loop for state */
         } /* end of loop for age */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        /* Confidence intervalle of pij  */
   chdir(path);        /*
   replace(pathc,path);          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
 /*-------- arguments in the command line --------*/          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   strcpy(fileres,"r");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   strcat(fileres, optionfilefiname);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   strcat(fileres,".txt");    /* Other files have txt extension */          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   /*---------arguments file --------*/  
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        first1=1;
     printf("Problem with optionfile %s\n",optionfile);        for (k2=1; k2<=(nlstate);k2++){
     goto end;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   }            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   strcpy(filereso,"o");            for (k1=1; k1<=(nlstate);k1++){
   strcat(filereso,fileres);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if((ficparo=fopen(filereso,"w"))==NULL) {                if(l1==k1) continue;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   /* Reads comments: lines beginning with '#' */                  if ((int)age %5==0){
   while((c=getc(ficpar))=='#' && c!= EOF){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     ungetc(c,ficpar);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fgets(line, MAXLINE, ficpar);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     puts(line);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     fputs(line,ficparo);                    mu2=mu[j][(int) age]/stepm*YEARM;
   }                    c12=cv12/sqrt(v1*v2);
   ungetc(c,ficpar);                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   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);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   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);                    /* Eigen vectors */
   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);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 while((c=getc(ficpar))=='#' && c!= EOF){                    /*v21=sqrt(1.-v11*v11); *//* error */
     ungetc(c,ficpar);                    v21=(lc1-v1)/cv12*v11;
     fgets(line, MAXLINE, ficpar);                    v12=-v21;
     puts(line);                    v22=v11;
     fputs(line,ficparo);                    tnalp=v21/v11;
   }                    if(first1==1){
   ungetc(c,ficpar);                      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);
                        }
   covar=matrix(0,NCOVMAX,1,n);                    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);
   cptcovn=0;                    /*printf(fignu*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   ncovmodel=2+cptcovn;                    if(first==1){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                      first=0;
                        fprintf(ficgp,"\nset parametric;unset label");
   /* Read guess parameters */                      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);
   /* Reads comments: lines beginning with '#' */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   while((c=getc(ficpar))=='#' && c!= EOF){                      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);
     ungetc(c,ficpar);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     puts(line);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     fputs(line,ficparo);                      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);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     for(i=1; i <=nlstate; i++)                    }else{
     for(j=1; j <=nlstate+ndeath-1; j++){                      first=0;
       fscanf(ficpar,"%1d%1d",&i1,&j1);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
       fprintf(ficparo,"%1d%1d",i1,j1);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       printf("%1d%1d",i,j);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       for(k=1; k<=ncovmodel;k++){                      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",\
         fscanf(ficpar," %lf",&param[i][j][k]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         printf(" %lf",param[i][j][k]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficparo," %lf",param[i][j][k]);                    }/* if first */
       }                  } /* age mod 5 */
       fscanf(ficpar,"\n");                } /* end loop age */
       printf("\n");                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
       fprintf(ficparo,"\n");                first=1;
     }              } /*l12 */
              } /* k12 */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          } /*l1 */
         }/* k1 */
   p=param[1][1];      } /* loop covariates */
      }
   /* Reads comments: lines beginning with '#' */    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     ungetc(c,ficpar);    free_vector(xp,1,npar);
     fgets(line, MAXLINE, ficpar);    fclose(ficresprob);
     puts(line);    fclose(ficresprobcov);
     fputs(line,ficparo);    fclose(ficresprobcor);
   }    fclose(ficgp);
   ungetc(c,ficpar);    fclose(fichtm);
   }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){  /******************* Printing html file ***********/
     for(j=1; j <=nlstate+ndeath-1; j++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       fscanf(ficpar,"%1d%1d",&i1,&j1);                    int lastpass, int stepm, int weightopt, char model[],\
       printf("%1d%1d",i,j);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       fprintf(ficparo,"%1d%1d",i1,j1);                    int popforecast, int estepm ,\
       for(k=1; k<=ncovmodel;k++){                    double jprev1, double mprev1,double anprev1, \
         fscanf(ficpar,"%le",&delti3[i][j][k]);                    double jprev2, double mprev2,double anprev2){
         printf(" %le",delti3[i][j][k]);    int jj1, k1, i1, cpt;
         fprintf(ficparo," %le",delti3[i][j][k]);    /*char optionfilehtm[FILENAMELENGTH];*/
       }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       fscanf(ficpar,"\n");      printf("Problem with %s \n",optionfilehtm), exit(0);
       printf("\n");      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficparo,"\n");    }
     }  
   }     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   delti=delti3[1][1];   - 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
   /* Reads comments: lines beginning with '#' */   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   while((c=getc(ficpar))=='#' && c!= EOF){   - Life expectancies by age and initial health status (estepm=%2d months): 
     ungetc(c,ficpar);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     fgets(line, MAXLINE, ficpar);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     puts(line);  
     fputs(line,ficparo);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   }  
   ungetc(c,ficpar);   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){   jj1=0;
     fscanf(ficpar,"%s",&str);   for(k1=1; k1<=m;k1++){
     printf("%s",str);     for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficparo,"%s",str);       jj1++;
     for(j=1; j <=i; j++){       if (cptcovn > 0) {
       fscanf(ficpar," %le",&matcov[i][j]);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       printf(" %.5le",matcov[i][j]);         for (cpt=1; cpt<=cptcoveff;cpt++) 
       fprintf(ficparo," %.5le",matcov[i][j]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     fscanf(ficpar,"\n");       }
     printf("\n");       /* Pij */
     fprintf(ficparo,"\n");       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);     
   for(i=1; i <=npar; i++)       /* Quasi-incidences */
     for(j=i+1;j<=npar;j++)       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>
       matcov[i][j]=matcov[j][i];  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
             /* Stable prevalence in each health state */
   printf("\n");         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     /*-------- Rewriting paramater file ----------*/         }
      strcpy(rfileres,"r");    /* "Rparameterfile */       for(cpt=1; cpt<=nlstate;cpt++) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
      strcat(rfileres,".");    /* */  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */       }
     if((ficres =fopen(rfileres,"w"))==NULL) {       fprintf(fichtm,"\n<br>- Total life expectancy by age and
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  health expectancies in states (1) and (2): e%s%d.png<br>
     }  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     fprintf(ficres,"#%s\n",version);     } /* end i1 */
       }/* End k1 */
     /*-------- data file ----------*/   fprintf(fichtm,"</ul>");
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     n= lastobs;   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     severity = vector(1,maxwav);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     outcome=imatrix(1,maxwav+1,1,n);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     num=ivector(1,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 
     moisnais=vector(1,n);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     annais=vector(1,n);   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
     moisdc=vector(1,n);  
     andc=vector(1,n);  /*  if(popforecast==1) fprintf(fichtm,"\n */
     agedc=vector(1,n);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     cod=ivector(1,n);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     weight=vector(1,n);  /*      <br>",fileres,fileres,fileres,fileres); */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  /*  else  */
     mint=matrix(1,maxwav,1,n);  /*    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); */
     anint=matrix(1,maxwav,1,n);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);       m=cptcoveff;
     tab=ivector(1,NCOVMAX);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     ncodemax=ivector(1,8);  
    jj1=0;
     i=1;   for(k1=1; k1<=m;k1++){
     while (fgets(line, MAXLINE, fic) != NULL)    {     for(i1=1; i1<=ncodemax[k1];i1++){
       if ((i >= firstobs) && (i <=lastobs)) {       jj1++;
               if (cptcovn > 0) {
         for (j=maxwav;j>=1;j--){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);         for (cpt=1; cpt<=cptcoveff;cpt++) 
           strcpy(line,stra);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       }
         }       for(cpt=1; cpt<=nlstate;cpt++) {
                 fprintf(fichtm,"<br>- Observed and period prevalence (with confident
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  interval) in state (%d): v%s%d%d.png <br>
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     } /* end i1 */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);   }/* End k1 */
    fprintf(fichtm,"</ul>");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  fclose(fichtm);
         for (j=ncovcol;j>=1;j--){  }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  /******************* Gnuplot file **************/
         num[i]=atol(stra);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           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;}*/    int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         i=i+1;      printf("Problem with file %s",optionfilegnuplot);
       }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }    }
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/    /*#ifdef windows */
   imx=i-1; /* Number of individuals */      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   /* for (i=1; i<=imx; i++){  m=pow(2,cptcoveff);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;   /* 1eme*/
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    for (cpt=1; cpt<= nlstate ; cpt ++) {
     }*/     for (k1=1; k1<= m ; k1 ++) {
    /*  for (i=1; i<=imx; i++){       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
      if (s[4][i]==9)  s[4][i]=-1;       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
      printf("%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<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* Calculation of the number of parameter from char model*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
   Tvar=ivector(1,15);       }
   Tprod=ivector(1,15);       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);
   Tvaraff=ivector(1,15);       for (i=1; i<= nlstate ; i ++) {
   Tvard=imatrix(1,15,1,2);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   Tage=ivector(1,15);               else fprintf(ficgp," \%%*lf (\%%*lf)");
           } 
   if (strlen(model) >1){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     j=0, j1=0, k1=1, k2=1;       for (i=1; i<= nlstate ; i ++) {
     j=nbocc(model,'+');         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     j1=nbocc(model,'*');         else fprintf(ficgp," \%%*lf (\%%*lf)");
     cptcovn=j+1;       }  
     cptcovprod=j1;       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         }
     strcpy(modelsav,model);    }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    /*2 eme*/
       printf("Error. Non available option model=%s ",model);    
       goto end;    for (k1=1; k1<= m ; k1 ++) { 
     }      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(i=(j+1); i>=1;i--){      
       cutv(stra,strb,modelsav,'+');      for (i=1; i<= nlstate+1 ; i ++) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        k=2*i;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       /*scanf("%d",i);*/        for (j=1; j<= nlstate+1 ; j ++) {
       if (strchr(strb,'*')) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         cutv(strd,strc,strb,'*');          else fprintf(ficgp," \%%*lf (\%%*lf)");
         if (strcmp(strc,"age")==0) {        }   
           cptcovprod--;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           cutv(strb,stre,strd,'V');        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           Tvar[i]=atoi(stre);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           cptcovage++;        for (j=1; j<= nlstate+1 ; j ++) {
             Tage[cptcovage]=i;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             /*printf("stre=%s ", stre);*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }        }   
         else if (strcmp(strd,"age")==0) {        fprintf(ficgp,"\" t\"\" w l 0,");
           cptcovprod--;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
           cutv(strb,stre,strc,'V');        for (j=1; j<= nlstate+1 ; j ++) {
           Tvar[i]=atoi(stre);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           cptcovage++;          else fprintf(ficgp," \%%*lf (\%%*lf)");
           Tage[cptcovage]=i;        }   
         }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else {        else fprintf(ficgp,"\" t\"\" w l 0,");
           cutv(strb,stre,strc,'V');      }
           Tvar[i]=ncovcol+k1;    }
           cutv(strb,strc,strd,'V');    
           Tprod[k1]=i;    /*3eme*/
           Tvard[k1][1]=atoi(strc);    
           Tvard[k1][2]=atoi(stre);    for (k1=1; k1<= m ; k1 ++) { 
           Tvar[cptcovn+k2]=Tvard[k1][1];      for (cpt=1; cpt<= nlstate ; cpt ++) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        k=2+nlstate*(2*cpt-2);
           for (k=1; k<=lastobs;k++)        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
           k1++;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           k2=k2+2;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       else {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        /*  scanf("%d",i);*/          
       cutv(strd,strc,strb,'V');        */
       Tvar[i]=atoi(strc);        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);
       strcpy(modelsav,stra);            
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        } 
         scanf("%d",i);*/      }
     }    }
 }    
      /* CV preval stable (period) */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    for (k1=1; k1<= m ; k1 ++) { 
   printf("cptcovprod=%d ", cptcovprod);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   scanf("%d ",i);*/        k=3;
     fclose(fic);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     /*  if(mle==1){*/        
     if (weightopt != 1) { /* Maximisation without weights*/        for (i=1; i<= nlstate ; i ++)
       for(i=1;i<=n;i++) weight[i]=1.0;          fprintf(ficgp,"+$%d",k+i+1);
     }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     /*-calculation of age at interview from date of interview and age at death -*/        
     agev=matrix(1,maxwav,1,imx);        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     for (i=1; i<=imx; i++) {        for (i=1; i< nlstate ; i ++) {
       for(m=2; (m<= maxwav); m++) {          l=3+(nlstate+ndeath)*cpt;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          fprintf(ficgp,"+$%d",l+i+1);
          anint[m][i]=9999;        }
          s[m][i]=-1;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
        }      } 
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    }  
       }    
     }    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
     for (i=1; i<=imx; i++)  {      for(k=1; k <=(nlstate+ndeath); k++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        if (k != i) {
       for(m=1; (m<= maxwav); m++){          for(j=1; j <=ncovmodel; j++){
         if(s[m][i] >0){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           if (s[m][i] >= nlstate+1) {            jk++; 
             if(agedc[i]>0)            fprintf(ficgp,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)          }
                 agev[m][i]=agedc[i];        }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      }
            else {     }
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
               agev[m][i]=-1;       for(jk=1; jk <=m; jk++) {
               }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
             }         if (ng==2)
           }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           else if(s[m][i] !=9){ /* Should no more exist */         else
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);           fprintf(ficgp,"\nset title \"Probability\"\n");
             if(mint[m][i]==99 || anint[m][i]==9999)         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
               agev[m][i]=1;         i=1;
             else if(agev[m][i] <agemin){         for(k2=1; k2<=nlstate; k2++) {
               agemin=agev[m][i];           k3=i;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/           for(k=1; k<=(nlstate+ndeath); k++) {
             }             if (k != k2){
             else if(agev[m][i] >agemax){               if(ng==2)
               agemax=agev[m][i];                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/               else
             }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
             /*agev[m][i]=anint[m][i]-annais[i];*/               ij=1;
             /*   agev[m][i] = age[i]+2*m;*/               for(j=3; j <=ncovmodel; j++) {
           }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           else { /* =9 */                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             agev[m][i]=1;                   ij++;
             s[m][i]=-1;                 }
           }                 else
         }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         else /*= 0 Unknown */               }
           agev[m][i]=1;               fprintf(ficgp,")/(1");
       }               
                   for(k1=1; k1 <=nlstate; k1++){   
     }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     for (i=1; i<=imx; i++)  {                 ij=1;
       for(m=1; (m<= maxwav); m++){                 for(j=3; j <=ncovmodel; j++){
         if (s[m][i] > (nlstate+ndeath)) {                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           printf("Error: Wrong value in nlstate or ndeath\n");                       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           goto end;                     ij++;
         }                   }
       }                   else
     }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                 fprintf(ficgp,")");
                }
     free_vector(severity,1,maxwav);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     free_imatrix(outcome,1,maxwav+1,1,n);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     free_vector(moisnais,1,n);               i=i+ncovmodel;
     free_vector(annais,1,n);             }
     /* free_matrix(mint,1,maxwav,1,n);           } /* end k */
        free_matrix(anint,1,maxwav,1,n);*/         } /* end k2 */
     free_vector(moisdc,1,n);       } /* end jk */
     free_vector(andc,1,n);     } /* end ng */
      fclose(ficgp); 
      }  /* end gnuplot */
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  /*************** Moving average **************/
      int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
       Tcode=ivector(1,100);    double age;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                             a covariate has 2 modalities */
          if (cptcovn<1) modcovmax=1; /* At least 1 pass */
    codtab=imatrix(1,100,1,10);  
    h=0;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
    m=pow(2,cptcoveff);      if(mobilav==1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
    for(k=1;k<=cptcoveff; k++){      for (age=bage; age<=fage; age++)
      for(i=1; i <=(m/pow(2,k));i++){        for (i=1; i<=nlstate;i++)
        for(j=1; j <= ncodemax[k]; j++){          for (cptcod=1;cptcod<=modcovmax;cptcod++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            h++;      /* We keep the original values on the extreme ages bage, fage and for 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/         we use a 5 terms etc. until the borders are no more concerned. 
          }      */ 
        }      for (mob=3;mob <=mobilavrange;mob=mob+2){
      }        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
    }          for (i=1; i<=nlstate;i++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       codtab[1][2]=1;codtab[2][2]=2; */              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
    /* for(i=1; i <=m ;i++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
       for(k=1; k <=cptcovn; k++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
       }                }
       printf("\n");              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
       }            }
       scanf("%d",i);*/          }
            }/* end age */
    /* Calculates basic frequencies. Computes observed prevalence at single age      }/* end mob */
        and prints on file fileres'p'. */    }else return -1;
     return 0;
      }/* End movingaverage */
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /************** Forecasting ******************/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* proj1, year, month, day of starting projection 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       agemin, agemax range of age
             dateprev1 dateprev2 range of dates during which prevalence is computed
     /* For Powell, parameters are in a vector p[] starting at p[1]       anproj2 year of en of projection (same day and month as proj1).
        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) */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     if(mle==1){    double agec; /* generic age */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     }    double *popeffectif,*popcount;
        double ***p3mat;
     /*--------- results files --------------*/    double ***mobaverage;
     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);    char fileresf[FILENAMELENGTH];
    
     agelim=AGESUP;
    jk=1;    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    strcpy(fileresf,"f"); 
    for(i=1,jk=1; i <=nlstate; i++){    strcat(fileresf,fileres);
      for(k=1; k <=(nlstate+ndeath); k++){    if((ficresf=fopen(fileresf,"w"))==NULL) {
        if (k != i)      printf("Problem with forecast resultfile: %s\n", fileresf);
          {      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    printf("Computing forecasting: result on file '%s' \n", fileresf);
            for(j=1; j <=ncovmodel; j++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
              jk++;  
            }    if (mobilav!=0) {
            printf("\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            fprintf(ficres,"\n");      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);
    }      }
  if(mle==1){    }
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    stepsize=(int) (stepm+YEARM-1)/YEARM;
     hesscov(matcov, p, npar, delti, ftolhess, func);    if (stepm<=12) stepsize=1;
  }    if(estepm < stepm){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
     printf("# Scales (for hessian or gradient estimation)\n");    }
      for(i=1,jk=1; i <=nlstate; i++){    else  hstepm=estepm;   
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    hstepm=hstepm/stepm; 
           fprintf(ficres,"%1d%1d",i,j);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
           printf("%1d%1d",i,j);                                 fractional in yp1 */
           for(k=1; k<=ncovmodel;k++){    anprojmean=yp;
             printf(" %.5e",delti[jk]);    yp2=modf((yp1*12),&yp);
             fprintf(ficres," %.5e",delti[jk]);    mprojmean=yp;
             jk++;    yp1=modf((yp2*30.5),&yp);
           }    jprojmean=yp;
           printf("\n");    if(jprojmean==0) jprojmean=1;
           fprintf(ficres,"\n");    if(mprojmean==0) jprojmean=1;
         }  
       }    i1=cptcoveff;
      }    if (cptcovn < 1){i1=1;}
        
     k=1;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     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");    
     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(ficresf,"#****** Routine prevforecast **\n");
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;  /*            if (h==(int)(YEARM*yearp)){ */
       i1=(i-1)/(ncovmodel*nlstate)+1;    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/        k=k+1;
       fprintf(ficres,"%3d",i);        fprintf(ficresf,"\n#******");
       printf("%3d",i);        for(j=1;j<=cptcoveff;j++) {
       for(j=1; j<=i;j++){          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficres," %.5e",matcov[i][j]);        }
         printf(" %.5e",matcov[i][j]);        fprintf(ficresf,"******\n");
       }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       fprintf(ficres,"\n");        for(j=1; j<=nlstate+ndeath;j++){ 
       printf("\n");          for(i=1; i<=nlstate;i++)              
       k++;            fprintf(ficresf," p%d%d",i,j);
     }          fprintf(ficresf," p.%d",j);
            }
     while((c=getc(ficpar))=='#' && c!= EOF){        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       ungetc(c,ficpar);          fprintf(ficresf,"\n");
       fgets(line, MAXLINE, ficpar);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       puts(line);  
       fputs(line,ficparo);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     }            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     ungetc(c,ficpar);            nhstepm = nhstepm/hstepm; 
     estepm=0;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            oldm=oldms;savm=savms;
     if (estepm==0 || estepm < stepm) estepm=stepm;            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     if (fage <= 2) {          
       bage = ageminpar;            for (h=0; h<=nhstepm; h++){
       fage = agemaxpar;              if (h*hstepm/YEARM*stepm ==yearp) {
     }                fprintf(ficresf,"\n");
                    for(j=1;j<=cptcoveff;j++) 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);              } 
                for(j=1; j<=nlstate+ndeath;j++) {
     while((c=getc(ficpar))=='#' && c!= EOF){                ppij=0.;
     ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {
     fgets(line, MAXLINE, ficpar);                  if (mobilav==1) 
     puts(line);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     fputs(line,ficparo);                  else {
   }                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   ungetc(c,ficpar);                  }
                    if (h*hstepm/YEARM*stepm== yearp) {
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   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);                } /* end i */
                      if (h*hstepm/YEARM*stepm==yearp) {
   while((c=getc(ficpar))=='#' && c!= EOF){                  fprintf(ficresf," %.3f", ppij);
     ungetc(c,ficpar);                }
     fgets(line, MAXLINE, ficpar);              }/* end j */
     puts(line);            } /* end h */
     fputs(line,ficparo);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          } /* end agec */
   ungetc(c,ficpar);        } /* end yearp */
        } /* end cptcod */
     } /* end  cptcov */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    fclose(ficresf);
   fprintf(ficparo,"pop_based=%d\n",popbased);    }
   fprintf(ficres,"pop_based=%d\n",popbased);    
    /************** Forecasting *****not tested NB*************/
   while((c=getc(ficpar))=='#' && c!= EOF){  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){
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     puts(line);    int *popage;
     fputs(line,ficparo);    double calagedatem, agelim, kk1, kk2;
   }    double *popeffectif,*popcount;
   ungetc(c,ficpar);    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
   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);    char filerespop[FILENAMELENGTH];
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
 while((c=getc(ficpar))=='#' && c!= EOF){    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     puts(line);    
     fputs(line,ficparo);    
   }    strcpy(filerespop,"pop"); 
   ungetc(c,ficpar);    strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      printf("Problem with forecast resultfile: %s\n", filerespop);
   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(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
 /*------------ gnuplot -------------*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  
      if (mobilav!=0) {
 /*------------ free_vector  -------------*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  chdir(path);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  free_ivector(wav,1,imx);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      }
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);    stepsize=(int) (stepm+YEARM-1)/YEARM;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    if (stepm<=12) stepsize=1;
  fclose(ficparo);    
  fclose(ficres);    agelim=AGESUP;
     
 /*--------- index.htm --------*/    hstepm=1;
     hstepm=hstepm/stepm; 
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    
     if (popforecast==1) {
        if((ficpop=fopen(popfile,"r"))==NULL) {
   /*--------------- Prevalence limit --------------*/        printf("Problem with population file : %s\n",popfile);exit(0);
          fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   strcpy(filerespl,"pl");      } 
   strcat(filerespl,fileres);      popage=ivector(0,AGESUP);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      popeffectif=vector(0,AGESUP);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      popcount=vector(0,AGESUP);
   }      
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      i=1;   
   fprintf(ficrespl,"#Prevalence limit\n");      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   fprintf(ficrespl,"#Age ");     
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      imx=i;
   fprintf(ficrespl,"\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
      }
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k=k+1;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficrespop,"\n#******");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1;j<=cptcoveff;j++) {
   k=0;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   agebase=ageminpar;        }
   agelim=agemaxpar;        fprintf(ficrespop,"******\n");
   ftolpl=1.e-10;        fprintf(ficrespop,"# Age");
   i1=cptcoveff;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   if (cptcovn < 1){i1=1;}        if (popforecast==1)  fprintf(ficrespop," [Population]");
         
   for(cptcov=1;cptcov<=i1;cptcov++){        for (cpt=0; cpt<=0;cpt++) { 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         k=k+1;          
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
         fprintf(ficrespl,"\n#******");            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         for(j=1;j<=cptcoveff;j++)            nhstepm = nhstepm/hstepm; 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            
         fprintf(ficrespl,"******\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    oldm=oldms;savm=savms;
         for (age=agebase; age<=agelim; age++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          
           fprintf(ficrespl,"%.0f",age );            for (h=0; h<=nhstepm; h++){
           for(i=1; i<=nlstate;i++)              if (h==(int) (calagedatem+YEARM*cpt)) {
           fprintf(ficrespl," %.5f", prlim[i][i]);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           fprintf(ficrespl,"\n");              } 
         }              for(j=1; j<=nlstate+ndeath;j++) {
       }                kk1=0.;kk2=0;
     }                for(i=1; i<=nlstate;i++) {              
   fclose(ficrespl);                  if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   /*------------- h Pij x at various ages ------------*/                  else {
                      kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                  }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                if (h==(int)(calagedatem+12*cpt)){
   }                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   printf("Computing pij: result on file '%s' \n", filerespij);                    /*fprintf(ficrespop," %.3f", kk1);
                        if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;                }
   /*if (stepm<=24) stepsize=2;*/              }
               for(i=1; i<=nlstate;i++){
   agelim=AGESUP;                kk1=0.;
   hstepm=stepsize*YEARM; /* Every year of age */                  for(j=1; j<=nlstate;j++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                    }
   k=0;                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   for(cptcov=1;cptcov<=i1;cptcov++){              }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
         fprintf(ficrespij,"\n#****** ");                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         for(j=1;j<=cptcoveff;j++)            }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         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 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           oldm=oldms;savm=savms;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           fprintf(ficrespij,"# Age");            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           for(i=1; i<=nlstate;i++)            nhstepm = nhstepm/hstepm; 
             for(j=1; j<=nlstate+ndeath;j++)            
               fprintf(ficrespij," %1d-%1d",i,j);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");            oldm=oldms;savm=savms;
            for (h=0; h<=nhstepm; h++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            for (h=0; h<=nhstepm; h++){
             for(i=1; i<=nlstate;i++)              if (h==(int) (calagedatem+YEARM*cpt)) {
               for(j=1; j<=nlstate+ndeath;j++)                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              } 
             fprintf(ficrespij,"\n");              for(j=1; j<=nlstate+ndeath;j++) {
              }                kk1=0.;kk2=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                for(i=1; i<=nlstate;i++) {              
           fprintf(ficrespij,"\n");                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
         }                }
     }                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   }              }
             }
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
   fclose(ficrespij);        }
      } 
     }
   /*---------- Forecasting ------------------*/   
   if((stepm == 1) && (strcmp(model,".")==0)){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    if (popforecast==1) {
   }      free_ivector(popage,0,AGESUP);
   else{      free_vector(popeffectif,0,AGESUP);
     erreur=108;      free_vector(popcount,0,AGESUP);
     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);    }
   }    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   /*---------- Health expectancies and variances ------------*/  }
   
   strcpy(filerest,"t");  /***********************************************/
   strcat(filerest,fileres);  /**************** Main Program *****************/
   if((ficrest=fopen(filerest,"w"))==NULL) {  /***********************************************/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }  int main(int argc, char *argv[])
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   strcpy(filerese,"e");    double agedeb, agefin,hf;
   strcat(filerese,fileres);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double fret;
   }    double **xi,tmp,delta;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
     double dum; /* Dummy variable */
  strcpy(fileresv,"v");    double ***p3mat;
   strcat(fileresv,fileres);    double ***mobaverage;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int *indx;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    char line[MAXLINE], linepar[MAXLINE];
   }    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    int firstobs=1, lastobs=10;
   calagedate=-1;    int sdeb, sfin; /* Status at beginning and end */
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    int c,  h , cpt,l;
     int ju,jl, mi;
   k=0;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   for(cptcov=1;cptcov<=i1;cptcov++){    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
       k=k+1;    int mobilav=0,popforecast=0;
       fprintf(ficrest,"\n#****** ");    int hstepm, nhstepm;
       for(j=1;j<=cptcoveff;j++)    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
       fprintf(ficrest,"******\n");  
     double bage, fage, age, agelim, agebase;
       fprintf(ficreseij,"\n#****** ");    double ftolpl=FTOL;
       for(j=1;j<=cptcoveff;j++)    double **prlim;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double *severity;
       fprintf(ficreseij,"******\n");    double ***param; /* Matrix of parameters */
     double  *p;
       fprintf(ficresvij,"\n#****** ");    double **matcov; /* Matrix of covariance */
       for(j=1;j<=cptcoveff;j++)    double ***delti3; /* Scale */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double *delti; /* Scale */
       fprintf(ficresvij,"******\n");    double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *epj, vepp;
       oldm=oldms;savm=savms;    double kk1, kk2;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    char *alph[]={"a","a","b","c","d","e"}, str[4];
       oldm=oldms;savm=savms;  
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);  
        char z[1]="c", occ;
   #include <sys/time.h>
    #include <time.h>
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   
       fprintf(ficrest,"\n");    /* long total_usecs;
        struct timeval start_time, end_time;
       epj=vector(1,nlstate+1);    
       for(age=bage; age <=fage ;age++){       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    getcwd(pathcd, size);
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    printf("\n%s",version);
             prlim[i][i]=probs[(int)age][i][k];    if(argc <=1){
         }      printf("\nEnter the parameter file name: ");
              scanf("%s",pathtot);
         fprintf(ficrest," %4.0f",age);    }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    else{
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      strcpy(pathtot,argv[1]);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    }
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
           }    /*cygwin_split_path(pathtot,path,optionfile);
           epj[nlstate+1] +=epj[j];      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
         }    /* cutv(path,optionfile,pathtot,'\\');*/
   
         for(i=1, vepp=0.;i <=nlstate;i++)    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
           for(j=1;j <=nlstate;j++)    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             vepp += vareij[i][j][(int)age];    chdir(path);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    replace(pathc,path);
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    /*-------- arguments in the command line --------*/
         }  
         fprintf(ficrest,"\n");    /* Log file */
       }    strcat(filelog, optionfilefiname);
     }    strcat(filelog,".log");    /* */
   }    if((ficlog=fopen(filelog,"w"))==NULL)    {
 free_matrix(mint,1,maxwav,1,n);      printf("Problem with logfile %s\n",filelog);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      goto end;
     free_vector(weight,1,n);    }
   fclose(ficreseij);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fclose(ficresvij);    fprintf(ficlog,"\n%s",version);
   fclose(ficrest);    fprintf(ficlog,"\nEnter the parameter file name: ");
   fclose(ficpar);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   free_vector(epj,1,nlstate+1);    fflush(ficlog);
    
   /*------- Variance limit prevalence------*/      /* */
     strcpy(fileres,"r");
   strcpy(fileresvpl,"vpl");    strcat(fileres, optionfilefiname);
   strcat(fileresvpl,fileres);    strcat(fileres,".txt");    /* Other files have txt extension */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    /*---------arguments file --------*/
     exit(0);  
   }    if((ficpar=fopen(optionfile,"r"))==NULL)    {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   k=0;      goto end;
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    strcpy(filereso,"o");
       fprintf(ficresvpl,"\n#****** ");    strcat(filereso,fileres);
       for(j=1;j<=cptcoveff;j++)    if((ficparo=fopen(filereso,"w"))==NULL) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficresvpl,"******\n");      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
            goto end;
       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);    /* Reads comments: lines beginning with '#' */
     }    while((c=getc(ficpar))=='#' && c!= EOF){
  }      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   fclose(ficresvpl);      puts(line);
       fputs(line,ficparo);
   /*---------- End : free ----------------*/    }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    ungetc(c,ficpar);
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    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);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
      fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
      while((c=getc(ficpar))=='#' && c!= EOF){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      ungetc(c,ficpar);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fgets(line, MAXLINE, ficpar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      puts(line);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      fputs(line,ficparo);
      }
   free_matrix(matcov,1,npar,1,npar);    ungetc(c,ficpar);
   free_vector(delti,1,npar);    
   free_matrix(agev,1,maxwav,1,imx);     
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   if(erreur >0)    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
      
   /* 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);*/    /* Read guess parameters */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /* Reads comments: lines beginning with '#' */
   /*------ End -----------*/    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
  end:      puts(line);
   /* chdir(pathcd);*/      fputs(line,ficparo);
  /*system("wgnuplot graph.plt");*/    }
  /*system("../gp37mgw/wgnuplot graph.plt");*/    ungetc(c,ficpar);
  /*system("cd ../gp37mgw");*/    
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
  strcpy(plotcmd,GNUPLOTPROGRAM);    for(i=1; i <=nlstate; i++)
  strcat(plotcmd," ");      for(j=1; j <=nlstate+ndeath-1; j++){
  strcat(plotcmd,optionfilegnuplot);        fscanf(ficpar,"%1d%1d",&i1,&j1);
  system(plotcmd);        fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
  /*#ifdef windows*/          printf("%1d%1d",i,j);
   while (z[0] != 'q') {        fprintf(ficlog,"%1d%1d",i,j);
     /* chdir(path); */        for(k=1; k<=ncovmodel;k++){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          fscanf(ficpar," %lf",&param[i][j][k]);
     scanf("%s",z);          if(mle==1){
     if (z[0] == 'c') system("./imach");            printf(" %lf",param[i][j][k]);
     else if (z[0] == 'e') system(optionfilehtm);            fprintf(ficlog," %lf",param[i][j][k]);
     else if (z[0] == 'g') system(plotcmd);          }
     else if (z[0] == 'q') exit(0);          else
   }            fprintf(ficlog," %lf",param[i][j][k]);
   /*#endif */          fprintf(ficparo," %lf",param[i][j][k]);
 }        }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.41.2.2  
changed lines
  Added in v.1.80

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