Diff for /imach/src/imach.c between versions 1.35 and 1.74

version 1.35, 2002/03/26 17:08:39 version 1.74, 2003/05/02 18:51:41
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
      movingaverage()
     varevsij() 
 int erreur; /* Error number */    if popbased==1 varevsij(,popbased)
 int nvar;    total life expectancies
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Variance of stable prevalence
 int npar=NPARMAX;   end
 int nlstate=2; /* Number of live states */  */
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  
    
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <math.h>
 int maxwav; /* Maxim number of waves */  #include <stdio.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdlib.h>
 int mle, weightopt;  #include <unistd.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define MAXLINE 256
 double jmean; /* Mean space between 2 waves */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define FILENAMELENGTH 80
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define DEBUG*/
 FILE *ficgp,*ficresprob,*ficpop;  #define windows
 FILE *ficreseij;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
  FILE  *ficresvpl;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   char fileresvpl[FILENAMELENGTH];  
   #define NINTERVMAX 8
 #define NR_END 1  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FREE_ARG char*  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FTOL 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 #define NRANSI  #define YEARM 12. /* Number of months per year */
 #define ITMAX 200  #define AGESUP 130
   #define AGEBASE 40
 #define TOL 2.0e-4  #ifdef windows
   #define DIRSEPARATOR '\\'
 #define CGOLD 0.3819660  #define ODIRSEPARATOR '/'
 #define ZEPS 1.0e-10  #else
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 #define GOLD 1.618034  #endif
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char version[80]="Imach version 0.95, February 2003, INED-EUROREVES ";
   int erreur; /* Error number */
 static double maxarg1,maxarg2;  int nvar;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int ndeath=1; /* Number of dead states */
 #define rint(a) floor(a+0.5)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int *wav; /* Number of waves for this individuual 0 is possible */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 int imx;  int mle, weightopt;
 int stepm;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /* Stepm, step in month: minimum step interpolation*/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 int m,nb;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  double jmean; /* Mean space between 2 waves */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **pmmij, ***probs, ***mobaverage;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double dateintmean=0;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 double *weight;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 int **s; /* Status */  FILE *ficresprobmorprev;
 double *agedc, **covar, idx;  FILE *fichtm; /* Html File */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  FILE  *ficresvij;
 double ftolhess; /* Tolerance for computing hessian */  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 /**************** split *************************/  char fileresvpl[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    char *s;                             /* pointer */  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  char filelog[FILENAMELENGTH]; /* Log file */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char filerest[FILENAMELENGTH];
 #ifdef windows  char fileregp[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  char popfile[FILENAMELENGTH];
 #else  
    s = strrchr( path, '/' );            /* find last / */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  #define NR_END 1
 #if     defined(__bsd__)                /* get current working directory */  #define FREE_ARG char*
       extern char       *getwd( );  #define FTOL 1.0e-10
   
       if ( getwd( dirc ) == NULL ) {  #define NRANSI 
 #else  #define ITMAX 200 
       extern char       *getcwd( );  
   #define TOL 2.0e-4 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  #define CGOLD 0.3819660 
          return( GLOCK_ERROR_GETCWD );  #define ZEPS 1.0e-10 
       }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  #define GOLD 1.618034 
       s++;                              /* after this, the filename */  #define GLIMIT 100.0 
       l2 = strlen( s );                 /* length of filename */  #define TINY 1.0e-20 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  static double maxarg1,maxarg2;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       dirc[l1-l2] = 0;                  /* add zero */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    }    
    l1 = strlen( dirc );                 /* length of directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #ifdef windows  #define rint(a) floor(a+0.5)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  static double sqrarg;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #endif  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    s = strrchr( name, '.' );            /* find last / */  
    s++;  int imx; 
    strcpy(ext,s);                       /* save extension */  int stepm;
    l1= strlen( name);  /* Stepm, step in month: minimum step interpolation*/
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  int estepm;
    finame[l1-l2]= 0;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    return( 0 );                         /* we're done */  
 }  int m,nb;
   int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /******************************************/  double **pmmij, ***probs;
   double dateintmean=0;
 void replace(char *s, char*t)  
 {  double *weight;
   int i;  int **s; /* Status */
   int lg=20;  double *agedc, **covar, idx;
   i=0;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     (s[i] = t[i]);  double ftolhess; /* Tolerance for computing hessian */
     if (t[i]== '\\') s[i]='/';  
   }  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 int nbocc(char *s, char occ)    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   int i,j=0;  
   int lg=20;    l1 = strlen(path );                   /* length of path */
   i=0;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   lg=strlen(s);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for(i=0; i<= lg; i++) {    if ( ss == NULL ) {                   /* no directory, so use current */
   if  (s[i] == occ ) j++;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   return j;      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 void cutv(char *u,char *v, char*t, char occ)        return( GLOCK_ERROR_GETCWD );
 {      }
   int i,lg,j,p=0;      strcpy( name, path );               /* we've got it */
   i=0;    } else {                              /* strip direcotry from path */
   for(j=0; j<=strlen(t)-1; j++) {      ss++;                               /* after this, the filename */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      l2 = strlen( ss );                  /* length of filename */
   }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
   lg=strlen(t);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for(j=0; j<p; j++) {      dirc[l1-l2] = 0;                    /* add zero */
     (u[j] = t[j]);    }
   }    l1 = strlen( dirc );                  /* length of directory */
      u[p]='\0';  #ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    for(j=0; j<= lg; j++) {  #else
     if (j>=(p+1))(v[j-p-1] = t[j]);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   }  #endif
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /********************** nrerror ********************/    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 void nrerror(char error_text[])    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   fprintf(stderr,"ERREUR ...\n");    finame[l1-l2]= 0;
   fprintf(stderr,"%s\n",error_text);    return( 0 );                          /* we're done */
   exit(1);  }
 }  
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  /******************************************/
 {  
   double *v;  void replace(char *s, char*t)
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  {
   if (!v) nrerror("allocation failure in vector");    int i;
   return v-nl+NR_END;    int lg=20;
 }    i=0;
     lg=strlen(t);
 /************************ free vector ******************/    for(i=0; i<= lg; i++) {
 void free_vector(double*v, int nl, int nh)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   free((FREE_ARG)(v+nl-NR_END));    }
 }  }
   
 /************************ivector *******************************/  int nbocc(char *s, char occ)
 int *ivector(long nl,long nh)  {
 {    int i,j=0;
   int *v;    int lg=20;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    i=0;
   if (!v) nrerror("allocation failure in ivector");    lg=strlen(s);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }    if  (s[i] == occ ) j++;
     }
 /******************free ivector **************************/    return j;
 void free_ivector(int *v, long nl, long nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u is ended by char occ excluding it
 /******************* imatrix *******************************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 int **imatrix(long nrl, long nrh, long ncl, long nch)       gives u="abcedf" and v="ghi2j" */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    int i,lg,j,p=0;
 {    i=0;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    for(j=0; j<=strlen(t)-1; j++) {
   int **m;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      }
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    lg=strlen(t);
   if (!m) nrerror("allocation failure 1 in matrix()");    for(j=0; j<p; j++) {
   m += NR_END;      (u[j] = t[j]);
   m -= nrl;    }
         u[p]='\0';
    
   /* allocate rows and set pointers to them */     for(j=0; j<= lg; j++) {
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));      if (j>=(p+1))(v[j-p-1] = t[j]);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    }
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
    /********************** nrerror ********************/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    void nrerror(char error_text[])
   /* return pointer to array of pointers to rows */  {
   return m;    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 /****************** free_imatrix *************************/  }
 void free_imatrix(m,nrl,nrh,ncl,nch)  /*********************** vector *******************/
       int **m;  double *vector(int nl, int nh)
       long nch,ncl,nrh,nrl;  {
      /* free an int matrix allocated by imatrix() */    double *v;
 {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if (!v) nrerror("allocation failure in vector");
   free((FREE_ARG) (m+nrl-NR_END));    return v-nl+NR_END;
 }  }
   
 /******************* matrix *******************************/  /************************ free vector ******************/
 double **matrix(long nrl, long nrh, long ncl, long nch)  void free_vector(double*v, int nl, int nh)
 {  {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    free((FREE_ARG)(v+nl-NR_END));
   double **m;  }
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /************************ivector *******************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  int *ivector(long nl,long nh)
   m += NR_END;  {
   m -= nrl;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!v) nrerror("allocation failure in ivector");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return v-nl+NR_END;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /******************free ivector **************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_ivector(int *v, long nl, long nh)
   return m;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /******************* imatrix *******************************/
 {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   free((FREE_ARG)(m+nrl-NR_END));  { 
 }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 /******************* ma3x *******************************/    
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    /* allocate pointers to rows */ 
 {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double ***m;    m += NR_END; 
     m -= nrl; 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    /* allocate rows and set pointers to them */ 
   m -= nrl;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl] += NR_END; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m[nrl] -= ncl; 
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    /* return pointer to array of pointers to rows */ 
     return m; 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  } 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /****************** free_imatrix *************************/
   m[nrl][ncl] -= nll;  void free_imatrix(m,nrl,nrh,ncl,nch)
   for (j=ncl+1; j<=nch; j++)        int **m;
     m[nrl][j]=m[nrl][j-1]+nlay;        long nch,ncl,nrh,nrl; 
         /* free an int matrix allocated by imatrix() */ 
   for (i=nrl+1; i<=nrh; i++) {  { 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     for (j=ncl+1; j<=nch; j++)    free((FREE_ARG) (m+nrl-NR_END)); 
       m[i][j]=m[i][j-1]+nlay;  } 
   }  
   return m;  /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 /*************************free ma3x ************************/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    double **m;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()");
   free((FREE_ARG)(m+nrl-NR_END));    m += NR_END;
 }    m -= nrl;
   
 /***************** f1dim *************************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 extern int ncom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 extern double *pcom,*xicom;    m[nrl] += NR_END;
 extern double (*nrfunc)(double []);    m[nrl] -= ncl;
    
 double f1dim(double x)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {    return m;
   int j;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   double f;     */
   double *xt;  }
    
   xt=vector(1,ncom);  /*************************free matrix ************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   f=(*nrfunc)(xt);  {
   free_vector(xt,1,ncom);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return f;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /*****************brent *************************/  /******************* ma3x *******************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 {  {
   int iter;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double a,b,d,etemp;    double ***m;
   double fu,fv,fw,fx;  
   double ftemp;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m) nrerror("allocation failure 1 in matrix()");
   double e=0.0;    m += NR_END;
      m -= nrl;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   x=w=v=bx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   fw=fv=fx=(*f)(x);    m[nrl] += NR_END;
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] -= ncl;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    m[nrl][ncl] += NR_END;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    m[nrl][ncl] -= nll;
 #endif    for (j=ncl+1; j<=nch; j++) 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      m[nrl][j]=m[nrl][j-1]+nlay;
       *xmin=x;    
       return fx;    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     ftemp=fu;      for (j=ncl+1; j<=nch; j++) 
     if (fabs(e) > tol1) {        m[i][j]=m[i][j-1]+nlay;
       r=(x-w)*(fx-fv);    }
       q=(x-v)*(fx-fw);    return m; 
       p=(x-v)*q-(x-w)*r;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       q=2.0*(q-r);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       if (q > 0.0) p = -p;    */
       q=fabs(q);  }
       etemp=e;  
       e=d;  /*************************free ma3x ************************/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  {
       else {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         d=p/q;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         u=x+d;    free((FREE_ARG)(m+nrl-NR_END));
         if (u-a < tol2 || b-u < tol2)  }
           d=SIGN(tol1,xm-x);  
       }  /***************** f1dim *************************/
     } else {  extern int ncom; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));   
     fu=(*f)(u);  double f1dim(double x) 
     if (fu <= fx) {  { 
       if (u >= x) a=x; else b=x;    int j; 
       SHFT(v,w,x,u)    double f;
         SHFT(fv,fw,fx,fu)    double *xt; 
         } else {   
           if (u < x) a=u; else b=u;    xt=vector(1,ncom); 
           if (fu <= fw || w == x) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
             v=w;    f=(*nrfunc)(xt); 
             w=u;    free_vector(xt,1,ncom); 
             fv=fw;    return f; 
             fw=fu;  } 
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /*****************brent *************************/
             fv=fu;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           }  { 
         }    int iter; 
   }    double a,b,d,etemp;
   nrerror("Too many iterations in brent");    double fu,fv,fw,fx;
   *xmin=x;    double ftemp;
   return fx;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 }    double e=0.0; 
    
 /****************** mnbrak ***********************/    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    x=w=v=bx; 
             double (*func)(double))    fw=fv=fx=(*f)(x); 
 {    for (iter=1;iter<=ITMAX;iter++) { 
   double ulim,u,r,q, dum;      xm=0.5*(a+b); 
   double fu;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
        /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   *fa=(*func)(*ax);      printf(".");fflush(stdout);
   *fb=(*func)(*bx);      fprintf(ficlog,".");fflush(ficlog);
   if (*fb > *fa) {  #ifdef DEBUG
     SHFT(dum,*ax,*bx,dum)      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);
       SHFT(dum,*fb,*fa,dum)      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)))) { */
   *cx=(*bx)+GOLD*(*bx-*ax);  #endif
   *fc=(*func)(*cx);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   while (*fb > *fc) {        *xmin=x; 
     r=(*bx-*ax)*(*fb-*fc);        return fx; 
     q=(*bx-*cx)*(*fb-*fa);      } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      ftemp=fu;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      if (fabs(e) > tol1) { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        r=(x-w)*(fx-fv); 
     if ((*bx-u)*(u-*cx) > 0.0) {        q=(x-v)*(fx-fw); 
       fu=(*func)(u);        p=(x-v)*q-(x-w)*r; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        q=2.0*(q-r); 
       fu=(*func)(u);        if (q > 0.0) p = -p; 
       if (fu < *fc) {        q=fabs(q); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        etemp=e; 
           SHFT(*fb,*fc,fu,(*func)(u))        e=d; 
           }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       u=ulim;        else { 
       fu=(*func)(u);          d=p/q; 
     } else {          u=x+d; 
       u=(*cx)+GOLD*(*cx-*bx);          if (u-a < tol2 || b-u < tol2) 
       fu=(*func)(u);            d=SIGN(tol1,xm-x); 
     }        } 
     SHFT(*ax,*bx,*cx,u)      } else { 
       SHFT(*fa,*fb,*fc,fu)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
 }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 /*************** linmin ************************/      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 int ncom;        SHFT(v,w,x,u) 
 double *pcom,*xicom;          SHFT(fv,fw,fx,fu) 
 double (*nrfunc)(double []);          } else { 
              if (u < x) a=u; else b=u; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))            if (fu <= fw || w == x) { 
 {              v=w; 
   double brent(double ax, double bx, double cx,              w=u; 
                double (*f)(double), double tol, double *xmin);              fv=fw; 
   double f1dim(double x);              fw=fu; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,            } else if (fu <= fv || v == x || v == w) { 
               double *fc, double (*func)(double));              v=u; 
   int j;              fv=fu; 
   double xx,xmin,bx,ax;            } 
   double fx,fb,fa;          } 
      } 
   ncom=n;    nrerror("Too many iterations in brent"); 
   pcom=vector(1,n);    *xmin=x; 
   xicom=vector(1,n);    return fx; 
   nrfunc=func;  } 
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /****************** mnbrak ***********************/
     xicom[j]=xi[j];  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   ax=0.0;              double (*func)(double)) 
   xx=1.0;  { 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double ulim,u,r,q, dum;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double fu; 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *fa=(*func)(*ax); 
 #endif    *fb=(*func)(*bx); 
   for (j=1;j<=n;j++) {    if (*fb > *fa) { 
     xi[j] *= xmin;      SHFT(dum,*ax,*bx,dum) 
     p[j] += xi[j];        SHFT(dum,*fb,*fa,dum) 
   }        } 
   free_vector(xicom,1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
   free_vector(pcom,1,n);    *fc=(*func)(*cx); 
 }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 /*************** powell ************************/      q=(*bx-*cx)*(*fb-*fa); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             double (*func)(double []))        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   void linmin(double p[], double xi[], int n, double *fret,      if ((*bx-u)*(u-*cx) > 0.0) { 
               double (*func)(double []));        fu=(*func)(u); 
   int i,ibig,j;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double del,t,*pt,*ptt,*xit;        fu=(*func)(u); 
   double fp,fptt;        if (fu < *fc) { 
   double *xits;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   pt=vector(1,n);            SHFT(*fb,*fc,fu,(*func)(u)) 
   ptt=vector(1,n);            } 
   xit=vector(1,n);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   xits=vector(1,n);        u=ulim; 
   *fret=(*func)(p);        fu=(*func)(u); 
   for (j=1;j<=n;j++) pt[j]=p[j];      } else { 
   for (*iter=1;;++(*iter)) {        u=(*cx)+GOLD*(*cx-*bx); 
     fp=(*fret);        fu=(*func)(u); 
     ibig=0;      } 
     del=0.0;      SHFT(*ax,*bx,*cx,u) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=n;i++)        } 
       printf(" %d %.12f",i, p[i]);  } 
     printf("\n");  
     for (i=1;i<=n;i++) {  /*************** linmin ************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  int ncom; 
 #ifdef DEBUG  double *pcom,*xicom;
       printf("fret=%lf \n",*fret);  double (*nrfunc)(double []); 
 #endif   
       printf("%d",i);fflush(stdout);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       linmin(p,xit,n,fret,func);  { 
       if (fabs(fptt-(*fret)) > del) {    double brent(double ax, double bx, double cx, 
         del=fabs(fptt-(*fret));                 double (*f)(double), double tol, double *xmin); 
         ibig=i;    double f1dim(double x); 
       }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #ifdef DEBUG                double *fc, double (*func)(double)); 
       printf("%d %.12e",i,(*fret));    int j; 
       for (j=1;j<=n;j++) {    double xx,xmin,bx,ax; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    double fx,fb,fa;
         printf(" x(%d)=%.12e",j,xit[j]);   
       }    ncom=n; 
       for(j=1;j<=n;j++)    pcom=vector(1,n); 
         printf(" p=%.12e",p[j]);    xicom=vector(1,n); 
       printf("\n");    nrfunc=func; 
 #endif    for (j=1;j<=n;j++) { 
     }      pcom[j]=p[j]; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      xicom[j]=xi[j]; 
 #ifdef DEBUG    } 
       int k[2],l;    ax=0.0; 
       k[0]=1;    xx=1.0; 
       k[1]=-1;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       printf("Max: %.12e",(*func)(p));    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       for (j=1;j<=n;j++)  #ifdef DEBUG
         printf(" %.12e",p[j]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for(l=0;l<=1;l++) {  #endif
         for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      xi[j] *= xmin; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      p[j] += xi[j]; 
         }    } 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    free_vector(xicom,1,n); 
       }    free_vector(pcom,1,n); 
 #endif  } 
   
   /*************** powell ************************/
       free_vector(xit,1,n);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       free_vector(xits,1,n);              double (*func)(double [])) 
       free_vector(ptt,1,n);  { 
       free_vector(pt,1,n);    void linmin(double p[], double xi[], int n, double *fret, 
       return;                double (*func)(double [])); 
     }    int i,ibig,j; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double del,t,*pt,*ptt,*xit;
     for (j=1;j<=n;j++) {    double fp,fptt;
       ptt[j]=2.0*p[j]-pt[j];    double *xits;
       xit[j]=p[j]-pt[j];    pt=vector(1,n); 
       pt[j]=p[j];    ptt=vector(1,n); 
     }    xit=vector(1,n); 
     fptt=(*func)(ptt);    xits=vector(1,n); 
     if (fptt < fp) {    *fret=(*func)(p); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if (t < 0.0) {    for (*iter=1;;++(*iter)) { 
         linmin(p,xit,n,fret,func);      fp=(*fret); 
         for (j=1;j<=n;j++) {      ibig=0; 
           xi[j][ibig]=xi[j][n];      del=0.0; 
           xi[j][n]=xit[j];      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      for (i=1;i<=n;i++) 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        printf(" %d %.12f",i, p[i]);
         for(j=1;j<=n;j++)      fprintf(ficlog," %d %.12f",i, p[i]);
           printf(" %.12e",xit[j]);      printf("\n");
         printf("\n");      fprintf(ficlog,"\n");
 #endif      for (i=1;i<=n;i++) { 
       }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     }        fptt=(*fret); 
   }  #ifdef DEBUG
 }        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
 /**** Prevalence limit ****************/  #endif
         printf("%d",i);fflush(stdout);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        fprintf(ficlog,"%d",i);fflush(ficlog);
 {        linmin(p,xit,n,fret,func); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        if (fabs(fptt-(*fret)) > del) { 
      matrix by transitions matrix until convergence is reached */          del=fabs(fptt-(*fret)); 
           ibig=i; 
   int i, ii,j,k;        } 
   double min, max, maxmin, maxmax,sumnew=0.;  #ifdef DEBUG
   double **matprod2();        printf("%d %.12e",i,(*fret));
   double **out, cov[NCOVMAX], **pmij();        fprintf(ficlog,"%d %.12e",i,(*fret));
   double **newm;        for (j=1;j<=n;j++) {
   double agefin, delaymax=50 ; /* Max number of years to converge */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   for (ii=1;ii<=nlstate+ndeath;ii++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=nlstate+ndeath;j++){        }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
    cov[1]=1.;        }
          printf("\n");
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficlog,"\n");
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #endif
     newm=savm;      } 
     /* Covariates have to be included here again */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      cov[2]=agefin;  #ifdef DEBUG
          int k[2],l;
       for (k=1; k<=cptcovn;k++) {        k[0]=1;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        k[1]=-1;
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (j=1;j<=n;j++) {
       for (k=1; k<=cptcovprod;k++)          printf(" %.12e",p[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog," %.12e",p[j]);
         }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        printf("\n");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        fprintf(ficlog,"\n");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        for(l=0;l<=1;l++) {
     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++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     savm=oldm;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     oldm=newm;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     maxmax=0.;          }
     for(j=1;j<=nlstate;j++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       min=1.;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       max=0.;        }
       for(i=1; i<=nlstate; i++) {  #endif
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);        free_vector(xit,1,n); 
         max=FMAX(max,prlim[i][j]);        free_vector(xits,1,n); 
         min=FMIN(min,prlim[i][j]);        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
       maxmin=max-min;        return; 
       maxmax=FMAX(maxmax,maxmin);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     if(maxmax < ftolpl){      for (j=1;j<=n;j++) { 
       return prlim;        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 /*************** transition probabilities ***************/      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        if (t < 0.0) { 
 {          linmin(p,xit,n,fret,func); 
   double s1, s2;          for (j=1;j<=n;j++) { 
   /*double t34;*/            xi[j][ibig]=xi[j][n]; 
   int i,j,j1, nc, ii, jj;            xi[j][n]=xit[j]; 
           }
     for(i=1; i<= nlstate; i++){  #ifdef DEBUG
     for(j=1; j<i;j++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         /*s2 += param[i][j][nc]*cov[nc];*/          for(j=1;j<=n;j++){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            printf(" %.12e",xit[j]);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            fprintf(ficlog," %.12e",xit[j]);
       }          }
       ps[i][j]=s2;          printf("\n");
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          fprintf(ficlog,"\n");
     }  #endif
     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];    } 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  } 
       }  
       ps[i][j]=s2;  /**** Prevalence limit (stable prevalence)  ****************/
     }  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     /*ps[3][2]=1;*/  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(i=1; i<= nlstate; i++){       matrix by transitions matrix until convergence is reached */
      s1=0;  
     for(j=1; j<i; j++)    int i, ii,j,k;
       s1+=exp(ps[i][j]);    double min, max, maxmin, maxmax,sumnew=0.;
     for(j=i+1; j<=nlstate+ndeath; j++)    double **matprod2();
       s1+=exp(ps[i][j]);    double **out, cov[NCOVMAX], **pmij();
     ps[i][i]=1./(s1+1.);    double **newm;
     for(j=1; j<i; j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (j=1;j<=nlstate+ndeath;j++){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* end i */      }
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){     cov[1]=1.;
     for(jj=1; jj<= nlstate+ndeath; jj++){   
       ps[ii][jj]=0;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       ps[ii][ii]=1;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     }      newm=savm;
   }      /* Covariates have to be included here again */
        cov[2]=agefin;
     
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        for (k=1; k<=cptcovn;k++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      printf("%lf ",ps[ii][jj]);          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
    }        }
     printf("\n ");        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     printf("\n ");printf("%lf ",cov[2]);*/          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++) printf("%f ",x[i]);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   goto end;*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     return ps;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
 /**************** Product of 2 matrices ******************/      savm=oldm;
       oldm=newm;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      maxmax=0.;
 {      for(j=1;j<=nlstate;j++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        min=1.;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        max=0.;
   /* in, b, out are matrice of pointers which should have been initialized        for(i=1; i<=nlstate; i++) {
      before: only the contents of out is modified. The function returns          sumnew=0;
      a pointer to pointers identical to out */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   long i, j, k;          prlim[i][j]= newm[i][j]/(1-sumnew);
   for(i=nrl; i<= nrh; i++)          max=FMAX(max,prlim[i][j]);
     for(k=ncolol; k<=ncoloh; k++)          min=FMIN(min,prlim[i][j]);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        }
         out[i][k] +=in[i][j]*b[j][k];        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   return out;      }
 }      if(maxmax < ftolpl){
         return prlim;
       }
 /************* Higher Matrix Product ***************/    }
   }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /*************** transition probabilities ***************/ 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double s1, s2;
      (typically every 2 years instead of every month which is too big).    /*double t34;*/
      Model is determined by parameters x and covariates have to be    int i,j,j1, nc, ii, jj;
      included manually here.  
       for(i=1; i<= nlstate; i++){
      */      for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i, j, d, h, k;          /*s2 += param[i][j][nc]*cov[nc];*/
   double **out, cov[NCOVMAX];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double **newm;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   /* Hstepm could be zero and should return the unit matrix */        ps[i][j]=s2;
   for (i=1;i<=nlstate+ndeath;i++)        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);      for(j=i+1; j<=nlstate+ndeath;j++){
       po[i][j][0]=(i==j ? 1.0 : 0.0);        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];
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   for(h=1; h <=nhstepm; h++){        }
     for(d=1; d <=hstepm; d++){        ps[i][j]=s2;
       newm=savm;      }
       /* Covariates have to be included here again */    }
       cov[1]=1.;      /*ps[3][2]=1;*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for(i=1; i<= nlstate; i++){
       for (k=1; k<=cptcovage;k++)       s1=0;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for(j=1; j<i; j++)
       for (k=1; k<=cptcovprod;k++)        s1+=exp(ps[i][j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      for(j=1; j<i; j++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      for(j=i+1; j<=nlstate+ndeath; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        ps[i][j]= exp(ps[i][j])*ps[i][i];
       savm=oldm;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       oldm=newm;    } /* end i */
     }  
     for(i=1; i<=nlstate+ndeath; i++)    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(j=1;j<=nlstate+ndeath;j++) {      for(jj=1; jj<= nlstate+ndeath; jj++){
         po[i][j][h]=newm[i][j];        ps[ii][jj]=0;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        ps[ii][ii]=1;
          */      }
       }    }
   } /* end h */  
   return po;  
 }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
 /*************** log-likelihood *************/     }
 double func( double *x)      printf("\n ");
 {      }
   int i, ii, j, k, mi, d, kk;      printf("\n ");printf("%lf ",cov[2]);*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*
   double **out;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double sw; /* Sum of weights */    goto end;*/
   double lli; /* Individual log likelihood */      return ps;
   long ipmx;  }
   /*extern weight */  
   /* We are differentiating ll according to initial status */  /**************** Product of 2 matrices ******************/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     printf(" %d\n",s[4][i]);  {
   */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   cov[1]=1.;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   for(k=1; k<=nlstate; k++) ll[k]=0.;       before: only the contents of out is modified. The function returns
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){       a pointer to pointers identical to out */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    long i, j, k;
     for(mi=1; mi<= wav[i]-1; mi++){    for(i=nrl; i<= nrh; i++)
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(k=ncolol; k<=ncoloh; k++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       for(d=0; d<dh[mi][i]; d++){          out[i][k] +=in[i][j]*b[j][k];
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return out;
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  
          /************* Higher Matrix Product ***************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         savm=oldm;  {
         oldm=newm;    /* Computes the transition matrix starting at age 'age' over 
               'nhstepm*hstepm*stepm' months (i.e. until
               age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       } /* end mult */       nhstepm*hstepm matrices. 
             Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       (typically every 2 years instead of every month which is too big 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/       for the memory).
       ipmx +=1;       Model is determined by parameters x and covariates have to be 
       sw += weight[i];       included manually here. 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */       */
   } /* end of individual */  
     int i, j, d, h, k;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double **out, cov[NCOVMAX];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double **newm;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;    /* Hstepm could be zero and should return the unit matrix */
 }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
 /*********** Maximum Likelihood Estimation ***************/        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(h=1; h <=nhstepm; h++){
   int i,j, iter;      for(d=1; d <=hstepm; d++){
   double **xi,*delti;        newm=savm;
   double fret;        /* Covariates have to be included here again */
   xi=matrix(1,npar,1,npar);        cov[1]=1.;
   for (i=1;i<=npar;i++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       xi[i][j]=(i==j ? 1.0 : 0.0);        for (k=1; k<=cptcovage;k++)
   printf("Powell\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   powell(p,xi,npar,ftol,&iter,&fret,func);        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]]];
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 /**** Computes Hessian and covariance matrix ***/                     pmij(pmmij,cov,ncovmodel,x,nlstate));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        savm=oldm;
 {        oldm=newm;
   double  **a,**y,*x,pd;      }
   double **hess;      for(i=1; i<=nlstate+ndeath; i++)
   int i, j,jk;        for(j=1;j<=nlstate+ndeath;j++) {
   int *indx;          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]);
   double hessii(double p[], double delta, int theta, double delti[]);           */
   double hessij(double p[], double delti[], int i, int j);        }
   void lubksb(double **a, int npar, int *indx, double b[]) ;    } /* end h */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    return po;
   }
   hess=matrix(1,npar,1,npar);  
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*************** log-likelihood *************/
   for (i=1;i<=npar;i++){  double func( double *x)
     printf("%d",i);fflush(stdout);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    int i, ii, j, k, mi, d, kk;
     /*printf(" %f ",p[i]);*/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     /*printf(" %lf ",hess[i][i]);*/    double **out;
   }    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   for (i=1;i<=npar;i++) {    int s1, s2;
     for (j=1;j<=npar;j++)  {    double bbh, survp;
       if (j>i) {    long ipmx;
         printf(".%d%d",i,j);fflush(stdout);    /*extern weight */
         hess[i][j]=hessij(p,delti,i,j);    /* We are differentiating ll according to initial status */
         hess[j][i]=hess[i][j];        /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         /*printf(" %lf ",hess[i][j]);*/    /*for(i=1;i<imx;i++) 
       }      printf(" %d\n",s[4][i]);
     }    */
   }    cov[1]=1.;
   printf("\n");  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
      if(mle==1){
   a=matrix(1,npar,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   y=matrix(1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   x=vector(1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   indx=ivector(1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++)            for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   ludcmp(a,npar,indx,&pd);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   for (j=1;j<=npar;j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1;i<=npar;i++) x[i]=0;            newm=savm;
     x[j]=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     lubksb(a,npar,indx,x);            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       matcov[i][j]=x[i];            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   printf("\n#Hessian matrix#\n");            oldm=newm;
   for (i=1;i<=npar;i++) {          } /* end mult */
     for (j=1;j<=npar;j++) {        
       printf("%.3e ",hess[i][j]);          /*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.
     printf("\n");           * 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
   /* Recompute Inverse */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   for (i=1;i<=npar;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * probability in order to take into account the bias as a fraction of the way
   ludcmp(a,npar,indx,&pd);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   /*  printf("\n#Hessian matrix recomputed#\n");           * 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. 
   for (j=1;j<=npar;j++) {           */
     for (i=1;i<=npar;i++) x[i]=0;          s1=s[mw[mi][i]][i];
     x[j]=1;          s2=s[mw[mi+1][i]][i];
     lubksb(a,npar,indx,x);          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++){          /* bias is positive if real duration
       y[i][j]=x[i];           * is higher than the multiple of stepm and negative otherwise.
       printf("%.3e ",y[i][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]));*/
     printf("\n");          if( s2 > nlstate){ 
   }            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   */               to the likelihood is the probability to die between last step unit time and current 
                step unit time, which is also the differences between probability to die before dh 
   free_matrix(a,1,npar,1,npar);               and probability to die before dh-stepm . 
   free_matrix(y,1,npar,1,npar);               In version up to 0.92 likelihood was computed
   free_vector(x,1,npar);          as if date of death was unknown. Death was treated as any other
   free_ivector(indx,1,npar);          health state: the date of the interview describes the actual state
   free_matrix(hess,1,npar,1,npar);          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
 }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
 /*************** hessian matrix ****************/          contribution is smaller and very dependent of the step unit
 double hessii( double x[], double delta, int theta, double delti[])          stepm. It is no more the probability to die between last interview
 {          and month of death but the probability to survive from last
   int i;          interview up to one month before death multiplied by the
   int l=1, lmax=20;          probability to die within a month. Thanks to Chris
   double k1,k2;          Jackson for correcting this bug.  Former versions increased
   double p2[NPARMAX+1];          mortality artificially. The bad side is that we add another loop
   double res;          which slows down the processing. The difference can be up to 10%
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          lower mortality.
   double fx;            */
   int k=0,kmax=10;            lli=log(out[s1][s2] - savm[s1][s2]);
   double l1;          }else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fx=func(x);            /*  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];          } 
   for(l=0 ; l <=lmax; l++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     l1=pow(10,l);          /*if(lli ==000.0)*/
     delts=delt;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for(k=1 ; k <kmax; k=k+1){          ipmx +=1;
       delt = delta*(l1*k);          sw += weight[i];
       p2[theta]=x[theta] +delt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       k1=func(p2)-fx;        } /* end of wave */
       p2[theta]=x[theta]-delt;      } /* end of individual */
       k2=func(p2)-fx;    }  else if(mle==2){
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
 #ifdef DEBUG          for (ii=1;ii<=nlstate+ndeath;ii++)
       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 (j=1;j<=nlstate+ndeath;j++){
 #endif              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            }
         k=kmax;          for(d=0; d<=dh[mi][i]; d++){
       }            newm=savm;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         k=kmax; l=lmax*10.;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            }
         delts=delt;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   delti[theta]=delts;          } /* end mult */
   return res;        
            /*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 
 double hessij( double x[], double delti[], int thetai,int thetaj)           * (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
   int i;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int l=1, l1, lmax=20;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double k1,k2,k3,k4,res,fx;           * probability in order to take into account the bias as a fraction of the way
   double p2[NPARMAX+1];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int k;           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   fx=func(x);           * For stepm > 1 the results are less biased than in previous versions. 
   for (k=1; k<=2; k++) {           */
     for (i=1;i<=npar;i++) p2[i]=x[i];          s1=s[mw[mi][i]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;          s2=s[mw[mi+1][i]][i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          bbh=(double)bh[mi][i]/(double)stepm; 
     k1=func(p2)-fx;          /* bias is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
     p2[thetai]=x[thetai]+delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     k2=func(p2)-fx;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     p2[thetai]=x[thetai]-delti[thetai]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*if(lli ==000.0)*/
     k3=func(p2)-fx;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
     p2[thetai]=x[thetai]-delti[thetai]/k;          sw += weight[i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     k4=func(p2)-fx;        } /* end of wave */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      } /* end of individual */
 #ifdef DEBUG    }  else if(mle==3){  /* exponential inter-extrapolation */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 #endif        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   return res;          for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************** Inverse of matrix **************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void ludcmp(double **a, int n, int *indx, double *d)            }
 {          for(d=0; d<dh[mi][i]; d++){
   int i,imax,j,k;            newm=savm;
   double big,dum,sum,temp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *vv;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   vv=vector(1,n);            }
   *d=1.0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (i=1;i<=n;i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     big=0.0;            savm=oldm;
     for (j=1;j<=n;j++)            oldm=newm;
       if ((temp=fabs(a[i][j])) > big) big=temp;          } /* end mult */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        
     vv[i]=1.0/big;          /*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.
   for (j=1;j<=n;j++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<j;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       sum=a[i][j];           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       a[i][j]=sum;           * (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
     big=0.0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for (i=j;i<=n;i++) {           * -stepm/2 to stepm/2 .
       sum=a[i][j];           * For stepm=1 the results are the same as for previous versions of Imach.
       for (k=1;k<j;k++)           * For stepm > 1 the results are less biased than in previous versions. 
         sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;          s1=s[mw[mi][i]][i];
       if ( (dum=vv[i]*fabs(sum)) >= big) {          s2=s[mw[mi+1][i]][i];
         big=dum;          bbh=(double)bh[mi][i]/(double)stepm; 
         imax=i;          /* bias is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
     }           */
     if (j != imax) {          /* 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 (k=1;k<=n;k++) {          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 */
         dum=a[imax][k];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         a[imax][k]=a[j][k];          /*if(lli ==000.0)*/
         a[j][k]=dum;          /*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;
       *d = -(*d);          sw += weight[i];
       vv[imax]=vv[j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     indx[j]=imax;      } /* end of individual */
     if (a[j][j] == 0.0) a[j][j]=TINY;    }else{  /* ml=4 no inter-extrapolation */
     if (j != n) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       dum=1.0/(a[j][j]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   free_vector(vv,1,n);  /* Doesn't work */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 ;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 void lubksb(double **a, int n, int *indx, double b[])            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i,ii=0,ip,j;            for (kk=1; kk<=cptcovage;kk++) {
   double sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   for (i=1;i<=n;i++) {          
     ip=indx[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     sum=b[ip];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     b[ip]=b[i];            savm=oldm;
     if (ii)            oldm=newm;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          } /* end mult */
     else if (sum) ii=i;        
     b[i]=sum;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   }          ipmx +=1;
   for (i=n;i>=1;i--) {          sw += weight[i];
     sum=b[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        } /* end of wave */
     b[i]=sum/a[i][i];      } /* end of individual */
   }    } /* End of if */
 }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 /************ Frequencies ********************/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    return -l;
 {  /* Some frequencies */  }
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /*********** Maximum Likelihood Estimation ***************/
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    int i,j, iter;
      double **xi;
   pp=vector(1,nlstate);    double fret;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    xi=matrix(1,npar,1,npar);
   strcpy(fileresp,"p");    for (i=1;i<=npar;i++)
   strcat(fileresp,fileres);      for (j=1;j<=npar;j++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     exit(0);    powell(p,xi,npar,ftol,&iter,&fret,func);
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   j1=0;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
    
   for(k1=1; k1<=j;k1++){  /**** Computes Hessian and covariance matrix ***/
     for(i1=1; i1<=ncodemax[k1];i1++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       j1++;  {
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double  **a,**y,*x,pd;
         scanf("%d", i);*/    double **hess;
       for (i=-1; i<=nlstate+ndeath; i++)      int i, j,jk;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int *indx;
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;    double hessii(double p[], double delta, int theta, double delti[]);
          double hessij(double p[], double delti[], int i, int j);
       dateintsum=0;    void lubksb(double **a, int npar, int *indx, double b[]) ;
       k2cpt=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
       for (i=1; i<=imx; i++) {  
         bool=1;    hess=matrix(1,npar,1,npar);
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)    printf("\nCalculation of the hessian matrix. Wait...\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
               bool=0;    for (i=1;i<=npar;i++){
         }      printf("%d",i);fflush(stdout);
         if (bool==1) {      fprintf(ficlog,"%d",i);fflush(ficlog);
           for(m=firstpass; m<=lastpass; m++){      hess[i][i]=hessii(p,ftolhess,i,delti);
             k2=anint[m][i]+(mint[m][i]/12.);      /*printf(" %f ",p[i]);*/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      /*printf(" %lf ",hess[i][i]);*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    
               if (m<lastpass) {    for (i=1;i<=npar;i++) {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for (j=1;j<=npar;j++)  {
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        if (j>i) { 
               }          printf(".%d%d",i,j);fflush(stdout);
                        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          hess[i][j]=hessij(p,delti,i,j);
                 dateintsum=dateintsum+k2;          hess[j][i]=hess[i][j];    
                 k2cpt++;          /*printf(" %lf ",hess[i][j]);*/
               }        }
             }      }
           }    }
         }    printf("\n");
       }    fprintf(ficlog,"\n");
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       if  (cptcovn>0) {    
         fprintf(ficresp, "\n#********** Variable ");    a=matrix(1,npar,1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    y=matrix(1,npar,1,npar);
         fprintf(ficresp, "**********\n#");    x=vector(1,npar);
       }    indx=ivector(1,npar);
       for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++)
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       fprintf(ficresp, "\n");    ludcmp(a,npar,indx,&pd);
        
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for (j=1;j<=npar;j++) {
         if(i==(int)agemax+3)      for (i=1;i<=npar;i++) x[i]=0;
           printf("Total");      x[j]=1;
         else      lubksb(a,npar,indx,x);
           printf("Age %d", i);      for (i=1;i<=npar;i++){ 
         for(jk=1; jk <=nlstate ; jk++){        matcov[i][j]=x[i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
             pp[jk] += freq[jk][m][i];    }
         }  
         for(jk=1; jk <=nlstate ; jk++){    printf("\n#Hessian matrix#\n");
           for(m=-1, pos=0; m <=0 ; m++)    fprintf(ficlog,"\n#Hessian matrix#\n");
             pos += freq[jk][m][i];    for (i=1;i<=npar;i++) { 
           if(pp[jk]>=1.e-10)      for (j=1;j<=npar;j++) { 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        printf("%.3e ",hess[i][j]);
           else        fprintf(ficlog,"%.3e ",hess[i][j]);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      }
         }      printf("\n");
       fprintf(ficlog,"\n");
         for(jk=1; jk <=nlstate ; jk++){    }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];    /* Recompute Inverse */
         }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         for(jk=1,pos=0; jk <=nlstate ; jk++)    ludcmp(a,npar,indx,&pd);
           pos += pp[jk];  
         for(jk=1; jk <=nlstate ; jk++){    /*  printf("\n#Hessian matrix recomputed#\n");
           if(pos>=1.e-5)  
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for (j=1;j<=npar;j++) {
           else      for (i=1;i<=npar;i++) x[i]=0;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      x[j]=1;
           if( i <= (int) agemax){      lubksb(a,npar,indx,x);
             if(pos>=1.e-5){      for (i=1;i<=npar;i++){ 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        y[i][j]=x[i];
               probs[i][jk][j1]= pp[jk]/pos;        printf("%.3e ",y[i][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]);*/        fprintf(ficlog,"%.3e ",y[i][j]);
             }      }
             else      printf("\n");
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      fprintf(ficlog,"\n");
           }    }
         }    */
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)    free_matrix(a,1,npar,1,npar);
           for(m=-1; m <=nlstate+ndeath; m++)    free_matrix(y,1,npar,1,npar);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    free_vector(x,1,npar);
         if(i <= (int) agemax)    free_ivector(indx,1,npar);
           fprintf(ficresp,"\n");    free_matrix(hess,1,npar,1,npar);
         printf("\n");  
       }  
     }  }
   }  
   dateintmean=dateintsum/k2cpt;  /*************** hessian matrix ****************/
    double hessii( double x[], double delta, int theta, double delti[])
   fclose(ficresp);  {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int i;
   free_vector(pp,1,nlstate);    int l=1, lmax=20;
      double k1,k2;
   /* End of Freq */    double p2[NPARMAX+1];
 }    double res;
     double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 /************ Prevalence ********************/    double fx;
 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 k=0,kmax=10;
 {  /* Some frequencies */    double l1;
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    fx=func(x);
   double ***freq; /* Frequencies */    for (i=1;i<=npar;i++) p2[i]=x[i];
   double *pp;    for(l=0 ; l <=lmax; l++){
   double pos, k2;      l1=pow(10,l);
       delts=delt;
   pp=vector(1,nlstate);      for(k=1 ; k <kmax; k=k+1){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        k1=func(p2)-fx;
   j1=0;        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   j=cptcoveff;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
  for(k1=1; k1<=j;k1++){  #ifdef DEBUG
     for(i1=1; i1<=ncodemax[k1];i1++){        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);
       j1++;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
       for (i=-1; i<=nlstate+ndeath; i++)          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           for(m=agemin; m <= agemax+3; m++)          k=kmax;
             freq[i][jk][m]=0;        }
              else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for (i=1; i<=imx; i++) {          k=kmax; l=lmax*10.;
         bool=1;        }
         if  (cptcovn>0) {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           for (z1=1; z1<=cptcoveff; z1++)          delts=delt;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;      }
         }    }
         if (bool==1) {    delti[theta]=delts;
           for(m=firstpass; m<=lastpass; m++){    return res; 
             k2=anint[m][i]+(mint[m][i]/12.);    
             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;  double hessij( double x[], double delti[], int thetai,int thetaj)
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  {
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    int i;
             }    int l=1, l1, lmax=20;
           }    double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
       }    int k;
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){    fx=func(x);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (k=1; k<=2; k++) {
               pp[jk] += freq[jk][m][i];      for (i=1;i<=npar;i++) p2[i]=x[i];
           }      p2[thetai]=x[thetai]+delti[thetai]/k;
           for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             for(m=-1, pos=0; m <=0 ; m++)      k1=func(p2)-fx;
             pos += freq[jk][m][i];    
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
              p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          for(jk=1; jk <=nlstate ; jk++){      k2=func(p2)-fx;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    
              pp[jk] += freq[jk][m][i];      p2[thetai]=x[thetai]-delti[thetai]/k;
          }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                k3=func(p2)-fx;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    
       p2[thetai]=x[thetai]-delti[thetai]/k;
          for(jk=1; jk <=nlstate ; jk++){                p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            if( i <= (int) agemax){      k4=func(p2)-fx;
              if(pos>=1.e-5){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                probs[i][jk][j1]= pp[jk]/pos;  #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;
     }  }
   }  
    /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  { 
   free_vector(pp,1,nlstate);    int i,imax,j,k; 
      double big,dum,sum,temp; 
 }  /* End of Freq */    double *vv; 
    
 /************* Waves Concatenation ***************/    vv=vector(1,n); 
     *d=1.0; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    for (i=1;i<=n;i++) { 
 {      big=0.0; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for (j=1;j<=n;j++) 
      Death is a valid wave (if date is known).        if ((temp=fabs(a[i][j])) > big) big=temp; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      vv[i]=1.0/big; 
      and mw[mi+1][i]. dh depends on stepm.    } 
      */    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
   int i, mi, m;        sum=a[i][j]; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      double sum=0., jmean=0.;*/        a[i][j]=sum; 
       } 
   int j, k=0,jk, ju, jl;      big=0.0; 
   double sum=0.;      for (i=j;i<=n;i++) { 
   jmin=1e+5;        sum=a[i][j]; 
   jmax=-1;        for (k=1;k<j;k++) 
   jmean=0.;          sum -= a[i][k]*a[k][j]; 
   for(i=1; i<=imx; i++){        a[i][j]=sum; 
     mi=0;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     m=firstpass;          big=dum; 
     while(s[m][i] <= nlstate){          imax=i; 
       if(s[m][i]>=1)        } 
         mw[++mi][i]=m;      } 
       if(m >=lastpass)      if (j != imax) { 
         break;        for (k=1;k<=n;k++) { 
       else          dum=a[imax][k]; 
         m++;          a[imax][k]=a[j][k]; 
     }/* end while */          a[j][k]=dum; 
     if (s[m][i] > nlstate){        } 
       mi++;     /* Death is another wave */        *d = -(*d); 
       /* if(mi==0)  never been interviewed correctly before death */        vv[imax]=vv[j]; 
          /* Only death is a correct wave */      } 
       mw[mi][i]=m;      indx[j]=imax; 
     }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
     wav[i]=mi;        dum=1.0/(a[j][j]); 
     if(mi==0)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      } 
   }    } 
     free_vector(vv,1,n);  /* Doesn't work */
   for(i=1; i<=imx; i++){  ;
     for(mi=1; mi<wav[i];mi++){  } 
       if (stepm <=0)  
         dh[mi][i]=1;  void lubksb(double **a, int n, int *indx, double b[]) 
       else{  { 
         if (s[mw[mi+1][i]][i] > nlstate) {    int i,ii=0,ip,j; 
           if (agedc[i] < 2*AGESUP) {    double sum; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);   
           if(j==0) j=1;  /* Survives at least one month after exam */    for (i=1;i<=n;i++) { 
           k=k+1;      ip=indx[i]; 
           if (j >= jmax) jmax=j;      sum=b[ip]; 
           if (j <= jmin) jmin=j;      b[ip]=b[i]; 
           sum=sum+j;      if (ii) 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           }      else if (sum) ii=i; 
         }      b[i]=sum; 
         else{    } 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    for (i=n;i>=1;i--) { 
           k=k+1;      sum=b[i]; 
           if (j >= jmax) jmax=j;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           else if (j <= jmin)jmin=j;      b[i]=sum/a[i][i]; 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    } 
           sum=sum+j;  } 
         }  
         jk= j/stepm;  /************ Frequencies ********************/
         jl= j -jk*stepm;  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)
         ju= j -(jk+1)*stepm;  {  /* Some frequencies */
         if(jl <= -ju)    
           dh[mi][i]=jk;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         else    int first;
           dh[mi][i]=jk+1;    double ***freq; /* Frequencies */
         if(dh[mi][i]==0)    double *pp, **prop;
           dh[mi][i]=1; /* At least one step */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       }    FILE *ficresp;
     }    char fileresp[FILENAMELENGTH];
   }    
   jmean=sum/k;    pp=vector(1,nlstate);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    prop=matrix(1,nlstate,iagemin,iagemax+3);
  }    strcpy(fileresp,"p");
 /*********** Tricode ****************************/    strcat(fileresp,fileres);
 void tricode(int *Tvar, int **nbcode, int imx)    if((ficresp=fopen(fileresp,"w"))==NULL) {
 {      printf("Problem with prevalence resultfile: %s\n", fileresp);
   int Ndum[20],ij=1, k, j, i;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   int cptcode=0;      exit(0);
   cptcoveff=0;    }
      freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   for (k=0; k<19; k++) Ndum[k]=0;    j1=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;    
     j=cptcoveff;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);    first=1;
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    for(k1=1; k1<=j;k1++){
       if (ij > cptcode) cptcode=ij;      for(i1=1; i1<=ncodemax[k1];i1++){
     }        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for (i=0; i<=cptcode; i++) {          scanf("%d", i);*/
       if(Ndum[i]!=0) ncodemax[j]++;        for (i=-1; i<=nlstate+ndeath; i++)  
     }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     ij=1;            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1; i<=nlstate; i++)  
       for (k=0; k<=19; k++) {        for(m=iagemin; m <= iagemax+3; m++)
         if (Ndum[k] != 0) {          prop[i][m]=0;
           nbcode[Tvar[j]][ij]=k;        
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/        dateintsum=0;
           ij++;        k2cpt=0;
         }        for (i=1; i<=imx; i++) {
         if (ij > ncodemax[j]) break;          bool=1;
       }            if  (cptcovn>0) {
     }            for (z1=1; z1<=cptcoveff; z1++) 
   }                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
  for (k=0; k<19; k++) Ndum[k]=0;          }
           if (bool==1){
  for (i=1; i<=ncovmodel-2; i++) {            for(m=firstpass; m<=lastpass; m++){
       ij=Tvar[i];              k2=anint[m][i]+(mint[m][i]/12.);
       Ndum[ij]++;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
  ij=1;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
  for (i=1; i<=10; i++) {                if (m<lastpass) {
    if((Ndum[i]!=0) && (i<=ncovcol)){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      Tvaraff[ij]=i;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      ij++;                }
    }                
  }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                    dateintsum=dateintsum+k2;
     cptcoveff=ij-1;                  k2cpt++;
 }                }
               }
 /*********** Health Expectancies ****************/            }
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        }
 {         
   /* Health expectancies */        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   int i, j, nhstepm, hstepm, h, nstepm, k;  
   double age, agelim, hf;        if  (cptcovn>0) {
   double ***p3mat;          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficreseij,"# Health expectancies\n");          fprintf(ficresp, "**********\n#");
   fprintf(ficreseij,"# Age");        }
   for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++) 
     for(j=1; j<=nlstate;j++)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficresp, "\n");
   fprintf(ficreseij,"\n");        
         for(i=iagemin; i <= iagemax+3; i++){
   k=1;             /* For example stepm=6 months */          if(i==iagemax+3){
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */            fprintf(ficlog,"Total");
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */          }else{
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            if(first==1){
      nhstepm is the number of hstepm from age to agelim              first=0;
      nstepm is the number of stepm from age to agelin.              printf("See log file for details...\n");
      Look at hpijx to understand the reason of that which relies in memory size            }
      and note for a fixed period like k years */            fprintf(ficlog,"Age %d", i);
   /* 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          for(jk=1; jk <=nlstate ; jk++){
      means that if the survival funtion is printed only each two years of age and if            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same              pp[jk] += freq[jk][m][i]; 
      results. So we changed our mind and took the option of the best precision.          }
   */          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   agelim=AGESUP;            if(pp[jk]>=1.e-10){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(first==1){
     /* nhstepm age range expressed in number of stepm */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     /* if (stepm >= YEARM) hstepm=1;*/            }else{
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              if(first==1)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<=nlstate;j++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){              pp[jk] += freq[jk][m][i];
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          }       
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         }            pos += pp[jk];
     fprintf(ficreseij,"%3.0f",age );            posprop += prop[jk][i];
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            if(pos>=1.e-5){
       }              if(first==1)
     fprintf(ficreseij,"\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }            }else{
 }              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /************ Variance ******************/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            }
 {            if( i <= iagemax){
   /* Variance of health expectancies */              if(pos>=1.e-5){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double **newm;                probs[i][jk][j1]= pp[jk]/pos;
   double **dnewm,**doldm;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int i, j, nhstepm, hstepm, h, nstepm, kk;              }
   int k, cptcode;              else
   double *xp;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double **gp, **gm;            }
   double ***gradg, ***trgradg;          }
   double ***p3mat;          
   double age,agelim, hf;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int theta;            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");              if(first==1)
   fprintf(ficresvij,"# Age");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   for(i=1; i<=nlstate;i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(j=1; j<=nlstate;j++)              }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          if(i <= iagemax)
   fprintf(ficresvij,"\n");            fprintf(ficresp,"\n");
           if(first==1)
   xp=vector(1,npar);            printf("Others in log...\n");
   dnewm=matrix(1,nlstate,1,npar);          fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate,1,nlstate);        }
        }
   kk=1;             /* For example stepm=6 months */    }
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */    dateintmean=dateintsum/k2cpt; 
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */   
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    fclose(ficresp);
      nhstepm is the number of hstepm from age to agelim    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
      nstepm is the number of stepm from age to agelin.    free_vector(pp,1,nlstate);
      Look at hpijx to understand the reason of that which relies in memory size    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      and note for a fixed period like k years */    /* End of Freq */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  }
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if  /************ Prevalence ********************/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  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)
      results. So we changed our mind and took the option of the best precision.  {  
   */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */       in each health status at the date of interview (if between dateprev1 and dateprev2).
   agelim = AGESUP;       We still use firstpass and lastpass as another selection.
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double ***freq; /* Frequencies */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double *pp, **prop;
     gp=matrix(0,nhstepm,1,nlstate);    double pos,posprop; 
     gm=matrix(0,nhstepm,1,nlstate);    double  y2; /* in fractional years */
     int iagemin, iagemax;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    iagemin= (int) agemin;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    iagemax= (int) agemax;
       }    /*pp=vector(1,nlstate);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      prop=matrix(1,nlstate,iagemin,iagemax+3); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    j=cptcoveff;
           prlim[i][i]=probs[(int)age][i][ij];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }    
      for(k1=1; k1<=j;k1++){
       for(j=1; j<= nlstate; j++){      for(i1=1; i1<=ncodemax[k1];i1++){
         for(h=0; h<=nhstepm; h++){        j1++;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for (i=1; i<=nlstate; i++)  
         }          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0.0;
           
       for(i=1; i<=npar; i++) /* Computes gradient */        for (i=1; i<=imx; i++) { /* Each individual */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          bool=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            if  (cptcovn>0) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       if (popbased==1) {                bool=0;
         for(i=1; i<=nlstate;i++)          } 
           prlim[i][i]=probs[(int)age][i][ij];          if (bool==1) { 
       }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for(j=1; j<= nlstate; j++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for(h=0; h<=nhstepm; h++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                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(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];
       for(j=1; j<= nlstate; j++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
         for(h=0; h<=nhstepm; h++){                } 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              }
         }            } /* end selection of waves */
     } /* End theta */          }
         }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        for(i=iagemin; i <= iagemax+3; i++){  
           
     for(h=0; h<=nhstepm; h++)          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       for(j=1; j<=nlstate;j++)            posprop += prop[jk][i]; 
         for(theta=1; theta <=npar; theta++)          } 
           trgradg[h][j][theta]=gradg[h][theta][j];  
           for(jk=1; jk <=nlstate ; jk++){     
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            if( i <=  iagemax){ 
     for(i=1;i<=nlstate;i++)              if(posprop>=1.e-5){ 
       for(j=1;j<=nlstate;j++)                probs[i][jk][j1]= prop[jk][i]/posprop;
         vareij[i][j][(int)age] =0.;              } 
             } 
     for(h=0;h<=nhstepm;h++){          }/* end jk */ 
       for(k=0;k<=nhstepm;k++){        }/* end i */ 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      } /* end i1 */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    } /* end k1 */
         for(i=1;i<=nlstate;i++)    
           for(j=1;j<=nlstate;j++)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    /*free_vector(pp,1,nlstate);*/
       }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     }  }  /* End of prevalence */
   
     fprintf(ficresvij,"%.0f ",age );  /************* Waves Concatenation ***************/
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  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)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  {
       }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficresvij,"\n");       Death is a valid wave (if date is known).
     free_matrix(gp,0,nhstepm,1,nlstate);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     free_matrix(gm,0,nhstepm,1,nlstate);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);       and mw[mi+1][i]. dh depends on stepm.
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);       */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */    int i, mi, m;
      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   free_vector(xp,1,npar);       double sum=0., jmean=0.;*/
   free_matrix(doldm,1,nlstate,1,npar);    int first;
   free_matrix(dnewm,1,nlstate,1,nlstate);    int j, k=0,jk, ju, jl;
     double sum=0.;
 }    first=0;
     jmin=1e+5;
 /************ Variance of prevlim ******************/    jmax=-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)    jmean=0.;
 {    for(i=1; i<=imx; i++){
   /* Variance of prevalence limit */      mi=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      m=firstpass;
   double **newm;      while(s[m][i] <= nlstate){
   double **dnewm,**doldm;        if(s[m][i]>=1)
   int i, j, nhstepm, hstepm;          mw[++mi][i]=m;
   int k, cptcode;        if(m >=lastpass)
   double *xp;          break;
   double *gp, *gm;        else
   double **gradg, **trgradg;          m++;
   double age,agelim;      }/* end while */
   int theta;      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        /* if(mi==0)  never been interviewed correctly before death */
   fprintf(ficresvpl,"# Age");           /* Only death is a correct wave */
   for(i=1; i<=nlstate;i++)        mw[mi][i]=m;
       fprintf(ficresvpl," %1d-%1d",i,i);      }
   fprintf(ficresvpl,"\n");  
       wav[i]=mi;
   xp=vector(1,npar);      if(mi==0){
   dnewm=matrix(1,nlstate,1,npar);        if(first==0){
   doldm=matrix(1,nlstate,1,nlstate);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
            first=1;
   hstepm=1*YEARM; /* Every year of age */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        if(first==1){
   agelim = AGESUP;          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* end mi==0 */
     if (stepm >= YEARM) hstepm=1;    }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);    for(i=1; i<=imx; i++){
     gp=vector(1,nlstate);      for(mi=1; mi<wav[i];mi++){
     gm=vector(1,nlstate);        if (stepm <=0)
           dh[mi][i]=1;
     for(theta=1; theta <=npar; theta++){        else{
       for(i=1; i<=npar; i++){ /* Computes gradient */          if (s[mw[mi+1][i]][i] > nlstate) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (agedc[i] < 2*AGESUP) {
       }            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            if(j==0) j=1;  /* Survives at least one month after exam */
       for(i=1;i<=nlstate;i++)            k=k+1;
         gp[i] = prlim[i][i];            if (j >= jmax) jmax=j;
                if (j <= jmin) jmin=j;
       for(i=1; i<=npar; i++) /* Computes gradient */            sum=sum+j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for(i=1;i<=nlstate;i++)            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         gm[i] = prlim[i][i];            }
           }
       for(i=1;i<=nlstate;i++)          else{
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     } /* End theta */            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
     trgradg =matrix(1,nlstate,1,npar);            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
     for(j=1; j<=nlstate;j++)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(theta=1; theta <=npar; theta++)            /*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]);*/
         trgradg[j][theta]=gradg[theta][j];            sum=sum+j;
           }
     for(i=1;i<=nlstate;i++)          jk= j/stepm;
       varpl[i][(int)age] =0.;          jl= j -jk*stepm;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          ju= j -(jk+1)*stepm;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          if(mle <=1){ 
     for(i=1;i<=nlstate;i++)            if(jl==0){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              dh[mi][i]=jk;
               bh[mi][i]=0;
     fprintf(ficresvpl,"%.0f ",age );            }else{ /* We want a negative bias in order to only have interpolation ie
     for(i=1; i<=nlstate;i++)                    * at the price of an extra matrix product in likelihood */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              dh[mi][i]=jk+1;
     fprintf(ficresvpl,"\n");              bh[mi][i]=ju;
     free_vector(gp,1,nlstate);            }
     free_vector(gm,1,nlstate);          }else{
     free_matrix(gradg,1,npar,1,nlstate);            if(jl <= -ju){
     free_matrix(trgradg,1,nlstate,1,npar);              dh[mi][i]=jk;
   } /* End age */              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   free_vector(xp,1,npar);                                   */
   free_matrix(doldm,1,nlstate,1,npar);            }
   free_matrix(dnewm,1,nlstate,1,nlstate);            else{
               dh[mi][i]=jk+1;
 }              bh[mi][i]=ju;
             }
 /************ Variance of one-step probabilities  ******************/            if(dh[mi][i]==0){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)              dh[mi][i]=1; /* At least one step */
 {              bh[mi][i]=ju; /* At least one step */
   int i, j;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   int k=0, cptcode;            }
   double **dnewm,**doldm;          }
   double *xp;        } /* end if mle */
   double *gp, *gm;      } /* end wave */
   double **gradg, **trgradg;    }
   double age,agelim, cov[NCOVMAX];    jmean=sum/k;
   int theta;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   char fileresprob[FILENAMELENGTH];    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);  /*********** Tricode ****************************/
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  void tricode(int *Tvar, int **nbcode, int imx)
     printf("Problem with resultfile: %s\n", fileresprob);  {
   }    
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    int Ndum[20],ij=1, k, j, i, maxncov=19;
      int cptcode=0;
     cptcoveff=0; 
   xp=vector(1,npar);   
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    for (k=1; k<=7; k++) ncodemax[k]=0;
    
   cov[1]=1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   for (age=bage; age<=fage; age ++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     cov[2]=age;                                 modality*/ 
     gradg=matrix(1,npar,1,9);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     trgradg=matrix(1,9,1,npar);        Ndum[ij]++; /*store the modality */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                             Tvar[j]. If V=sex and male is 0 and 
     for(theta=1; theta <=npar; theta++){                                         female is 1, then  cptcode=1.*/
       for(i=1; i<=npar; i++)      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
            for (i=0; i<=cptcode; i++) {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
          }
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){      ij=1; 
         for(j=1; j<=(nlstate+ndeath);j++){      for (i=1; i<=ncodemax[j]; i++) {
            k=k+1;        for (k=0; k<= maxncov; k++) {
           gp[k]=pmmij[i][j];          if (Ndum[k] != 0) {
         }            nbcode[Tvar[j]][ij]=k; 
       }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             
       for(i=1; i<=npar; i++)            ij++;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
              if (ij > ncodemax[j]) break; 
         }  
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      } 
       k=0;    }  
       for(i=1; i<=(nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
           k=k+1;  
           gm[k]=pmmij[i][j];   for (i=1; i<=ncovmodel-2; i++) { 
         }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       }     ij=Tvar[i];
           Ndum[ij]++;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)   }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }   ij=1;
    for (i=1; i<= maxncov; i++) {
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)     if((Ndum[i]!=0) && (i<=ncovcol)){
       for(theta=1; theta <=npar; theta++)       Tvaraff[ij]=i; /*For printing */
       trgradg[j][theta]=gradg[theta][j];       ij++;
       }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);   }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);   
    cptcoveff=ij-1; /*Number of simple covariates*/
      pmij(pmmij,cov,ncovmodel,x,nlstate);  }
   
      k=0;  /*********** Health Expectancies ****************/
      for(i=1; i<=(nlstate+ndeath); i++){  
        for(j=1; j<=(nlstate+ndeath);j++){  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 )
          k=k+1;  
          gm[k]=pmmij[i][j];  {
         }    /* Health expectancies */
      }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
          double age, agelim, hf;
      /*printf("\n%d ",(int)age);    double ***p3mat,***varhe;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double **dnewm,**doldm;
            double *xp;
     double **gp, **gm;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double ***gradg, ***trgradg;
      }*/    int theta;
   
   fprintf(ficresprob,"\n%d ",(int)age);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    
   }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    for(i=1; i<=nlstate;i++)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for(j=1; j<=nlstate;j++)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficreseij,"\n");
 }  
  free_vector(xp,1,npar);    if(estepm < stepm){
 fclose(ficresprob);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
 }    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
 /******************* Printing html file ***********/     * This is mainly to measure the difference between two models: for example
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \     * if stepm=24 months pijx are given only every 2 years and by summing them
  int lastpass, int stepm, int weightopt, char model[],\     * we are calculating an estimate of the Life Expectancy assuming a linear 
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \     * progression in between and thus overestimating or underestimating according
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\     * to the curvature of the survival function. If, for the same date, we 
  char version[], int popforecast ){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   int jj1, k1, i1, cpt;     * to compare the new estimate of Life expectancy with the same linear 
   FILE *fichtm;     * hypothesis. A more precise result, taking into account a more precise
   /*char optionfilehtm[FILENAMELENGTH];*/     * curvature will be obtained if estepm is as small as stepm. */
   
   strcpy(optionfilehtm,optionfile);    /* For example we decided to compute the life expectancy with the smallest unit */
   strcat(optionfilehtm,".htm");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       nhstepm is the number of hstepm from age to agelim 
     printf("Problem with %s \n",optionfilehtm), exit(0);       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 */
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n       survival function given by stepm (the optimization length). Unfortunately it
 \n       means that if the survival funtion is printed only each two years of age and if
 Total number of observations=%d <br>\n       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n       results. So we changed our mind and took the option of the best precision.
 <hr  size=\"2\" color=\"#EC5E5E\">    */
  <ul><li>Outputs files<br>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    agelim=AGESUP;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n      /* nhstepm age range expressed in number of stepm */
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
  - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
  fprintf(fichtm,"\n      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      gp=matrix(0,nhstepm,1,nlstate*nlstate);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
  if(popforecast==1) fprintf(fichtm,"\n      /* Computed by stepm unit matrices, product of hstepm matrices, stored
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         <br>",fileres,fileres,fileres,fileres);   
  else  
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 fprintf(fichtm," <li>Graphs</li><p>");  
       /* Computing Variances of health expectancies */
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
  jj1=0;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  for(k1=1; k1<=m;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        jj1++;    
        if (cptcovn > 0) {        cptj=0;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(j=1; j<= nlstate; j++){
          for (cpt=1; cpt<=cptcoveff;cpt++)          for(i=1; i<=nlstate; i++){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            cptj=cptj+1;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
        }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
        for(cpt=1; cpt<nlstate;cpt++){        }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       
        }        for(i=1; i<=npar; i++) 
     for(cpt=1; cpt<=nlstate;cpt++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 interval) in state (%d): v%s%d%d.gif <br>        
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          cptj=0;
      }        for(j=1; j<= nlstate; j++){
      for(cpt=1; cpt<=nlstate;cpt++) {          for(i=1;i<=nlstate;i++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            cptj=cptj+1;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
      }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            }
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
 fprintf(fichtm,"\n</body>");        for(j=1; j<= nlstate*nlstate; j++)
    }          for(h=0; h<=nhstepm-1; h++){
    }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 fclose(fichtm);          }
 }       } 
      
 /******************* Gnuplot file **************/  /* End theta */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
        for(h=0; h<=nhstepm-1; h++)
   strcpy(optionfilegnuplot,optionfilefiname);        for(j=1; j<=nlstate*nlstate;j++)
   strcat(optionfilegnuplot,".gp.txt");          for(theta=1; theta <=npar; theta++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
     printf("Problem with file %s",optionfilegnuplot);       
   }  
        for(i=1;i<=nlstate*nlstate;i++)
 #ifdef windows        for(j=1;j<=nlstate*nlstate;j++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);          varhe[i][j][(int)age] =0.;
 #endif  
 m=pow(2,cptcoveff);       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  /* 1eme*/       for(h=0;h<=nhstepm-1;h++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(k=0;k<=nhstepm-1;k++){
    for (k1=1; k1<= m ; k1 ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 #ifdef windows          for(i=1;i<=nlstate*nlstate;i++)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            for(j=1;j<=nlstate*nlstate;j++)
 #endif              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 #ifdef unix        }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      }
 #endif      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 }            
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      fprintf(ficreseij,"%3.0f",age );
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      cptj=0;
      for (i=1; i<= nlstate ; i ++) {      for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          cptj++;
 }            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix      fprintf(ficreseij,"\n");
 fprintf(ficgp,"\nset ter gif small size 400,300");     
 #endif      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
    }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   /*2 eme*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   for (k1=1; k1<= m ; k1 ++) {    printf("\n");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    fprintf(ficlog,"\n");
      
     for (i=1; i<= nlstate+1 ; i ++) {    free_vector(xp,1,npar);
       k=2*i;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    /************ Variance ******************/
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  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)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  {
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* Variance of health expectancies */
       for (j=1; j<= nlstate+1 ; j ++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* double **newm;*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double **dnewm,**doldm;
 }      double **dnewmp,**doldmp;
       fprintf(ficgp,"\" t\"\" w l 0,");    int i, j, nhstepm, hstepm, h, nstepm ;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    int k, cptcode;
       for (j=1; j<= nlstate+1 ; j ++) {    double *xp;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double **gp, **gm;  /* for var eij */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***gradg, ***trgradg; /*for var eij */
 }      double **gradgp, **trgradgp; /* for var p point j */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    double *gpp, *gmp; /* for var p point j */
       else fprintf(ficgp,"\" t\"\" w l 0,");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     }    double ***p3mat;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double age,agelim, hf;
   }    double ***mobaverage;
      int theta;
   /*3eme*/    char digit[4];
     char digitp[25];
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {    char fileresprobmorprev[FILENAMELENGTH];
       k=2+nlstate*(cpt-1);  
       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);    if(popbased==1){
       for (i=1; i< nlstate ; i ++) {      if(mobilav!=0)
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        strcpy(digitp,"-populbased-mobilav-");
       }      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    else 
     }      strcpy(digitp,"-stablbased-");
    
   /* CV preval stat */    if (mobilav!=0) {
     for (k1=1; k1<= m ; k1 ++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for (cpt=1; cpt<nlstate ; cpt ++) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       k=3;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
       for (i=1; i< nlstate ; i ++)    }
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    strcpy(fileresprobmorprev,"prmorprev"); 
          sprintf(digit,"%-d",ij);
       l=3+(nlstate+ndeath)*cpt;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for (i=1; i< nlstate ; i ++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         l=3+(nlstate+ndeath)*cpt;    strcat(fileresprobmorprev,fileres);
         fprintf(ficgp,"+$%d",l+i+1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   }      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   /* proba elementaires */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(i=1,jk=1; i <=nlstate; i++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficresprobmorprev," p.%-d SE",j);
       if (k != i) {      for(i=1; i<=nlstate;i++)
         for(j=1; j <=ncovmodel; j++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
            }  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficresprobmorprev,"\n");
           jk++;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           fprintf(ficgp,"\n");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      exit(0);
     }    }
     }    else{
       fprintf(ficgp,"\n# Routine varevsij");
     for(jk=1; jk <=m; jk++) {    }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    i=1;      printf("Problem with html file: %s\n", optionfilehtm);
    for(k2=1; k2<=nlstate; k2++) {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      k3=i;      exit(0);
      for(k=1; k<=(nlstate+ndeath); k++) {    }
        if (k != k2){    else{
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      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");
 ij=1;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    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");
           else    for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
           fprintf(ficgp,")/(1");    fprintf(ficresvij,"\n");
          
         for(k1=1; k1 <=nlstate; k1++){      xp=vector(1,npar);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    dnewm=matrix(1,nlstate,1,npar);
 ij=1;    doldm=matrix(1,nlstate,1,nlstate);
           for(j=3; j <=ncovmodel; j++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           }    gpp=vector(nlstate+1,nlstate+ndeath);
           else    gmp=vector(nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           }    
           fprintf(ficgp,")");    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    else  hstepm=estepm;   
         i=i+ncovmodel;    /* For example we decided to compute the life expectancy with the smallest unit */
        }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      }       nhstepm is the number of hstepm from age to agelim 
    }       nstepm is the number of stepm from age to agelin. 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);       Look at hpijx to understand the reason of that which relies in memory size
    }       and note for a fixed period like k years */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficgp);       survival function given by stepm (the optimization length). Unfortunately it
 }  /* end gnuplot */       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
 /*************** Moving average **************/    */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   int i, cpt, cptcod;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for (i=1; i<=nlstate;i++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           mobaverage[(int)agedeb][i][cptcod]=0.;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      gm=matrix(0,nhstepm,1,nlstate);
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){      for(theta=1; theta <=npar; theta++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
            if (popbased==1) {
 }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
 /************** Forecasting ******************/          }else{ /* mobilav */ 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          }
   int *popage;        }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    
   double *popeffectif,*popcount;        for(j=1; j<= nlstate; j++){
   double ***p3mat;          for(h=0; h<=nhstepm; h++){
   char fileresf[FILENAMELENGTH];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  agelim=AGESUP;          }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        }
         /* This for computing probability of death (h=1 means
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
   strcpy(fileresf,"f");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcat(fileresf,fileres);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   if((ficresf=fopen(fileresf,"w"))==NULL) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     printf("Problem with forecast resultfile: %s\n", fileresf);        }    
   }        /* end probability of death */
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (mobilav==1) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     movingaverage(agedeb, fage, ageminpar, mobaverage);        if (popbased==1) {
   }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;              prlim[i][i]=probs[(int)age][i][ij];
   if (stepm<=12) stepsize=1;          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   agelim=AGESUP;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   hstepm=1;        }
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);        for(j=1; j<= nlstate; j++){
   anprojmean=yp;          for(h=0; h<=nhstepm; h++){
   yp2=modf((yp1*12),&yp);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   mprojmean=yp;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   yp1=modf((yp2*30.5),&yp);          }
   jprojmean=yp;        }
   if(jprojmean==0) jprojmean=1;        /* This for computing probability of death (h=1 means
   if(mprojmean==0) jprojmean=1;           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for(cptcov=1;cptcov<=i2;cptcov++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       k=k+1;        }    
       fprintf(ficresf,"\n#******");        /* end probability of death */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<= nlstate; j++) /* vareij */
       }          for(h=0; h<=nhstepm; h++){
       fprintf(ficresf,"******\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       fprintf(ficresf,"# StartingAge FinalAge");          }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
              for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        }
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        } /* End theta */
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;      for(h=0; h<=nhstepm; h++) /* veij */
                  for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(theta=1; theta <=npar; theta++)
           oldm=oldms;savm=savms;            trgradg[h][j][theta]=gradg[h][theta][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
              for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           for (h=0; h<=nhstepm; h++){        for(theta=1; theta <=npar; theta++)
             if (h==(int) (calagedate+YEARM*cpt)) {          trgradgp[j][theta]=gradgp[theta][j];
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               kk1=0.;kk2=0;      for(i=1;i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                      for(j=1;j<=nlstate;j++)
                 if (mobilav==1)          vareij[i][j][(int)age] =0.;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {      for(h=0;h<=nhstepm;h++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(k=0;k<=nhstepm;k++){
                 }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
               }          for(i=1;i<=nlstate;i++)
               if (h==(int)(calagedate+12*cpt)){            for(j=1;j<=nlstate;j++)
                 fprintf(ficresf," %.3f", kk1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                                }
               }      }
             }    
           }      /* pptj */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
              /* end ppptj */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   fclose(ficresf);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 }   
 /************** Forecasting ******************/      if (popbased==1) {
 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){        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            prlim[i][i]=probs[(int)age][i][ij];
   int *popage;        }else{ /* mobilav */ 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(i=1; i<=nlstate;i++)
   double *popeffectif,*popcount;            prlim[i][i]=mobaverage[(int)age][i][ij];
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];      }
                
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* This for computing probability of death (h=1 means
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   agelim=AGESUP;         as a weighted average of prlim.
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
   strcpy(filerespop,"pop");      /* end probability of death */
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     printf("Problem with forecast resultfile: %s\n", filerespop);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        }
       } 
   if (mobilav==1) {      fprintf(ficresprobmorprev,"\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficresvij,"%.0f ",age );
   }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   if (stepm<=12) stepsize=1;        }
        fprintf(ficresvij,"\n");
   agelim=AGESUP;      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   hstepm=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   hstepm=hstepm/stepm;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (popforecast==1) {    } /* End age */
     if((ficpop=fopen(popfile,"r"))==NULL) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
       printf("Problem with population file : %s\n",popfile);exit(0);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     popage=ivector(0,AGESUP);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     popeffectif=vector(0,AGESUP);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     popcount=vector(0,AGESUP);    /* 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)\";");
     i=1;    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  /*   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); */
     imx=i;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    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);
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /*  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);
       k=k+1;  */
       fprintf(ficrespop,"\n#******");    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xp,1,npar);
       }    free_matrix(doldm,1,nlstate,1,nlstate);
       fprintf(ficrespop,"******\n");    free_matrix(dnewm,1,nlstate,1,npar);
       fprintf(ficrespop,"# Age");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (cpt=0; cpt<=0;cpt++) {    fclose(ficresprobmorprev);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fclose(ficgp);
            fclose(fichtm);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  }  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /************ Variance of prevlim ******************/
            void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    /* Variance of prevalence limit */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
            double **newm;
           for (h=0; h<=nhstepm; h++){    double **dnewm,**doldm;
             if (h==(int) (calagedate+YEARM*cpt)) {    int i, j, nhstepm, hstepm;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int k, cptcode;
             }    double *xp;
             for(j=1; j<=nlstate+ndeath;j++) {    double *gp, *gm;
               kk1=0.;kk2=0;    double **gradg, **trgradg;
               for(i=1; i<=nlstate;i++) {                  double age,agelim;
                 if (mobilav==1)    int theta;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     
                 else {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fprintf(ficresvpl,"# Age");
                 }    for(i=1; i<=nlstate;i++)
               }        fprintf(ficresvpl," %1d-%1d",i,i);
               if (h==(int)(calagedate+12*cpt)){    fprintf(ficresvpl,"\n");
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);    xp=vector(1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    dnewm=matrix(1,nlstate,1,npar);
               }    doldm=matrix(1,nlstate,1,nlstate);
             }    
             for(i=1; i<=nlstate;i++){    hstepm=1*YEARM; /* Every year of age */
               kk1=0.;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                 for(j=1; j<=nlstate;j++){    agelim = AGESUP;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      if (stepm >= YEARM) hstepm=1;
             }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      gp=vector(1,nlstate);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      gm=vector(1,nlstate);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(theta=1; theta <=npar; theta++){
         }        for(i=1; i<=npar; i++){ /* Computes gradient */
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   /******/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          gp[i] = prlim[i][i];
         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<=npar; i++) /* Computes gradient */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           nhstepm = nhstepm/hstepm;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                  for(i=1;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          gm[i] = prlim[i][i];
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=1;i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
             if (h==(int) (calagedate+YEARM*cpt)) {      } /* End theta */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }      trgradg =matrix(1,nlstate,1,npar);
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;      for(j=1; j<=nlstate;j++)
               for(i=1; i<=nlstate;i++) {                      for(theta=1; theta <=npar; theta++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              trgradg[j][theta]=gradg[theta][j];
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      for(i=1;i<=nlstate;i++)
             }        varpl[i][(int)age] =0.;
           }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         }      for(i=1;i<=nlstate;i++)
       }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    }  
   }      fprintf(ficresvpl,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   if (popforecast==1) {      free_vector(gp,1,nlstate);
     free_ivector(popage,0,AGESUP);      free_vector(gm,1,nlstate);
     free_vector(popeffectif,0,AGESUP);      free_matrix(gradg,1,npar,1,nlstate);
     free_vector(popcount,0,AGESUP);      free_matrix(trgradg,1,nlstate,1,npar);
   }    } /* End age */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_vector(xp,1,npar);
   fclose(ficrespop);    free_matrix(doldm,1,nlstate,1,npar);
 }    free_matrix(dnewm,1,nlstate,1,nlstate);
   
 /***********************************************/  }
 /**************** Main Program *****************/  
 /***********************************************/  /************ 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)
 int main(int argc, char *argv[])  {
 {    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int k=0,l, cptcode;
   double agedeb, agefin,hf;    int first=1, first1;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
   double fret;    double *xp;
   double **xi,tmp,delta;    double *gp, *gm;
     double **gradg, **trgradg;
   double dum; /* Dummy variable */    double **mu;
   double ***p3mat;    double age,agelim, cov[NCOVMAX];
   int *indx;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   char line[MAXLINE], linepar[MAXLINE];    int theta;
   char title[MAXLINE];    char fileresprob[FILENAMELENGTH];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    char fileresprobcov[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    char fileresprobcor[FILENAMELENGTH];
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    double ***varpij;
   
   char filerest[FILENAMELENGTH];    strcpy(fileresprob,"prob"); 
   char fileregp[FILENAMELENGTH];    strcat(fileresprob,fileres);
   char popfile[FILENAMELENGTH];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      printf("Problem with resultfile: %s\n", fileresprob);
   int firstobs=1, lastobs=10;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   int sdeb, sfin; /* Status at beginning and end */    }
   int c,  h , cpt,l;    strcpy(fileresprobcov,"probcov"); 
   int ju,jl, mi;    strcat(fileresprobcov,fileres);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      printf("Problem with resultfile: %s\n", fileresprobcov);
   int mobilav=0,popforecast=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   int hstepm, nhstepm;    }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
   double bage, fage, age, agelim, agebase;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   double ftolpl=FTOL;      printf("Problem with resultfile: %s\n", fileresprobcor);
   double **prlim;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   double *severity;    }
   double ***param; /* Matrix of parameters */    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   double  *p;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   double **matcov; /* Matrix of covariance */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double ***delti3; /* Scale */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double *delti; /* Scale */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double ***eij, ***vareij;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double **varpl; /* Variances of prevalence limits by age */    
   double *epj, vepp;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   double kk1, kk2;    fprintf(ficresprob,"# Age");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";    fprintf(ficresprobcov,"# Age");
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   
     for(i=1; i<=nlstate;i++)
   char z[1]="c", occ;      for(j=1; j<=(nlstate+ndeath);j++){
 #include <sys/time.h>        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 #include <time.h>        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
   /* long total_usecs;   /* fprintf(ficresprob,"\n");
   struct timeval start_time, end_time;    fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */   */
   getcwd(pathcd, size);   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   printf("\n%s",version);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   if(argc <=1){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     printf("\nEnter the parameter file name: ");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     scanf("%s",pathtot);    first=1;
   }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   else{      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     strcpy(pathtot,argv[1]);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      exit(0);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    }
   /*cygwin_split_path(pathtot,path,optionfile);    else{
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      fprintf(ficgp,"\n# Routine varprob");
   /* cutv(path,optionfile,pathtot,'\\');*/    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      printf("Problem with html file: %s\n", optionfilehtm);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   chdir(path);      exit(0);
   replace(pathc,path);    }
     else{
 /*-------- arguments in the command line --------*/      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   strcat(fileres,".txt");    /* Other files have txt extension */      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   /*---------arguments file --------*/  
     }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    cov[1]=1;
     goto end;    tj=cptcoveff;
   }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   strcpy(filereso,"o");    for(t=1; t<=tj;t++){
   strcat(filereso,fileres);      for(i1=1; i1<=ncodemax[t];i1++){ 
   if((ficparo=fopen(filereso,"w"))==NULL) {        j1++;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        if  (cptcovn>0) {
   }          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Reads comments: lines beginning with '#' */          fprintf(ficresprob, "**********\n#\n");
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "\n#********** Variable "); 
     ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov, "**********\n#\n");
     puts(line);          
     fputs(line,ficparo);          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   ungetc(c,ficpar);          fprintf(ficgp, "**********\n#\n");
           
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          
   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(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor, "\n#********** Variable ");    
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficresprobcor, "**********\n#");    
   }        }
   ungetc(c,ficpar);        
          for (age=bage; age<=fage; age ++){ 
              cov[2]=age;
   covar=matrix(0,NCOVMAX,1,n);          for (k=1; k<=cptcovn;k++) {
   cptcovn=0;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   ncovmodel=2+cptcovn;          for (k=1; k<=cptcovprod;k++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            
   /* Read guess parameters */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   /* Reads comments: lines beginning with '#' */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){          gp=vector(1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);      
     puts(line);          for(theta=1; theta <=npar; theta++){
     fputs(line,ficparo);            for(i=1; i<=npar; i++)
   }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   ungetc(c,ficpar);            
              pmij(pmmij,cov,ncovmodel,xp,nlstate);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            
     for(i=1; i <=nlstate; i++)            k=0;
     for(j=1; j <=nlstate+ndeath-1; j++){            for(i=1; i<= (nlstate); i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"%1d%1d",i1,j1);                k=k+1;
       printf("%1d%1d",i,j);                gp[k]=pmmij[i][j];
       for(k=1; k<=ncovmodel;k++){              }
         fscanf(ficpar," %lf",&param[i][j][k]);            }
         printf(" %lf",param[i][j][k]);            
         fprintf(ficparo," %lf",param[i][j][k]);            for(i=1; i<=npar; i++)
       }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       fscanf(ficpar,"\n");      
       printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficparo,"\n");            k=0;
     }            for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                k=k+1;
                 gm[k]=pmmij[i][j];
   p=param[1][1];              }
              }
   /* Reads comments: lines beginning with '#' */       
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     ungetc(c,ficpar);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fgets(line, MAXLINE, ficpar);          }
     puts(line);  
     fputs(line,ficparo);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   }            for(theta=1; theta <=npar; theta++)
   ungetc(c,ficpar);              trgradg[j][theta]=gradg[theta][j];
           
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   for(i=1; i <=nlstate; i++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     for(j=1; j <=nlstate+ndeath-1; j++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       fscanf(ficpar,"%1d%1d",&i1,&j1);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       printf("%1d%1d",i,j);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          
         printf(" %le",delti3[i][j][k]);          k=0;
         fprintf(ficparo," %le",delti3[i][j][k]);          for(i=1; i<=(nlstate); i++){
       }            for(j=1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar,"\n");              k=k+1;
       printf("\n");              mu[k][(int) age]=pmmij[i][j];
       fprintf(ficparo,"\n");            }
     }          }
   }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   delti=delti3[1][1];            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){          /*printf("\n%d ",(int)age);
     ungetc(c,ficpar);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fgets(line, MAXLINE, ficpar);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     puts(line);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fputs(line,ficparo);            }*/
   }  
   ungetc(c,ficpar);          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
   matcov=matrix(1,npar,1,npar);          fprintf(ficresprobcor,"\n%d ",(int)age);
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     printf("%s",str);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     fprintf(ficparo,"%s",str);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     for(j=1; j <=i; j++){            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       fscanf(ficpar," %le",&matcov[i][j]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       printf(" %.5le",matcov[i][j]);          }
       fprintf(ficparo," %.5le",matcov[i][j]);          i=0;
     }          for (k=1; k<=(nlstate);k++){
     fscanf(ficpar,"\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
     printf("\n");              i=i++;
     fprintf(ficparo,"\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   for(i=1; i <=npar; i++)              for (j=1; j<=i;j++){
     for(j=i+1;j<=npar;j++)                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       matcov[i][j]=matcov[j][i];                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                  }
   printf("\n");            }
           }/* end of loop for state */
         } /* end of loop for age */
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */        /* Confidence intervalle of pij  */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        /*
      strcat(rfileres,".");    /* */          fprintf(ficgp,"\nset noparametric;unset label");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     if((ficres =fopen(rfileres,"w"))==NULL) {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     fprintf(ficres,"#%s\n",version);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
              fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     /*-------- data file ----------*/        */
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     }        first1=1;
         for (k2=1; k2<=(nlstate);k2++){
     n= lastobs;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     severity = vector(1,maxwav);            if(l2==k2) continue;
     outcome=imatrix(1,maxwav+1,1,n);            j=(k2-1)*(nlstate+ndeath)+l2;
     num=ivector(1,n);            for (k1=1; k1<=(nlstate);k1++){
     moisnais=vector(1,n);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     annais=vector(1,n);                if(l1==k1) continue;
     moisdc=vector(1,n);                i=(k1-1)*(nlstate+ndeath)+l1;
     andc=vector(1,n);                if(i<=j) continue;
     agedc=vector(1,n);                for (age=bage; age<=fage; age ++){ 
     cod=ivector(1,n);                  if ((int)age %5==0){
     weight=vector(1,n);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     mint=matrix(1,maxwav,1,n);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     anint=matrix(1,maxwav,1,n);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     s=imatrix(1,maxwav+1,1,n);                    mu2=mu[j][(int) age]/stepm*YEARM;
     adl=imatrix(1,maxwav+1,1,n);                        c12=cv12/sqrt(v1*v2);
     tab=ivector(1,NCOVMAX);                    /* Computing eigen value of matrix of covariance */
     ncodemax=ivector(1,8);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     i=1;                    /* Eigen vectors */
     while (fgets(line, MAXLINE, fic) != NULL)    {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       if ((i >= firstobs) && (i <=lastobs)) {                    /*v21=sqrt(1.-v11*v11); *//* error */
                            v21=(lc1-v1)/cv12*v11;
         for (j=maxwav;j>=1;j--){                    v12=-v21;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                    v22=v11;
           strcpy(line,stra);                    tnalp=v21/v11;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    if(first1==1){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      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);
                            }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    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);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                    if(first==1){
                       first=0;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\nset parametric;unset label");
         for (j=ncovcol;j>=1;j--){                      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);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         }                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
         num[i]=atol(stra);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                              fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           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;}*/                      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);
         i=i+1;                      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),\
     }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     /* printf("ii=%d", ij);                    }else{
        scanf("%d",i);*/                      first=0;
   imx=i-1; /* Number of individuals */                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   /* for (i=1; i<=imx; i++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     }*/                    }/* if first */
                    } /* age mod 5 */
   /* for (i=1; i<=imx; i++){                } /* end loop age */
      if (s[4][i]==9)  s[4][i]=-1;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
      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]));}                first=1;
   */              } /*l12 */
              } /* k12 */
   /* Calculation of the number of parameter from char model*/          } /*l1 */
   Tvar=ivector(1,15);        }/* k1 */
   Tprod=ivector(1,15);      } /* loop covariates */
   Tvaraff=ivector(1,15);    }
   Tvard=imatrix(1,15,1,2);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   Tage=ivector(1,15);          free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        free_vector(xp,1,npar);
   if (strlen(model) >1){    fclose(ficresprob);
     j=0, j1=0, k1=1, k2=1;    fclose(ficresprobcov);
     j=nbocc(model,'+');    fclose(ficresprobcor);
     j1=nbocc(model,'*');    fclose(ficgp);
     cptcovn=j+1;    fclose(fichtm);
     cptcovprod=j1;  }
      
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  /******************* Printing html file ***********/
       printf("Error. Non available option model=%s ",model);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       goto end;                    int lastpass, int stepm, int weightopt, char model[],\
     }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                        int popforecast, int estepm ,\
     for(i=(j+1); i>=1;i--){                    double jprev1, double mprev1,double anprev1, \
       cutv(stra,strb,modelsav,'+');                    double jprev2, double mprev2,double anprev2){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    int jj1, k1, i1, cpt;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    /*char optionfilehtm[FILENAMELENGTH];*/
       /*scanf("%d",i);*/    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       if (strchr(strb,'*')) {      printf("Problem with %s \n",optionfilehtm), exit(0);
         cutv(strd,strc,strb,'*');      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
         if (strcmp(strc,"age")==0) {    }
           cptcovprod--;  
           cutv(strb,stre,strd,'V');     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
           Tvar[i]=atoi(stre);   - 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
           cptcovage++;   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
             Tage[cptcovage]=i;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
             /*printf("stre=%s ", stre);*/   - Life expectancies by age and initial health status (estepm=%2d months): 
         }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
         else if (strcmp(strd,"age")==0) {    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
           cptcovprod--;  
           cutv(strb,stre,strc,'V');  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           Tvar[i]=atoi(stre);  
           cptcovage++;   m=cptcoveff;
           Tage[cptcovage]=i;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         }  
         else {   jj1=0;
           cutv(strb,stre,strc,'V');   for(k1=1; k1<=m;k1++){
           Tvar[i]=ncovcol+k1;     for(i1=1; i1<=ncodemax[k1];i1++){
           cutv(strb,strc,strd,'V');       jj1++;
           Tprod[k1]=i;       if (cptcovn > 0) {
           Tvard[k1][1]=atoi(strc);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           Tvard[k1][2]=atoi(stre);         for (cpt=1; cpt<=cptcoveff;cpt++) 
           Tvar[cptcovn+k2]=Tvard[k1][1];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           for (k=1; k<=lastobs;k++)       }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       /* Pij */
           k1++;       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>
           k2=k2+2;  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
         }       /* Quasi-incidences */
       }       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>
       else {  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/         /* Stable prevalence in each health state */
        /*  scanf("%d",i);*/         for(cpt=1; cpt<nlstate;cpt++){
       cutv(strd,strc,strb,'V');           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
       Tvar[i]=atoi(strc);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
       }         }
       strcpy(modelsav,stra);         for(cpt=1; cpt<=nlstate;cpt++) {
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
         scanf("%d",i);*/  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     }       }
 }       fprintf(fichtm,"\n<br>- Total life expectancy by age and
    health expectancies in states (1) and (2): e%s%d.png<br>
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   printf("cptcovprod=%d ", cptcovprod);     } /* end i1 */
   scanf("%d ",i);*/   }/* End k1 */
     fclose(fic);   fprintf(fichtm,"</ul>");
   
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       for(i=1;i<=n;i++) weight[i]=1.0;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     }   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     /*-calculation of age at interview from date of interview and age at death -*/   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     agev=matrix(1,maxwav,1,imx);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     for (i=1; i<=imx; i++) {   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
       for(m=2; (m<= maxwav); m++) {   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;   if(popforecast==1) fprintf(fichtm,"\n
          s[m][i]=-1;   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
        }   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          <br>",fileres,fileres,fileres,fileres);
       }   else 
     }     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   m=cptcoveff;
       for(m=1; (m<= maxwav); m++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {   jj1=0;
             if(agedc[i]>0)   for(k1=1; k1<=m;k1++){
               if(moisdc[i]!=99 && andc[i]!=9999)     for(i1=1; i1<=ncodemax[k1];i1++){
                 agev[m][i]=agedc[i];       jj1++;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       if (cptcovn > 0) {
            else {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               if (andc[i]!=9999){         for (cpt=1; cpt<=cptcoveff;cpt++) 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
               agev[m][i]=-1;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               }       }
             }       for(cpt=1; cpt<=nlstate;cpt++) {
           }         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
           else if(s[m][i] !=9){ /* Should no more exist */  interval) in state (%d): v%s%d%d.png <br>
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
             if(mint[m][i]==99 || anint[m][i]==9999)       }
               agev[m][i]=1;     } /* end i1 */
             else if(agev[m][i] <agemin){   }/* End k1 */
               agemin=agev[m][i];   fprintf(fichtm,"</ul>");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  fclose(fichtm);
             }  }
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];  /******************* Gnuplot file **************/
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
             /*   agev[m][i] = age[i]+2*m;*/    int ng;
           }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           else { /* =9 */      printf("Problem with file %s",optionfilegnuplot);
             agev[m][i]=1;      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
             s[m][i]=-1;    }
           }  
         }    /*#ifdef windows */
         else /*= 0 Unknown */      fprintf(ficgp,"cd \"%s\" \n",pathc);
           agev[m][i]=1;      /*#endif */
       }  m=pow(2,cptcoveff);
        
     }   /* 1eme*/
     for (i=1; i<=imx; i++)  {    for (cpt=1; cpt<= nlstate ; cpt ++) {
       for(m=1; (m<= maxwav); m++){     for (k1=1; k1<= m ; k1 ++) {
         if (s[m][i] > (nlstate+ndeath)) {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           printf("Error: Wrong value in nlstate or ndeath\n");         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);
           goto end;  
         }       for (i=1; i<= nlstate ; i ++) {
       }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
     free_vector(severity,1,maxwav);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     free_imatrix(outcome,1,maxwav+1,1,n);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_vector(moisnais,1,n);       } 
     free_vector(annais,1,n);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     /* free_matrix(mint,1,maxwav,1,n);       for (i=1; i<= nlstate ; i ++) {
        free_matrix(anint,1,maxwav,1,n);*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     free_vector(moisdc,1,n);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_vector(andc,1,n);       }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         }
     wav=ivector(1,imx);    }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    /*2 eme*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    
        for (k1=1; k1<= m ; k1 ++) { 
     /* Concatenates waves */      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
       Tcode=ivector(1,100);        k=2*i;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       ncodemax[1]=1;        for (j=1; j<= nlstate+1 ; j ++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                else fprintf(ficgp," \%%*lf (\%%*lf)");
    codtab=imatrix(1,100,1,10);        }   
    h=0;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
    m=pow(2,cptcoveff);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
          fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
    for(k=1;k<=cptcoveff; k++){        for (j=1; j<= nlstate+1 ; j ++) {
      for(i=1; i <=(m/pow(2,k));i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        for(j=1; j <= ncodemax[k]; j++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        }   
            h++;        fprintf(ficgp,"\" t\"\" w l 0,");
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        for (j=1; j<= nlstate+1 ; j ++) {
          }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        }          else fprintf(ficgp," \%%*lf (\%%*lf)");
      }        }   
    }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        else fprintf(ficgp,"\" t\"\" w l 0,");
       codtab[1][2]=1;codtab[2][2]=2; */      }
    /* for(i=1; i <=m ;i++){    }
       for(k=1; k <=cptcovn; k++){    
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    /*3eme*/
       }    
       printf("\n");    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<= nlstate ; cpt ++) {
       scanf("%d",i);*/        k=2+nlstate*(2*cpt-2);
            fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    /* Calculates basic frequencies. Computes observed prevalence at single age        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
        and prints on file fileres'p'. */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     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 (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);
     /* 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){    
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    /* CV preval stat */
     }    for (k1=1; k1<= m ; k1 ++) { 
          for (cpt=1; cpt<nlstate ; cpt ++) {
     /*--------- results files --------------*/        k=3;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);        fprintf(ficgp,"\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);
         
    jk=1;        for (i=1; i< nlstate ; i ++)
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          fprintf(ficgp,"+$%d",k+i+1);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
    for(i=1,jk=1; i <=nlstate; i++){        
      for(k=1; k <=(nlstate+ndeath); k++){        l=3+(nlstate+ndeath)*cpt;
        if (k != i)        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
          {        for (i=1; i< nlstate ; i ++) {
            printf("%d%d ",i,k);          l=3+(nlstate+ndeath)*cpt;
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficgp,"+$%d",l+i+1);
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
              fprintf(ficres,"%f ",p[jk]);      } 
              jk++;    }  
            }    
            printf("\n");    /* proba elementaires */
            fprintf(ficres,"\n");    for(i=1,jk=1; i <=nlstate; i++){
          }      for(k=1; k <=(nlstate+ndeath); k++){
      }        if (k != i) {
    }          for(j=1; j <=ncovmodel; j++){
  if(mle==1){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     /* Computing hessian and covariance matrix */            jk++; 
     ftolhess=ftol; /* Usually correct */            fprintf(ficgp,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);          }
  }        }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      }
     printf("# Scales (for hessian or gradient estimation)\n");     }
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         if (j!=i) {       for(jk=1; jk <=m; jk++) {
           fprintf(ficres,"%1d%1d",i,j);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
           printf("%1d%1d",i,j);         if (ng==2)
           for(k=1; k<=ncovmodel;k++){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             printf(" %.5e",delti[jk]);         else
             fprintf(ficres," %.5e",delti[jk]);           fprintf(ficgp,"\nset title \"Probability\"\n");
             jk++;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           }         i=1;
           printf("\n");         for(k2=1; k2<=nlstate; k2++) {
           fprintf(ficres,"\n");           k3=i;
         }           for(k=1; k<=(nlstate+ndeath); k++) {
       }             if (k != k2){
      }               if(ng==2)
                     fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     k=1;               else
     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");                 fprintf(ficgp," exp(p%d+p%d*x",i,i+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");               ij=1;
     for(i=1;i<=npar;i++){               for(j=3; j <=ncovmodel; j++) {
       /*  if (k>nlstate) k=1;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       i1=(i-1)/(ncovmodel*nlstate)+1;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                   ij++;
       printf("%s%d%d",alph[k],i1,tab[i]);*/                 }
       fprintf(ficres,"%3d",i);                 else
       printf("%3d",i);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       for(j=1; j<=i;j++){               }
         fprintf(ficres," %.5e",matcov[i][j]);               fprintf(ficgp,")/(1");
         printf(" %.5e",matcov[i][j]);               
       }               for(k1=1; k1 <=nlstate; k1++){   
       fprintf(ficres,"\n");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       printf("\n");                 ij=1;
       k++;                 for(j=3; j <=ncovmodel; j++){
     }                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                         fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     while((c=getc(ficpar))=='#' && c!= EOF){                     ij++;
       ungetc(c,ficpar);                   }
       fgets(line, MAXLINE, ficpar);                   else
       puts(line);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       fputs(line,ficparo);                 }
     }                 fprintf(ficgp,")");
     ungetc(c,ficpar);               }
                 fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   i=i+ncovmodel;
     if (fage <= 2) {             }
       bage = ageminpar;           } /* end k */
       fage = agemaxpar;         } /* end k2 */
     }       } /* end jk */
         } /* end ng */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");     fclose(ficgp); 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);  }  /* end gnuplot */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);  
    
     while((c=getc(ficpar))=='#' && c!= EOF){  /*************** Moving average **************/
     ungetc(c,ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     fgets(line, MAXLINE, ficpar);  
     puts(line);    int i, cpt, cptcod;
     fputs(line,ficparo);    int modcovmax =1;
   }    int mobilavrange, mob;
   ungetc(c,ficpar);    double age;
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                             a covariate has 2 modalities */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
        
   while((c=getc(ficpar))=='#' && c!= EOF){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     ungetc(c,ficpar);      if(mobilav==1) mobilavrange=5; /* default */
     fgets(line, MAXLINE, ficpar);      else mobilavrange=mobilav;
     puts(line);      for (age=bage; age<=fage; age++)
     fputs(line,ficparo);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   ungetc(c,ficpar);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         we use a 5 terms etc. until the borders are no more concerned. 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   fprintf(ficparo,"pop_based=%d\n",popbased);            for (i=1; i<=nlstate;i++){
   fprintf(ficres,"pop_based=%d\n",popbased);              for (cptcod=1;cptcod<=modcovmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   while((c=getc(ficpar))=='#' && c!= EOF){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     ungetc(c,ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     fgets(line, MAXLINE, ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     puts(line);                }
     fputs(line,ficparo);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   }            }
   ungetc(c,ficpar);          }
         }/* end age */
   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);      }/* end mob */
 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);    }else return -1;
 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);    return 0;
   }/* End movingaverage */
   
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************** Forecasting ******************/
     fgets(line, MAXLINE, ficpar);  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){
     puts(line);    /* proj1, year, month, day of starting projection 
     fputs(line,ficparo);       agemin, agemax range of age
   }       dateprev1 dateprev2 range of dates during which prevalence is computed
   ungetc(c,ficpar);       anproj2 year of en of projection (same day and month as proj1).
     */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    int *popage;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double *popeffectif,*popcount;
     double ***p3mat;
 /*------------ gnuplot -------------*/    double ***mobaverage;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    char fileresf[FILENAMELENGTH];
    
 /*------------ free_vector  -------------*/    agelim=AGESUP;
  chdir(path);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
  free_ivector(wav,1,imx);    strcpy(fileresf,"f"); 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    strcat(fileresf,fileres);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      if((ficresf=fopen(fileresf,"w"))==NULL) {
  free_ivector(num,1,n);      printf("Problem with forecast resultfile: %s\n", fileresf);
  free_vector(agedc,1,n);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    }
  fclose(ficparo);    printf("Computing forecasting: result on file '%s' \n", fileresf);
  fclose(ficres);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
 /*--------- index.htm --------*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   /*--------------- Prevalence limit --------------*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
   strcpy(filerespl,"pl");      }
   strcat(filerespl,fileres);    }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   }    if (stepm<=12) stepsize=1;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if(estepm < stepm){
   fprintf(ficrespl,"#Prevalence limit\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
   fprintf(ficrespl,"#Age ");    }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    else  hstepm=estepm;   
   fprintf(ficrespl,"\n");  
      hstepm=hstepm/stepm; 
   prlim=matrix(1,nlstate,1,nlstate);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                                 fractional in yp1 */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    anprojmean=yp;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    yp2=modf((yp1*12),&yp);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    mprojmean=yp;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    yp1=modf((yp2*30.5),&yp);
   k=0;    jprojmean=yp;
   agebase=ageminpar;    if(jprojmean==0) jprojmean=1;
   agelim=agemaxpar;    if(mprojmean==0) jprojmean=1;
   ftolpl=1.e-10;  
   i1=cptcoveff;    i1=cptcoveff;
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
     
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
         k=k+1;    fprintf(ficresf,"#****** Routine prevforecast **\n");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
         for(j=1;j<=cptcoveff;j++)      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k=k+1;
         fprintf(ficrespl,"******\n");        fprintf(ficresf,"\n#******");
                for(j=1;j<=cptcoveff;j++) {
         for (age=agebase; age<=agelim; age++){          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]]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        }
           fprintf(ficrespl,"%.0f",age );        fprintf(ficresf,"******\n");
           for(i=1; i<=nlstate;i++)        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
           fprintf(ficrespl," %.5f", prlim[i][i]);        for(j=1; j<=nlstate+ndeath;j++){ 
           fprintf(ficrespl,"\n");          for(i=1; i<=nlstate;i++)              
         }            fprintf(ficresf," p%d%d",i,j);
       }          fprintf(ficresf," p.%d",j);
     }        }
   fclose(ficrespl);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
   /*------------- h Pij x at various ages ------------*/          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            nhstepm = nhstepm/hstepm; 
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing pij: result on file '%s' \n", filerespij);            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
   stepsize=(int) (stepm+YEARM-1)/YEARM;          
   /*if (stepm<=24) stepsize=2;*/            for (h=0; h<=nhstepm; h++){
               if (h==(int) (YEARM*yearp)) {
   agelim=AGESUP;                fprintf(ficresf,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */                for(j=1;j<=cptcoveff;j++) 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                  fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   k=0;              } 
   for(cptcov=1;cptcov<=i1;cptcov++){              for(j=1; j<=nlstate+ndeath;j++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                ppij=0.;
       k=k+1;                for(i=1; i<=nlstate;i++) {
         fprintf(ficrespij,"\n#****** ");                  if (mobilav==1) 
         for(j=1;j<=cptcoveff;j++)                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  else {
         fprintf(ficrespij,"******\n");                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                          }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                  if (h==(int)(YEARM*yearp))
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if (h==(int)(YEARM*yearp)){
           oldm=oldms;savm=savms;                  fprintf(ficresf," %.3f", ppij);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  }
           fprintf(ficrespij,"# Age");              }
           for(i=1; i<=nlstate;i++)            }
             for(j=1; j<=nlstate+ndeath;j++)            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               fprintf(ficrespij," %1d-%1d",i,j);          }
           fprintf(ficrespij,"\n");        }
           for (h=0; h<=nhstepm; h++){      }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    }
             for(i=1; i<=nlstate;i++)         
               for(j=1; j<=nlstate+ndeath;j++)    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    fclose(ficresf);
           }  }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");  /************** Forecasting *****not tested NB*************/
         }  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     }    
   }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
   fclose(ficrespij);    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    agelim=AGESUP;
     free_matrix(mint,1,maxwav,1,n);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    
     free_vector(weight,1,n);}    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   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);    strcpy(filerespop,"pop"); 
   }    strcat(filerespop,fileres);
      if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
   /*---------- Health expectancies and variances ------------*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
   strcpy(filerest,"t");    printf("Computing forecasting: result on file '%s' \n", filerespop);
   strcat(filerest,fileres);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   strcpy(filerese,"e");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(filerese,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
  strcpy(fileresv,"v");    
   strcat(fileresv,fileres);    agelim=AGESUP;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    hstepm=1;
   }    hstepm=hstepm/stepm; 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    
     if (popforecast==1) {
   k=0;      if((ficpop=fopen(popfile,"r"))==NULL) {
   for(cptcov=1;cptcov<=i1;cptcov++){        printf("Problem with population file : %s\n",popfile);exit(0);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       k=k+1;      } 
       fprintf(ficrest,"\n#****** ");      popage=ivector(0,AGESUP);
       for(j=1;j<=cptcoveff;j++)      popeffectif=vector(0,AGESUP);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      popcount=vector(0,AGESUP);
       fprintf(ficrest,"******\n");      
       i=1;   
       fprintf(ficreseij,"\n#****** ");      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       for(j=1;j<=cptcoveff;j++)     
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      imx=i;
       fprintf(ficreseij,"******\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fprintf(ficresvij,"******\n");        k=k+1;
         fprintf(ficrespop,"\n#******");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for(j=1;j<=cptcoveff;j++) {
       oldm=oldms;savm=savms;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficrespop,"******\n");
       oldm=oldms;savm=savms;        fprintf(ficrespop,"# Age");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
            if (popforecast==1)  fprintf(ficrespop," [Population]");
         
          for (cpt=0; cpt<=0;cpt++) { 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          
       fprintf(ficrest,"\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       epj=vector(1,nlstate+1);            nhstepm = nhstepm/hstepm; 
       for(age=bage; age <=fage ;age++){            
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (popbased==1) {            oldm=oldms;savm=savms;
           for(i=1; i<=nlstate;i++)            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             prlim[i][i]=probs[(int)age][i][k];          
         }            for (h=0; h<=nhstepm; h++){
                      if (h==(int) (calagedatem+YEARM*cpt)) {
         fprintf(ficrest," %4.0f",age);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              } 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              for(j=1; j<=nlstate+ndeath;j++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                kk1=0.;kk2=0;
           }                for(i=1; i<=nlstate;i++) {              
           epj[nlstate+1] +=epj[j];                  if (mobilav==1) 
         }                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         for(i=1, vepp=0.;i <=nlstate;i++)                  else {
           for(j=1;j <=nlstate;j++)                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
             vepp += vareij[i][j][(int)age];                  }
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));                }
         for(j=1;j <=nlstate;j++){                if (h==(int)(calagedatem+12*cpt)){
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
         }                    /*fprintf(ficrespop," %.3f", kk1);
         fprintf(ficrest,"\n");                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
       }                }
     }              }
   }              for(i=1; i<=nlstate;i++){
                 kk1=0.;
   fclose(ficreseij);                  for(j=1; j<=nlstate;j++){
   fclose(ficresvij);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   fclose(ficrest);                  }
   fclose(ficpar);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   free_vector(epj,1,nlstate+1);              }
    
   /*------- Variance limit prevalence------*/                if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   strcpy(fileresvpl,"vpl");            }
   strcat(fileresvpl,fileres);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);   
   }    /******/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   k=0;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   for(cptcov=1;cptcov<=i1;cptcov++){          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       k=k+1;            nhstepm = nhstepm/hstepm; 
       fprintf(ficresvpl,"\n#****** ");            
       for(j=1;j<=cptcoveff;j++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            oldm=oldms;savm=savms;
       fprintf(ficresvpl,"******\n");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                  for (h=0; h<=nhstepm; h++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);              if (h==(int) (calagedatem+YEARM*cpt)) {
       oldm=oldms;savm=savms;                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              } 
     }              for(j=1; j<=nlstate+ndeath;j++) {
  }                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
   fclose(ficresvpl);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
   /*---------- End : free ----------------*/                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              }
              }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
          }
       } 
   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);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      if (popforecast==1) {
   free_matrix(matcov,1,npar,1,npar);      free_ivector(popage,0,AGESUP);
   free_vector(delti,1,npar);      free_vector(popeffectif,0,AGESUP);
   free_matrix(agev,1,maxwav,1,imx);      free_vector(popcount,0,AGESUP);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if(erreur >0)    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("End of Imach with error or warning %d\n",erreur);    fclose(ficrespop);
   else   printf("End of Imach\n");  }
   /*  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);*/  /**************** Main Program *****************/
   /*printf("Total time was %d uSec.\n", total_usecs);*/  /***********************************************/
   /*------ End -----------*/  
   int main(int argc, char *argv[])
   {
  end:    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
 #ifdef windows    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   /* chdir(pathcd);*/    double agedeb, agefin,hf;
 #endif    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    double fret;
  /*system("cd ../gp37mgw");*/    double **xi,tmp,delta;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    double dum; /* Dummy variable */
  strcat(plotcmd," ");    double ***p3mat;
  strcat(plotcmd,optionfilegnuplot);    double ***mobaverage;
  system(plotcmd);    int *indx;
     char line[MAXLINE], linepar[MAXLINE];
 #ifdef windows    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   while (z[0] != 'q') {    int firstobs=1, lastobs=10;
     /* chdir(path); */    int sdeb, sfin; /* Status at beginning and end */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    int c,  h , cpt,l;
     scanf("%s",z);    int ju,jl, mi;
     if (z[0] == 'c') system("./imach");    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     else if (z[0] == 'e') system(optionfilehtm);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     else if (z[0] == 'g') system(plotcmd);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     else if (z[0] == 'q') exit(0);    int mobilav=0,popforecast=0;
   }    int hstepm, nhstepm;
 #endif    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
 }    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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  Added in v.1.74


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