Diff for /imach/src/imach.c between versions 1.38 and 1.74

version 1.38, 2002/04/03 12:19:36 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 estepm;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 int m,nb;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  FILE *ficlog;
 double **pmmij, ***probs, ***mobaverage;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double dateintmean=0;  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 double *weight;  FILE *ficreseij;
 int **s; /* Status */  char filerese[FILENAMELENGTH];
 double *agedc, **covar, idx;  FILE  *ficresvij;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char fileresvpl[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /**************** split *************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    char *s;                             /* pointer */  char filelog[FILENAMELENGTH]; /* Log file */
    int  l1, l2;                         /* length counters */  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
    l1 = strlen( path );                 /* length of path */  char popfile[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  
 #else  #define NR_END 1
    s = strrchr( path, '/' );            /* find last / */  #define FREE_ARG char*
 #endif  #define FTOL 1.0e-10
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  #define NRANSI 
       extern char       *getwd( );  #define ITMAX 200 
   
       if ( getwd( dirc ) == NULL ) {  #define TOL 2.0e-4 
 #else  
       extern char       *getcwd( );  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #endif  
          return( GLOCK_ERROR_GETCWD );  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
       strcpy( name, path );             /* we've got it */  #define TINY 1.0e-20 
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  static double maxarg1,maxarg2;
       l2 = strlen( s );                 /* length of filename */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       strcpy( name, s );                /* save file name */    
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       dirc[l1-l2] = 0;                  /* add zero */  #define rint(a) floor(a+0.5)
    }  
    l1 = strlen( dirc );                 /* length of directory */  static double sqrarg;
 #ifdef windows  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int imx; 
 #endif  int stepm;
    s = strrchr( name, '.' );            /* find last / */  /* Stepm, step in month: minimum step interpolation*/
    s++;  
    strcpy(ext,s);                       /* save extension */  int estepm;
    l1= strlen( name);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  int m,nb;
    finame[l1-l2]= 0;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    return( 0 );                         /* we're done */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double dateintmean=0;
   
 /******************************************/  double *weight;
   int **s; /* Status */
 void replace(char *s, char*t)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int i;  
   int lg=20;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   i=0;  double ftolhess; /* Tolerance for computing hessian */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  /**************** split *************************/
     (s[i] = t[i]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     if (t[i]== '\\') s[i]='/';  {
   }    char  *ss;                            /* pointer */
 }    int   l1, l2;                         /* length counters */
   
 int nbocc(char *s, char occ)    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,j=0;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int lg=20;    if ( ss == NULL ) {                   /* no directory, so use current */
   i=0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   lg=strlen(s);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(i=0; i<= lg; i++) {      /* get current working directory */
   if  (s[i] == occ ) j++;      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   return j;        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 void cutv(char *u,char *v, char*t, char occ)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   int i,lg,j,p=0;      l2 = strlen( ss );                  /* length of filename */
   i=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<=strlen(t)-1; j++) {      strcpy( name, ss );         /* save file name */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
     }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(j=0; j<p; j++) {  #ifdef windows
     (u[j] = t[j]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      u[p]='\0';    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
    for(j=0; j<= lg; j++) {    ss = strrchr( name, '.' );            /* find last / */
     if (j>=(p+1))(v[j-p-1] = t[j]);    ss++;
   }    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /********************** nrerror ********************/    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 void nrerror(char error_text[])    return( 0 );                          /* we're done */
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /******************************************/
 }  
 /*********************** vector *******************/  void replace(char *s, char*t)
 double *vector(int nl, int nh)  {
 {    int i;
   double *v;    int lg=20;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ivector *******************************/    int lg=20;
 int *ivector(long nl,long nh)    i=0;
 {    lg=strlen(s);
   int *v;    for(i=0; i<= lg; i++) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    if  (s[i] == occ ) j++;
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;    return j;
 }  }
   
 /******************free ivector **************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_ivector(int *v, long nl, long nh)  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(v+nl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************* imatrix *******************************/    i=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<=strlen(t)-1; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* allocate pointers to rows */      (u[j] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");       u[p]='\0';
   m += NR_END;  
   m -= nrl;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
      }
   /* allocate rows and set pointers to them */  }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   /* return pointer to array of pointers to rows */    exit(EXIT_FAILURE);
   return m;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    double *v;
       int **m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       long nch,ncl,nrh,nrl;    if (!v) nrerror("allocation failure in vector");
      /* free an int matrix allocated by imatrix() */    return v-nl+NR_END;
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* matrix *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /************************ivector *******************************/
   double **m;  int *ivector(long nl,long nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m -= nrl;    return v-nl+NR_END;
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_ivector(int *v, long nl, long nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /*************************free matrix ************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int **m; 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /******************* ma3x *******************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m += NR_END; 
 {    m -= nrl; 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    
     /* allocate rows and set pointers to them */ 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m += NR_END;    m[nrl] += NR_END; 
   m -= nrl;    m[nrl] -= ncl; 
     
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* return pointer to array of pointers to rows */ 
   m[nrl] -= ncl;    return m; 
   } 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /****************** free_imatrix *************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_imatrix(m,nrl,nrh,ncl,nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        int **m;
   m[nrl][ncl] += NR_END;        long nch,ncl,nrh,nrl; 
   m[nrl][ncl] -= nll;       /* free an int matrix allocated by imatrix() */ 
   for (j=ncl+1; j<=nch; j++)  { 
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   for (i=nrl+1; i<=nrh; i++) {  } 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /******************* matrix *******************************/
       m[i][j]=m[i][j-1]+nlay;  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
   return m;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /*************************free ma3x ************************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m -= nrl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /***************** f1dim *************************/    m[nrl] -= ncl;
 extern int ncom;  
 extern double *pcom,*xicom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double (*nrfunc)(double []);    return m;
      /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 double f1dim(double x)     */
 {  }
   int j;  
   double f;  /*************************free matrix ************************/
   double *xt;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
   xt=vector(1,ncom);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    free((FREE_ARG)(m+nrl-NR_END));
   f=(*nrfunc)(xt);  }
   free_vector(xt,1,ncom);  
   return f;  /******************* ma3x *******************************/
 }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
 /*****************brent *************************/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    double ***m;
 {  
   int iter;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double a,b,d,etemp;    if (!m) nrerror("allocation failure 1 in matrix()");
   double fu,fv,fw,fx;    m += NR_END;
   double ftemp;    m -= nrl;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   a=(ax < cx ? ax : cx);    m[nrl] += NR_END;
   b=(ax > cx ? ax : cx);    m[nrl] -= ncl;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl][ncl] += NR_END;
     printf(".");fflush(stdout);    m[nrl][ncl] -= nll;
 #ifdef DEBUG    for (j=ncl+1; j<=nch; j++) 
     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][j]=m[nrl][j-1]+nlay;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    
 #endif    for (i=nrl+1; i<=nrh; i++) {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       *xmin=x;      for (j=ncl+1; j<=nch; j++) 
       return fx;        m[i][j]=m[i][j-1]+nlay;
     }    }
     ftemp=fu;    return m; 
     if (fabs(e) > tol1) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       r=(x-w)*(fx-fv);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       q=(x-v)*(fx-fw);    */
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /*************************free ma3x ************************/
       q=fabs(q);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       etemp=e;  {
       e=d;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    free((FREE_ARG)(m+nrl-NR_END));
       else {  }
         d=p/q;  
         u=x+d;  /***************** f1dim *************************/
         if (u-a < tol2 || b-u < tol2)  extern int ncom; 
           d=SIGN(tol1,xm-x);  extern double *pcom,*xicom;
       }  extern double (*nrfunc)(double []); 
     } else {   
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double f1dim(double x) 
     }  { 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    int j; 
     fu=(*f)(u);    double f;
     if (fu <= fx) {    double *xt; 
       if (u >= x) a=x; else b=x;   
       SHFT(v,w,x,u)    xt=vector(1,ncom); 
         SHFT(fv,fw,fx,fu)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         } else {    f=(*nrfunc)(xt); 
           if (u < x) a=u; else b=u;    free_vector(xt,1,ncom); 
           if (fu <= fw || w == x) {    return f; 
             v=w;  } 
             w=u;  
             fv=fw;  /*****************brent *************************/
             fw=fu;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           } else if (fu <= fv || v == x || v == w) {  { 
             v=u;    int iter; 
             fv=fu;    double a,b,d,etemp;
           }    double fu,fv,fw,fx;
         }    double ftemp;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   nrerror("Too many iterations in brent");    double e=0.0; 
   *xmin=x;   
   return fx;    a=(ax < cx ? ax : cx); 
 }    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
 /****************** mnbrak ***********************/    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      xm=0.5*(a+b); 
             double (*func)(double))      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   double ulim,u,r,q, dum;      printf(".");fflush(stdout);
   double fu;      fprintf(ficlog,".");fflush(ficlog);
    #ifdef DEBUG
   *fa=(*func)(*ax);      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);
   *fb=(*func)(*bx);      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 (*fb > *fa) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     SHFT(dum,*ax,*bx,dum)  #endif
       SHFT(dum,*fb,*fa,dum)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
   *cx=(*bx)+GOLD*(*bx-*ax);        return fx; 
   *fc=(*func)(*cx);      } 
   while (*fb > *fc) {      ftemp=fu;
     r=(*bx-*ax)*(*fb-*fc);      if (fabs(e) > tol1) { 
     q=(*bx-*cx)*(*fb-*fa);        r=(x-w)*(fx-fv); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        q=(x-v)*(fx-fw); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        p=(x-v)*q-(x-w)*r; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        q=2.0*(q-r); 
     if ((*bx-u)*(u-*cx) > 0.0) {        if (q > 0.0) p = -p; 
       fu=(*func)(u);        q=fabs(q); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        etemp=e; 
       fu=(*func)(u);        e=d; 
       if (fu < *fc) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           SHFT(*fb,*fc,fu,(*func)(u))        else { 
           }          d=p/q; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {          u=x+d; 
       u=ulim;          if (u-a < tol2 || b-u < tol2) 
       fu=(*func)(u);            d=SIGN(tol1,xm-x); 
     } else {        } 
       u=(*cx)+GOLD*(*cx-*bx);      } else { 
       fu=(*func)(u);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
     SHFT(*ax,*bx,*cx,u)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       SHFT(*fa,*fb,*fc,fu)      fu=(*f)(u); 
       }      if (fu <= fx) { 
 }        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 /*************** linmin ************************/          SHFT(fv,fw,fx,fu) 
           } else { 
 int ncom;            if (u < x) a=u; else b=u; 
 double *pcom,*xicom;            if (fu <= fw || w == x) { 
 double (*nrfunc)(double []);              v=w; 
                w=u; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))              fv=fw; 
 {              fw=fu; 
   double brent(double ax, double bx, double cx,            } else if (fu <= fv || v == x || v == w) { 
                double (*f)(double), double tol, double *xmin);              v=u; 
   double f1dim(double x);              fv=fu; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,            } 
               double *fc, double (*func)(double));          } 
   int j;    } 
   double xx,xmin,bx,ax;    nrerror("Too many iterations in brent"); 
   double fx,fb,fa;    *xmin=x; 
      return fx; 
   ncom=n;  } 
   pcom=vector(1,n);  
   xicom=vector(1,n);  /****************** mnbrak ***********************/
   nrfunc=func;  
   for (j=1;j<=n;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     pcom[j]=p[j];              double (*func)(double)) 
     xicom[j]=xi[j];  { 
   }    double ulim,u,r,q, dum;
   ax=0.0;    double fu; 
   xx=1.0;   
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    *fa=(*func)(*ax); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *fb=(*func)(*bx); 
 #ifdef DEBUG    if (*fb > *fa) { 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      SHFT(dum,*ax,*bx,dum) 
 #endif        SHFT(dum,*fb,*fa,dum) 
   for (j=1;j<=n;j++) {        } 
     xi[j] *= xmin;    *cx=(*bx)+GOLD*(*bx-*ax); 
     p[j] += xi[j];    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
   free_vector(xicom,1,n);      r=(*bx-*ax)*(*fb-*fc); 
   free_vector(pcom,1,n);      q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /*************** powell ************************/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      if ((*bx-u)*(u-*cx) > 0.0) { 
             double (*func)(double []))        fu=(*func)(u); 
 {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   void linmin(double p[], double xi[], int n, double *fret,        fu=(*func)(u); 
               double (*func)(double []));        if (fu < *fc) { 
   int i,ibig,j;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double del,t,*pt,*ptt,*xit;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double fp,fptt;            } 
   double *xits;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   pt=vector(1,n);        u=ulim; 
   ptt=vector(1,n);        fu=(*func)(u); 
   xit=vector(1,n);      } else { 
   xits=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   *fret=(*func)(p);        fu=(*func)(u); 
   for (j=1;j<=n;j++) pt[j]=p[j];      } 
   for (*iter=1;;++(*iter)) {      SHFT(*ax,*bx,*cx,u) 
     fp=(*fret);        SHFT(*fa,*fb,*fc,fu) 
     ibig=0;        } 
     del=0.0;  } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /*************** linmin ************************/
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  int ncom; 
     for (i=1;i<=n;i++) {  double *pcom,*xicom;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  double (*nrfunc)(double []); 
       fptt=(*fret);   
 #ifdef DEBUG  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf("fret=%lf \n",*fret);  { 
 #endif    double brent(double ax, double bx, double cx, 
       printf("%d",i);fflush(stdout);                 double (*f)(double), double tol, double *xmin); 
       linmin(p,xit,n,fret,func);    double f1dim(double x); 
       if (fabs(fptt-(*fret)) > del) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         del=fabs(fptt-(*fret));                double *fc, double (*func)(double)); 
         ibig=i;    int j; 
       }    double xx,xmin,bx,ax; 
 #ifdef DEBUG    double fx,fb,fa;
       printf("%d %.12e",i,(*fret));   
       for (j=1;j<=n;j++) {    ncom=n; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    pcom=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xicom=vector(1,n); 
       }    nrfunc=func; 
       for(j=1;j<=n;j++)    for (j=1;j<=n;j++) { 
         printf(" p=%.12e",p[j]);      pcom[j]=p[j]; 
       printf("\n");      xicom[j]=xi[j]; 
 #endif    } 
     }    ax=0.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    xx=1.0; 
 #ifdef DEBUG    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       int k[2],l;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       k[0]=1;  #ifdef DEBUG
       k[1]=-1;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("Max: %.12e",(*func)(p));    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (j=1;j<=n;j++)  #endif
         printf(" %.12e",p[j]);    for (j=1;j<=n;j++) { 
       printf("\n");      xi[j] *= xmin; 
       for(l=0;l<=1;l++) {      p[j] += xi[j]; 
         for (j=1;j<=n;j++) {    } 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free_vector(xicom,1,n); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    free_vector(pcom,1,n); 
         }  } 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /*************** powell ************************/
 #endif  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   { 
       free_vector(xit,1,n);    void linmin(double p[], double xi[], int n, double *fret, 
       free_vector(xits,1,n);                double (*func)(double [])); 
       free_vector(ptt,1,n);    int i,ibig,j; 
       free_vector(pt,1,n);    double del,t,*pt,*ptt,*xit;
       return;    double fp,fptt;
     }    double *xits;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    pt=vector(1,n); 
     for (j=1;j<=n;j++) {    ptt=vector(1,n); 
       ptt[j]=2.0*p[j]-pt[j];    xit=vector(1,n); 
       xit[j]=p[j]-pt[j];    xits=vector(1,n); 
       pt[j]=p[j];    *fret=(*func)(p); 
     }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     fptt=(*func)(ptt);    for (*iter=1;;++(*iter)) { 
     if (fptt < fp) {      fp=(*fret); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      ibig=0; 
       if (t < 0.0) {      del=0.0; 
         linmin(p,xit,n,fret,func);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         for (j=1;j<=n;j++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
           xi[j][ibig]=xi[j][n];      for (i=1;i<=n;i++) 
           xi[j][n]=xit[j];        printf(" %d %.12f",i, p[i]);
         }      fprintf(ficlog," %d %.12f",i, p[i]);
 #ifdef DEBUG      printf("\n");
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      fprintf(ficlog,"\n");
         for(j=1;j<=n;j++)      for (i=1;i<=n;i++) { 
           printf(" %.12e",xit[j]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         printf("\n");        fptt=(*fret); 
 #endif  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
   }  #endif
 }        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
 /**** Prevalence limit ****************/        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          del=fabs(fptt-(*fret)); 
 {          ibig=i; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        } 
      matrix by transitions matrix until convergence is reached */  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   int i, ii,j,k;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double min, max, maxmin, maxmax,sumnew=0.;        for (j=1;j<=n;j++) {
   double **matprod2();          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double **out, cov[NCOVMAX], **pmij();          printf(" x(%d)=%.12e",j,xit[j]);
   double **newm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double agefin, delaymax=50 ; /* Max number of years to converge */        }
         for(j=1;j<=n;j++) {
   for (ii=1;ii<=nlstate+ndeath;ii++)          printf(" p=%.12e",p[j]);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog," p=%.12e",p[j]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
     }        printf("\n");
         fprintf(ficlog,"\n");
    cov[1]=1.;  #endif
        } 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #ifdef DEBUG
     newm=savm;        int k[2],l;
     /* Covariates have to be included here again */        k[0]=1;
      cov[2]=agefin;        k[1]=-1;
          printf("Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovn;k++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for (j=1;j<=n;j++) {
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        }
       for (k=1; k<=cptcovprod;k++)        printf("\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          for (j=1;j<=n;j++) {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
     savm=oldm;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     oldm=newm;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){  #endif
       min=1.;  
       max=0.;  
       for(i=1; i<=nlstate; i++) {        free_vector(xit,1,n); 
         sumnew=0;        free_vector(xits,1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        free_vector(ptt,1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);        free_vector(pt,1,n); 
         max=FMAX(max,prlim[i][j]);        return; 
         min=FMIN(min,prlim[i][j]);      } 
       }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       maxmin=max-min;      for (j=1;j<=n;j++) { 
       maxmax=FMAX(maxmax,maxmin);        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
     if(maxmax < ftolpl){        pt[j]=p[j]; 
       return prlim;      } 
     }      fptt=(*func)(ptt); 
   }      if (fptt < fp) { 
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 /*************** transition probabilities ***************/          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            xi[j][ibig]=xi[j][n]; 
 {            xi[j][n]=xit[j]; 
   double s1, s2;          }
   /*double t34;*/  #ifdef DEBUG
   int i,j,j1, nc, ii, jj;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(i=1; i<= nlstate; i++){          for(j=1;j<=n;j++){
     for(j=1; j<i;j++){            printf(" %.12e",xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            fprintf(ficlog," %.12e",xit[j]);
         /*s2 += param[i][j][nc]*cov[nc];*/          }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          printf("\n");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          fprintf(ficlog,"\n");
       }  #endif
       ps[i][j]=s2;        }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
     }    } 
     for(j=i+1; j<=nlstate+ndeath;j++){  } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /**** Prevalence limit (stable prevalence)  ****************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       ps[i][j]=s2;  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   }       matrix by transitions matrix until convergence is reached */
     /*ps[3][2]=1;*/  
     int i, ii,j,k;
   for(i=1; i<= nlstate; i++){    double min, max, maxmin, maxmax,sumnew=0.;
      s1=0;    double **matprod2();
     for(j=1; j<i; j++)    double **out, cov[NCOVMAX], **pmij();
       s1+=exp(ps[i][j]);    double **newm;
     for(j=i+1; j<=nlstate+ndeath; j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<i; j++)      for (j=1;j<=nlstate+ndeath;j++){
       ps[i][j]= exp(ps[i][j])*ps[i][i];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=i+1; j<=nlstate+ndeath; j++)      }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */     cov[1]=1.;
   } /* end i */   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(jj=1; jj<= nlstate+ndeath; jj++){      newm=savm;
       ps[ii][jj]=0;      /* Covariates have to be included here again */
       ps[ii][ii]=1;       cov[2]=agefin;
     }    
   }        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      printf("%lf ",ps[ii][jj]);        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 ");  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     printf("\n ");printf("%lf ",cov[2]);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 /*        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   goto end;*/  
     return ps;      savm=oldm;
 }      oldm=newm;
       maxmax=0.;
 /**************** Product of 2 matrices ******************/      for(j=1;j<=nlstate;j++){
         min=1.;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        max=0.;
 {        for(i=1; i<=nlstate; i++) {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          sumnew=0;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* in, b, out are matrice of pointers which should have been initialized          prlim[i][j]= newm[i][j]/(1-sumnew);
      before: only the contents of out is modified. The function returns          max=FMAX(max,prlim[i][j]);
      a pointer to pointers identical to out */          min=FMIN(min,prlim[i][j]);
   long i, j, k;        }
   for(i=nrl; i<= nrh; i++)        maxmin=max-min;
     for(k=ncolol; k<=ncoloh; k++)        maxmax=FMAX(maxmax,maxmin);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      }
         out[i][k] +=in[i][j]*b[j][k];      if(maxmax < ftolpl){
         return prlim;
   return out;      }
 }    }
   }
   
 /************* Higher Matrix Product ***************/  /*************** transition probabilities ***************/ 
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    double s1, s2;
      duration (i.e. until    /*double t34;*/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    int i,j,j1, nc, ii, jj;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).      for(i=1; i<= nlstate; i++){
      Model is determined by parameters x and covariates have to be      for(j=1; j<i;j++){
      included manually here.        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
      */          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i, j, d, h, k;        }
   double **out, cov[NCOVMAX];        ps[i][j]=s2;
   double **newm;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
   /* Hstepm could be zero and should return the unit matrix */      for(j=i+1; j<=nlstate+ndeath;j++){
   for (i=1;i<=nlstate+ndeath;i++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for (j=1;j<=nlstate+ndeath;j++){          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       oldm[i][j]=(i==j ? 1.0 : 0.0);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);        }
     }        ps[i][j]=s2;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      }
   for(h=1; h <=nhstepm; h++){    }
     for(d=1; d <=hstepm; d++){      /*ps[3][2]=1;*/
       newm=savm;  
       /* Covariates have to be included here again */    for(i=1; i<= nlstate; i++){
       cov[1]=1.;       s1=0;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for(j=1; j<i; j++)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        s1+=exp(ps[i][j]);
       for (k=1; k<=cptcovage;k++)      for(j=i+1; j<=nlstate+ndeath; j++)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        s1+=exp(ps[i][j]);
       for (k=1; k<=cptcovprod;k++)      ps[i][i]=1./(s1+1.);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    } /* end i */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       oldm=newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
     }        ps[ii][jj]=0;
     for(i=1; i<=nlstate+ndeath; i++)        ps[ii][ii]=1;
       for(j=1;j<=nlstate+ndeath;j++) {      }
         po[i][j][h]=newm[i][j];    }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  
       }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   } /* end h */      for(jj=1; jj<= nlstate+ndeath; jj++){
   return po;       printf("%lf ",ps[ii][jj]);
 }     }
       printf("\n ");
       }
 /*************** log-likelihood *************/      printf("\n ");printf("%lf ",cov[2]);*/
 double func( double *x)  /*
 {    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int i, ii, j, k, mi, d, kk;    goto end;*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      return ps;
   double **out;  }
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  /**************** Product of 2 matrices ******************/
   long ipmx;  
   /*extern weight */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   /*for(i=1;i<imx;i++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     printf(" %d\n",s[4][i]);    /* in, b, out are matrice of pointers which should have been initialized 
   */       before: only the contents of out is modified. The function returns
   cov[1]=1.;       a pointer to pointers identical to out */
     long i, j, k;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(i=nrl; i<= nrh; i++)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for(k=ncolol; k<=ncoloh; k++)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for(mi=1; mi<= wav[i]-1; mi++){          out[i][k] +=in[i][j]*b[j][k];
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return out;
       for(d=0; d<dh[mi][i]; d++){  }
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /************* Higher Matrix Product ***************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* Computes the transition matrix starting at age 'age' over 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       'nhstepm*hstepm*stepm' months (i.e. until
         savm=oldm;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         oldm=newm;       nhstepm*hstepm matrices. 
               Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               (typically every 2 years instead of every month which is too big 
       } /* end mult */       for the memory).
             Model is determined by parameters x and covariates have to be 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       included manually here. 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;       */
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int i, j, d, h, k;
     } /* end of wave */    double **out, cov[NCOVMAX];
   } /* end of individual */    double **newm;
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* Hstepm could be zero and should return the unit matrix */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for (i=1;i<=nlstate+ndeath;i++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for (j=1;j<=nlstate+ndeath;j++){
   return -l;        oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /*********** Maximum Likelihood Estimation ***************/    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        newm=savm;
 {        /* Covariates have to be included here again */
   int i,j, iter;        cov[1]=1.;
   double **xi,*delti;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double fret;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   xi=matrix(1,npar,1,npar);        for (k=1; k<=cptcovage;k++)
   for (i=1;i<=npar;i++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovprod;k++)
       xi[i][j]=(i==j ? 1.0 : 0.0);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 }        savm=oldm;
         oldm=newm;
 /**** Computes Hessian and covariance matrix ***/      }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(i=1; i<=nlstate+ndeath; i++)
 {        for(j=1;j<=nlstate+ndeath;j++) {
   double  **a,**y,*x,pd;          po[i][j][h]=newm[i][j];
   double **hess;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   int i, j,jk;           */
   int *indx;        }
     } /* end h */
   double hessii(double p[], double delta, int theta, double delti[]);    return po;
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /*************** log-likelihood *************/
   hess=matrix(1,npar,1,npar);  double func( double *x)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    int i, ii, j, k, mi, d, kk;
   for (i=1;i<=npar;i++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     printf("%d",i);fflush(stdout);    double **out;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double sw; /* Sum of weights */
     /*printf(" %f ",p[i]);*/    double lli; /* Individual log likelihood */
     /*printf(" %lf ",hess[i][i]);*/    int s1, s2;
   }    double bbh, survp;
      long ipmx;
   for (i=1;i<=npar;i++) {    /*extern weight */
     for (j=1;j<=npar;j++)  {    /* We are differentiating ll according to initial status */
       if (j>i) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         printf(".%d%d",i,j);fflush(stdout);    /*for(i=1;i<imx;i++) 
         hess[i][j]=hessij(p,delti,i,j);      printf(" %d\n",s[4][i]);
         hess[j][i]=hess[i][j];        */
         /*printf(" %lf ",hess[i][j]);*/    cov[1]=1.;
       }  
     }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   printf("\n");    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   a=matrix(1,npar,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   y=matrix(1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   x=vector(1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   indx=ivector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++)            }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          for(d=0; d<dh[mi][i]; d++){
   ludcmp(a,npar,indx,&pd);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (j=1;j<=npar;j++) {            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++) x[i]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     x[j]=1;            }
     lubksb(a,npar,indx,x);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=1;i<=npar;i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       matcov[i][j]=x[i];            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
         
   printf("\n#Hessian matrix#\n");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   for (i=1;i<=npar;i++) {          /* But now since version 0.9 we anticipate for bias and large stepm.
     for (j=1;j<=npar;j++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       printf("%.3e ",hess[i][j]);           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
     printf("\n");           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
   /* Recompute Inverse */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=npar;i++)           * -stepm/2 to stepm/2 .
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * For stepm=1 the results are the same as for previous versions of Imach.
   ludcmp(a,npar,indx,&pd);           * For stepm > 1 the results are less biased than in previous versions. 
            */
   /*  printf("\n#Hessian matrix recomputed#\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   for (j=1;j<=npar;j++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++) x[i]=0;          /* bias is positive if real duration
     x[j]=1;           * is higher than the multiple of stepm and negative otherwise.
     lubksb(a,npar,indx,x);           */
     for (i=1;i<=npar;i++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       y[i][j]=x[i];          if( s2 > nlstate){ 
       printf("%.3e ",y[i][j]);            /* 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 
     printf("\n");               step unit time, which is also the differences between probability to die before dh 
   }               and probability to die before dh-stepm . 
   */               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   free_matrix(a,1,npar,1,npar);          health state: the date of the interview describes the actual state
   free_matrix(y,1,npar,1,npar);          and not the date of a change in health state. The former idea was
   free_vector(x,1,npar);          to consider that at each interview the state was recorded
   free_ivector(indx,1,npar);          (healthy, disable or death) and IMaCh was corrected; but when we
   free_matrix(hess,1,npar,1,npar);          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
 }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
 /*************** hessian matrix ****************/          interview up to one month before death multiplied by the
 double hessii( double x[], double delta, int theta, double delti[])          probability to die within a month. Thanks to Chris
 {          Jackson for correcting this bug.  Former versions increased
   int i;          mortality artificially. The bad side is that we add another loop
   int l=1, lmax=20;          which slows down the processing. The difference can be up to 10%
   double k1,k2;          lower mortality.
   double p2[NPARMAX+1];            */
   double res;            lli=log(out[s1][s2] - savm[s1][s2]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          }else{
   double fx;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int k=0,kmax=10;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   double l1;          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fx=func(x);          /*if(lli ==000.0)*/
   for (i=1;i<=npar;i++) p2[i]=x[i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for(l=0 ; l <=lmax; l++){          ipmx +=1;
     l1=pow(10,l);          sw += weight[i];
     delts=delt;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(k=1 ; k <kmax; k=k+1){        } /* end of wave */
       delt = delta*(l1*k);      } /* end of individual */
       p2[theta]=x[theta] +delt;    }  else if(mle==2){
       k1=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       p2[theta]=x[theta]-delt;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       k2=func(p2)-fx;        for(mi=1; mi<= wav[i]-1; mi++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */          for (ii=1;ii<=nlstate+ndeath;ii++)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            }
 #endif          for(d=0; d<=dh[mi][i]; d++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            newm=savm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         k=kmax;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            }
         k=kmax; l=lmax*10.;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            savm=oldm;
         delts=delt;            oldm=newm;
       }          } /* end mult */
     }        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   delti[theta]=delts;          /* But now since version 0.9 we anticipate for bias and large stepm.
   return res;           * 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
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
 double hessij( double x[], double delti[], int thetai,int thetaj)           * (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
   int i;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int l=1, l1, lmax=20;           * -stepm/2 to stepm/2 .
   double k1,k2,k3,k4,res,fx;           * For stepm=1 the results are the same as for previous versions of Imach.
   double p2[NPARMAX+1];           * For stepm > 1 the results are less biased than in previous versions. 
   int k;           */
           s1=s[mw[mi][i]][i];
   fx=func(x);          s2=s[mw[mi+1][i]][i];
   for (k=1; k<=2; k++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++) p2[i]=x[i];          /* bias is positive if real duration
     p2[thetai]=x[thetai]+delti[thetai]/k;           * is higher than the multiple of stepm and negative otherwise.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           */
     k1=func(p2)-fx;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     k2=func(p2)-fx;          /*if(lli ==000.0)*/
            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     p2[thetai]=x[thetai]-delti[thetai]/k;          ipmx +=1;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          sw += weight[i];
     k3=func(p2)-fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
     p2[thetai]=x[thetai]-delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    }  else if(mle==3){  /* exponential inter-extrapolation */
     k4=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 #ifdef DEBUG        for(mi=1; mi<= wav[i]-1; mi++){
     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 (ii=1;ii<=nlstate+ndeath;ii++)
 #endif            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /************** Inverse of matrix **************/            newm=savm;
 void ludcmp(double **a, int n, int *indx, double *d)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   int i,imax,j,k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double big,dum,sum,temp;            }
   double *vv;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   vv=vector(1,n);            savm=oldm;
   *d=1.0;            oldm=newm;
   for (i=1;i<=n;i++) {          } /* end mult */
     big=0.0;        
     for (j=1;j<=n;j++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if ((temp=fabs(a[i][j])) > big) big=temp;          /* But now since version 0.9 we anticipate for bias and large stepm.
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     vv[i]=1.0/big;           * (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
   for (j=1;j<=n;j++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (i=1;i<j;i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       sum=a[i][j];           * probability in order to take into account the bias as a fraction of the way
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       a[i][j]=sum;           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
     big=0.0;           * For stepm > 1 the results are less biased than in previous versions. 
     for (i=j;i<=n;i++) {           */
       sum=a[i][j];          s1=s[mw[mi][i]][i];
       for (k=1;k<j;k++)          s2=s[mw[mi+1][i]][i];
         sum -= a[i][k]*a[k][j];          bbh=(double)bh[mi][i]/(double)stepm; 
       a[i][j]=sum;          /* bias is positive if real duration
       if ( (dum=vv[i]*fabs(sum)) >= big) {           * is higher than the multiple of stepm and negative otherwise.
         big=dum;           */
         imax=i;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
       }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     if (j != imax) {          /*if(lli ==000.0)*/
       for (k=1;k<=n;k++) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         dum=a[imax][k];          ipmx +=1;
         a[imax][k]=a[j][k];          sw += weight[i];
         a[j][k]=dum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       *d = -(*d);      } /* end of individual */
       vv[imax]=vv[j];    }else{  /* ml=4 no inter-extrapolation */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     indx[j]=imax;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;        for(mi=1; mi<= wav[i]-1; mi++){
     if (j != n) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       dum=1.0/(a[j][j]);            for (j=1;j<=nlstate+ndeath;j++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   free_vector(vv,1,n);  /* Doesn't work */          for(d=0; d<dh[mi][i]; d++){
 ;            newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 void lubksb(double **a, int n, int *indx, double b[])              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   int i,ii=0,ip,j;          
   double sum;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (i=1;i<=n;i++) {            savm=oldm;
     ip=indx[i];            oldm=newm;
     sum=b[ip];          } /* end mult */
     b[ip]=b[i];        
     if (ii)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ipmx +=1;
     else if (sum) ii=i;          sw += weight[i];
     b[i]=sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   for (i=n;i>=1;i--) {      } /* end of individual */
     sum=b[i];    } /* End of if */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     b[i]=sum/a[i][i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 }    return -l;
   }
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  
 {  /* Some frequencies */  /*********** Maximum Likelihood Estimation ***************/
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double ***freq; /* Frequencies */  {
   double *pp;    int i,j, iter;
   double pos, k2, dateintsum=0,k2cpt=0;    double **xi;
   FILE *ficresp;    double fret;
   char fileresp[FILENAMELENGTH];    xi=matrix(1,npar,1,npar);
      for (i=1;i<=npar;i++)
   pp=vector(1,nlstate);      for (j=1;j<=npar;j++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        xi[i][j]=(i==j ? 1.0 : 0.0);
   strcpy(fileresp,"p");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcat(fileresp,fileres);    powell(p,xi,npar,ftol,&iter,&fret,func);
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     exit(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));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  }
    
   j=cptcoveff;  /**** Computes Hessian and covariance matrix ***/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   for(k1=1; k1<=j;k1++){    double  **a,**y,*x,pd;
     for(i1=1; i1<=ncodemax[k1];i1++){    double **hess;
       j1++;    int i, j,jk;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    int *indx;
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      double hessii(double p[], double delta, int theta, double delti[]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double hessij(double p[], double delti[], int i, int j);
           for(m=agemin; m <= agemax+3; m++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
             freq[i][jk][m]=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
        
       dateintsum=0;    hess=matrix(1,npar,1,npar);
       k2cpt=0;  
       for (i=1; i<=imx; i++) {    printf("\nCalculation of the hessian matrix. Wait...\n");
         bool=1;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         if  (cptcovn>0) {    for (i=1;i<=npar;i++){
           for (z1=1; z1<=cptcoveff; z1++)      printf("%d",i);fflush(stdout);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      fprintf(ficlog,"%d",i);fflush(ficlog);
               bool=0;      hess[i][i]=hessii(p,ftolhess,i,delti);
         }      /*printf(" %f ",p[i]);*/
         if (bool==1) {      /*printf(" %lf ",hess[i][i]);*/
           for(m=firstpass; m<=lastpass; m++){    }
             k2=anint[m][i]+(mint[m][i]/12.);    
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (i=1;i<=npar;i++) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for (j=1;j<=npar;j++)  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;        if (j>i) { 
               if (m<lastpass) {          printf(".%d%d",i,j);fflush(stdout);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          hess[i][j]=hessij(p,delti,i,j);
               }          hess[j][i]=hess[i][j];    
                        /*printf(" %lf ",hess[i][j]);*/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        }
                 dateintsum=dateintsum+k2;      }
                 k2cpt++;    }
               }    printf("\n");
             }    fprintf(ficlog,"\n");
           }  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
            
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
       if  (cptcovn>0) {    x=vector(1,npar);
         fprintf(ficresp, "\n#********** Variable ");    indx=ivector(1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=1;i<=npar;i++)
         fprintf(ficresp, "**********\n#");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    for (j=1;j<=npar;j++) {
       fprintf(ficresp, "\n");      for (i=1;i<=npar;i++) x[i]=0;
            x[j]=1;
       for(i=(int)agemin; i <= (int)agemax+3; i++){      lubksb(a,npar,indx,x);
         if(i==(int)agemax+3)      for (i=1;i<=npar;i++){ 
           printf("Total");        matcov[i][j]=x[i];
         else      }
           printf("Age %d", i);    }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    printf("\n#Hessian matrix#\n");
             pp[jk] += freq[jk][m][i];    fprintf(ficlog,"\n#Hessian matrix#\n");
         }    for (i=1;i<=npar;i++) { 
         for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++) { 
           for(m=-1, pos=0; m <=0 ; m++)        printf("%.3e ",hess[i][j]);
             pos += freq[jk][m][i];        fprintf(ficlog,"%.3e ",hess[i][j]);
           if(pp[jk]>=1.e-10)      }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      printf("\n");
           else      fprintf(ficlog,"\n");
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    }
         }  
     /* Recompute Inverse */
         for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++)
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             pp[jk] += freq[jk][m][i];    ludcmp(a,npar,indx,&pd);
         }  
     /*  printf("\n#Hessian matrix recomputed#\n");
         for(jk=1,pos=0; jk <=nlstate ; jk++)  
           pos += pp[jk];    for (j=1;j<=npar;j++) {
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++) x[i]=0;
           if(pos>=1.e-5)      x[j]=1;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      lubksb(a,npar,indx,x);
           else      for (i=1;i<=npar;i++){ 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        y[i][j]=x[i];
           if( i <= (int) agemax){        printf("%.3e ",y[i][j]);
             if(pos>=1.e-5){        fprintf(ficlog,"%.3e ",y[i][j]);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      }
               probs[i][jk][j1]= pp[jk]/pos;      printf("\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      fprintf(ficlog,"\n");
             }    }
             else    */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  
           }    free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
            free_vector(x,1,npar);
         for(jk=-1; jk <=nlstate+ndeath; jk++)    free_ivector(indx,1,npar);
           for(m=-1; m <=nlstate+ndeath; m++)    free_matrix(hess,1,npar,1,npar);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  }
         printf("\n");  
       }  /*************** hessian matrix ****************/
     }  double hessii( double x[], double delta, int theta, double delti[])
   }  {
   dateintmean=dateintsum/k2cpt;    int i;
      int l=1, lmax=20;
   fclose(ficresp);    double k1,k2;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double p2[NPARMAX+1];
   free_vector(pp,1,nlstate);    double res;
      double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /* End of Freq */    double fx;
 }    int k=0,kmax=10;
     double l1;
 /************ Prevalence ********************/  
 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)    fx=func(x);
 {  /* Some frequencies */    for (i=1;i<=npar;i++) p2[i]=x[i];
      for(l=0 ; l <=lmax; l++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      l1=pow(10,l);
   double ***freq; /* Frequencies */      delts=delt;
   double *pp;      for(k=1 ; k <kmax; k=k+1){
   double pos, k2;        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   pp=vector(1,nlstate);        k1=func(p2)-fx;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   j1=0;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
   j=cptcoveff;  #ifdef DEBUG
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
          fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
  for(k1=1; k1<=j;k1++){  #endif
     for(i1=1; i1<=ncodemax[k1];i1++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       j1++;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
            k=kmax;
       for (i=-1; i<=nlstate+ndeath; i++)          }
         for (jk=-1; jk<=nlstate+ndeath; jk++)          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           for(m=agemin; m <= agemax+3; m++)          k=kmax; l=lmax*10.;
             freq[i][jk][m]=0;        }
              else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for (i=1; i<=imx; i++) {          delts=delt;
         bool=1;        }
         if  (cptcovn>0) {      }
           for (z1=1; z1<=cptcoveff; z1++)    }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    delti[theta]=delts;
               bool=0;    return res; 
         }    
         if (bool==1) {  }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  double hessij( double x[], double delti[], int thetai,int thetaj)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  {
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int i;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int l=1, l1, lmax=20;
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double k1,k2,k3,k4,res,fx;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    double p2[NPARMAX+1];
             }    int k;
           }  
         }    fx=func(x);
       }    for (k=1; k<=2; k++) {
         for(i=(int)agemin; i <= (int)agemax+3; i++){      for (i=1;i<=npar;i++) p2[i]=x[i];
           for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]+delti[thetai]/k;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
               pp[jk] += freq[jk][m][i];      k1=func(p2)-fx;
           }    
           for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]+delti[thetai]/k;
             for(m=-1, pos=0; m <=0 ; m++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             pos += freq[jk][m][i];      k2=func(p2)-fx;
         }    
              p2[thetai]=x[thetai]-delti[thetai]/k;
          for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      k3=func(p2)-fx;
              pp[jk] += freq[jk][m][i];    
          }      p2[thetai]=x[thetai]-delti[thetai]/k;
                p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
          for(jk=1; jk <=nlstate ; jk++){            #ifdef DEBUG
            if( i <= (int) agemax){      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);
              if(pos>=1.e-5){      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);
                probs[i][jk][j1]= pp[jk]/pos;  #endif
              }    }
            }    return res;
          }  }
            
         }  /************** Inverse of matrix **************/
     }  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
      int i,imax,j,k; 
      double big,dum,sum,temp; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double *vv; 
   free_vector(pp,1,nlstate);   
      vv=vector(1,n); 
 }  /* End of Freq */    *d=1.0; 
     for (i=1;i<=n;i++) { 
 /************* Waves Concatenation ***************/      big=0.0; 
       for (j=1;j<=n;j++) 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        if ((temp=fabs(a[i][j])) > big) big=temp; 
 {      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      vv[i]=1.0/big; 
      Death is a valid wave (if date is known).    } 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    for (j=1;j<=n;j++) { 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (i=1;i<j;i++) { 
      and mw[mi+1][i]. dh depends on stepm.        sum=a[i][j]; 
      */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   int i, mi, m;      } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      big=0.0; 
      double sum=0., jmean=0.;*/      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   int j, k=0,jk, ju, jl;        for (k=1;k<j;k++) 
   double sum=0.;          sum -= a[i][k]*a[k][j]; 
   jmin=1e+5;        a[i][j]=sum; 
   jmax=-1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   jmean=0.;          big=dum; 
   for(i=1; i<=imx; i++){          imax=i; 
     mi=0;        } 
     m=firstpass;      } 
     while(s[m][i] <= nlstate){      if (j != imax) { 
       if(s[m][i]>=1)        for (k=1;k<=n;k++) { 
         mw[++mi][i]=m;          dum=a[imax][k]; 
       if(m >=lastpass)          a[imax][k]=a[j][k]; 
         break;          a[j][k]=dum; 
       else        } 
         m++;        *d = -(*d); 
     }/* end while */        vv[imax]=vv[j]; 
     if (s[m][i] > nlstate){      } 
       mi++;     /* Death is another wave */      indx[j]=imax; 
       /* if(mi==0)  never been interviewed correctly before death */      if (a[j][j] == 0.0) a[j][j]=TINY; 
          /* Only death is a correct wave */      if (j != n) { 
       mw[mi][i]=m;        dum=1.0/(a[j][j]); 
     }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     wav[i]=mi;    } 
     if(mi==0)    free_vector(vv,1,n);  /* Doesn't work */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  ;
   }  } 
   
   for(i=1; i<=imx; i++){  void lubksb(double **a, int n, int *indx, double b[]) 
     for(mi=1; mi<wav[i];mi++){  { 
       if (stepm <=0)    int i,ii=0,ip,j; 
         dh[mi][i]=1;    double sum; 
       else{   
         if (s[mw[mi+1][i]][i] > nlstate) {    for (i=1;i<=n;i++) { 
           if (agedc[i] < 2*AGESUP) {      ip=indx[i]; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      sum=b[ip]; 
           if(j==0) j=1;  /* Survives at least one month after exam */      b[ip]=b[i]; 
           k=k+1;      if (ii) 
           if (j >= jmax) jmax=j;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           if (j <= jmin) jmin=j;      else if (sum) ii=i; 
           sum=sum+j;      b[i]=sum; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    } 
           }    for (i=n;i>=1;i--) { 
         }      sum=b[i]; 
         else{      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      b[i]=sum/a[i][i]; 
           k=k+1;    } 
           if (j >= jmax) jmax=j;  } 
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /************ Frequencies ********************/
           sum=sum+j;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
         }  {  /* Some frequencies */
         jk= j/stepm;    
         jl= j -jk*stepm;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         ju= j -(jk+1)*stepm;    int first;
         if(jl <= -ju)    double ***freq; /* Frequencies */
           dh[mi][i]=jk;    double *pp, **prop;
         else    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           dh[mi][i]=jk+1;    FILE *ficresp;
         if(dh[mi][i]==0)    char fileresp[FILENAMELENGTH];
           dh[mi][i]=1; /* At least one step */    
       }    pp=vector(1,nlstate);
     }    prop=matrix(1,nlstate,iagemin,iagemax+3);
   }    strcpy(fileresp,"p");
   jmean=sum/k;    strcat(fileresp,fileres);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    if((ficresp=fopen(fileresp,"w"))==NULL) {
  }      printf("Problem with prevalence resultfile: %s\n", fileresp);
 /*********** Tricode ****************************/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 void tricode(int *Tvar, int **nbcode, int imx)      exit(0);
 {    }
   int Ndum[20],ij=1, k, j, i;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   int cptcode=0;    j1=0;
   cptcoveff=0;    
      j=cptcoveff;
   for (k=0; k<19; k++) Ndum[k]=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (k=1; k<=7; k++) ncodemax[k]=0;  
     first=1;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {    for(k1=1; k1<=j;k1++){
       ij=(int)(covar[Tvar[j]][i]);      for(i1=1; i1<=ncodemax[k1];i1++){
       Ndum[ij]++;        j1++;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       if (ij > cptcode) cptcode=ij;          scanf("%d", i);*/
     }        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     for (i=0; i<=cptcode; i++) {            for(m=iagemin; m <= iagemax+3; m++)
       if(Ndum[i]!=0) ncodemax[j]++;              freq[i][jk][m]=0;
     }  
     ij=1;      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
     for (i=1; i<=ncodemax[j]; i++) {        
       for (k=0; k<=19; k++) {        dateintsum=0;
         if (Ndum[k] != 0) {        k2cpt=0;
           nbcode[Tvar[j]][ij]=k;        for (i=1; i<=imx; i++) {
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/          bool=1;
           ij++;          if  (cptcovn>0) {
         }            for (z1=1; z1<=cptcoveff; z1++) 
         if (ij > ncodemax[j]) break;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                  bool=0;
     }          }
   }            if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
  for (k=0; k<19; k++) Ndum[k]=0;              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
  for (i=1; i<=ncovmodel-2; i++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       ij=Tvar[i];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       Ndum[ij]++;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     }                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
  ij=1;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
  for (i=1; i<=10; i++) {                }
    if((Ndum[i]!=0) && (i<=ncovcol)){                
      Tvaraff[ij]=i;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
      ij++;                  dateintsum=dateintsum+k2;
    }                  k2cpt++;
  }                }
                }
     cptcoveff=ij-1;            }
 }          }
         }
 /*********** Health Expectancies ****************/         
         fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)  
 {        if  (cptcovn>0) {
   /* Health expectancies */          fprintf(ficresp, "\n#********** Variable "); 
   int i, j, nhstepm, hstepm, h, nstepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double age, agelim, hf;          fprintf(ficresp, "**********\n#");
   double ***p3mat;        }
          for(i=1; i<=nlstate;i++) 
   fprintf(ficreseij,"# Health expectancies\n");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   fprintf(ficreseij,"# Age");        fprintf(ficresp, "\n");
   for(i=1; i<=nlstate;i++)        
     for(j=1; j<=nlstate;j++)        for(i=iagemin; i <= iagemax+3; i++){
       fprintf(ficreseij," %1d-%1d",i,j);          if(i==iagemax+3){
   fprintf(ficreseij,"\n");            fprintf(ficlog,"Total");
           }else{
   if(estepm < stepm){            if(first==1){
     printf ("Problem %d lower than %d\n",estepm, stepm);              first=0;
   }              printf("See log file for details...\n");
   else  hstepm=estepm;              }
   /* We compute the life expectancy from trapezoids spaced every estepm months            fprintf(ficlog,"Age %d", i);
    * This is mainly to measure the difference between two models: for example          }
    * if stepm=24 months pijx are given only every 2 years and by summing them          for(jk=1; jk <=nlstate ; jk++){
    * we are calculating an estimate of the Life Expectancy assuming a linear            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
    * progression inbetween and thus overestimating or underestimating according              pp[jk] += freq[jk][m][i]; 
    * to the curvature of the survival function. If, for the same date, we          }
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          for(jk=1; jk <=nlstate ; jk++){
    * to compare the new estimate of Life expectancy with the same linear            for(m=-1, pos=0; m <=0 ; m++)
    * hypothesis. A more precise result, taking into account a more precise              pos += freq[jk][m][i];
    * curvature will be obtained if estepm is as small as stepm. */            if(pp[jk]>=1.e-10){
               if(first==1){
   /* For example we decided to compute the life expectancy with the smallest unit */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              }
      nhstepm is the number of hstepm from age to agelim              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      nstepm is the number of stepm from age to agelin.            }else{
      Look at hpijx to understand the reason of that which relies in memory size              if(first==1)
      and note for a fixed period like estepm months */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      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          }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.          for(jk=1; jk <=nlstate ; jk++){
   */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              pp[jk] += freq[jk][m][i];
           }       
   agelim=AGESUP;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            pos += pp[jk];
     /* nhstepm age range expressed in number of stepm */            posprop += prop[jk][i];
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          for(jk=1; jk <=nlstate ; jk++){
     /* if (stepm >= YEARM) hstepm=1;*/            if(pos>=1.e-5){
     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 prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }else{
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                if(first==1)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            if( i <= iagemax){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;              if(pos>=1.e-5){
           /* 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]);*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         }                probs[i][jk][j1]= pp[jk]/pos;
     fprintf(ficreseij,"%3.0f",age );                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     for(i=1; i<=nlstate;i++)              }
       for(j=1; j<=nlstate;j++){              else
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
     fprintf(ficreseij,"\n");          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
   }          for(jk=-1; jk <=nlstate+ndeath; jk++)
 }            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
 /************ Variance ******************/              if(first==1)
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   /* Variance of health expectancies */              }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          if(i <= iagemax)
   double **newm;            fprintf(ficresp,"\n");
   double **dnewm,**doldm;          if(first==1)
   int i, j, nhstepm, hstepm, h, nstepm ;            printf("Others in log...\n");
   int k, cptcode;          fprintf(ficlog,"\n");
   double *xp;        }
   double **gp, **gm;      }
   double ***gradg, ***trgradg;    }
   double ***p3mat;    dateintmean=dateintsum/k2cpt; 
   double age,agelim, hf;   
   int theta;    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    fprintf(ficresvij,"# Covariances of life expectancies\n");    free_vector(pp,1,nlstate);
   fprintf(ficresvij,"# Age");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   for(i=1; i<=nlstate;i++)    /* End of Freq */
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");  /************ Prevalence ********************/
   void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   xp=vector(1,npar);  {  
   dnewm=matrix(1,nlstate,1,npar);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   doldm=matrix(1,nlstate,1,nlstate);       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   if(estepm < stepm){    */
     printf ("Problem %d lower than %d\n",estepm, stepm);   
   }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   else  hstepm=estepm;      double ***freq; /* Frequencies */
   /* For example we decided to compute the life expectancy with the smallest unit */    double *pp, **prop;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double pos,posprop; 
      nhstepm is the number of hstepm from age to agelim    double  y2; /* in fractional years */
      nstepm is the number of stepm from age to agelin.    int iagemin, iagemax;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */    iagemin= (int) agemin;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    iagemax= (int) agemax;
      survival function given by stepm (the optimization length). Unfortunately it    /*pp=vector(1,nlstate);*/
      means that if the survival funtion is printed only each two years of age and if    prop=matrix(1,nlstate,iagemin,iagemax+3); 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      results. So we changed our mind and took the option of the best precision.    j1=0;
   */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    j=cptcoveff;
   agelim = AGESUP;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for(k1=1; k1<=j;k1++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for(i1=1; i1<=ncodemax[k1];i1++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        
     gp=matrix(0,nhstepm,1,nlstate);        for (i=1; i<=nlstate; i++)  
     gm=matrix(0,nhstepm,1,nlstate);          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
     for(theta=1; theta <=npar; theta++){       
       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;
       }          if  (cptcovn>0) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for (z1=1; z1<=cptcoveff; z1++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
       if (popbased==1) {          } 
         for(i=1; i<=nlstate;i++)          if (bool==1) { 
           prlim[i][i]=probs[(int)age][i][ij];            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 */
                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(j=1; j<= nlstate; j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for(h=0; h<=nhstepm; h++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                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); 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                      prop[s[m][i]][iagemax+3] += weight[i]; 
       for(i=1; i<=npar; i++) /* Computes gradient */                } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              } /* end selection of waves */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
          }
       if (popbased==1) {        for(i=iagemin; i <= iagemax+3; i++){  
         for(i=1; i<=nlstate;i++)          
           prlim[i][i]=probs[(int)age][i][ij];          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       }            posprop += prop[jk][i]; 
           } 
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){          for(jk=1; jk <=nlstate ; jk++){     
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            if( i <=  iagemax){ 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              if(posprop>=1.e-5){ 
         }                probs[i][jk][j1]= prop[jk][i]/posprop;
       }              } 
             } 
       for(j=1; j<= nlstate; j++)          }/* end jk */ 
         for(h=0; h<=nhstepm; h++){        }/* end i */ 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      } /* end i1 */
         }    } /* end k1 */
     } /* End theta */    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for(h=0; h<=nhstepm; h++)  }  /* End of prevalence */
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  /************* Waves Concatenation ***************/
           trgradg[h][j][theta]=gradg[h][theta][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)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  {
     for(i=1;i<=nlstate;i++)    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for(j=1;j<=nlstate;j++)       Death is a valid wave (if date is known).
         vareij[i][j][(int)age] =0.;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for(h=0;h<=nhstepm;h++){       and mw[mi+1][i]. dh depends on stepm.
       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]);    int i, mi, m;
         for(i=1;i<=nlstate;i++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           for(j=1;j<=nlstate;j++)       double sum=0., jmean=0.;*/
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    int first;
       }    int j, k=0,jk, ju, jl;
     }    double sum=0.;
     first=0;
     fprintf(ficresvij,"%.0f ",age );    jmin=1e+5;
     for(i=1; i<=nlstate;i++)    jmax=-1;
       for(j=1; j<=nlstate;j++){    jmean=0.;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    for(i=1; i<=imx; i++){
       }      mi=0;
     fprintf(ficresvij,"\n");      m=firstpass;
     free_matrix(gp,0,nhstepm,1,nlstate);      while(s[m][i] <= nlstate){
     free_matrix(gm,0,nhstepm,1,nlstate);        if(s[m][i]>=1)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          mw[++mi][i]=m;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        if(m >=lastpass)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          break;
   } /* End age */        else
            m++;
   free_vector(xp,1,npar);      }/* end while */
   free_matrix(doldm,1,nlstate,1,npar);      if (s[m][i] > nlstate){
   free_matrix(dnewm,1,nlstate,1,nlstate);        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
 }           /* Only death is a correct wave */
         mw[mi][i]=m;
 /************ 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)  
 {      wav[i]=mi;
   /* Variance of prevalence limit */      if(mi==0){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        if(first==0){
   double **newm;          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
   double **dnewm,**doldm;          first=1;
   int i, j, nhstepm, hstepm;        }
   int k, cptcode;        if(first==1){
   double *xp;          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   double *gp, *gm;        }
   double **gradg, **trgradg;      } /* end mi==0 */
   double age,agelim;    }
   int theta;  
        for(i=1; i<=imx; i++){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for(mi=1; mi<wav[i];mi++){
   fprintf(ficresvpl,"# Age");        if (stepm <=0)
   for(i=1; i<=nlstate;i++)          dh[mi][i]=1;
       fprintf(ficresvpl," %1d-%1d",i,i);        else{
   fprintf(ficresvpl,"\n");          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
   xp=vector(1,npar);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   dnewm=matrix(1,nlstate,1,npar);            if(j==0) j=1;  /* Survives at least one month after exam */
   doldm=matrix(1,nlstate,1,nlstate);            k=k+1;
              if (j >= jmax) jmax=j;
   hstepm=1*YEARM; /* Every year of age */            if (j <= jmin) jmin=j;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            sum=sum+j;
   agelim = AGESUP;            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            /*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]);*/
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
     gradg=matrix(1,npar,1,nlstate);          else{
     gp=vector(1,nlstate);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     gm=vector(1,nlstate);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
     for(theta=1; theta <=npar; theta++){            if (j >= jmax) jmax=j;
       for(i=1; i<=npar; i++){ /* Computes gradient */            else if (j <= jmin)jmin=j;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            sum=sum+j;
       for(i=1;i<=nlstate;i++)          }
         gp[i] = prlim[i][i];          jk= j/stepm;
              jl= j -jk*stepm;
       for(i=1; i<=npar; i++) /* Computes gradient */          ju= j -(jk+1)*stepm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          if(mle <=1){ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            if(jl==0){
       for(i=1;i<=nlstate;i++)              dh[mi][i]=jk;
         gm[i] = prlim[i][i];              bh[mi][i]=0;
             }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 */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              dh[mi][i]=jk+1;
     } /* End theta */              bh[mi][i]=ju;
             }
     trgradg =matrix(1,nlstate,1,npar);          }else{
             if(jl <= -ju){
     for(j=1; j<=nlstate;j++)              dh[mi][i]=jk;
       for(theta=1; theta <=npar; theta++)              bh[mi][i]=jl;       /* bias is positive if real duration
         trgradg[j][theta]=gradg[theta][j];                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
     for(i=1;i<=nlstate;i++)            }
       varpl[i][(int)age] =0.;            else{
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              dh[mi][i]=jk+1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              bh[mi][i]=ju;
     for(i=1;i<=nlstate;i++)            }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
     fprintf(ficresvpl,"%.0f ",age );              bh[mi][i]=ju; /* At least one step */
     for(i=1; i<=nlstate;i++)              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            }
     fprintf(ficresvpl,"\n");          }
     free_vector(gp,1,nlstate);        } /* end if mle */
     free_vector(gm,1,nlstate);      } /* end wave */
     free_matrix(gradg,1,npar,1,nlstate);    }
     free_matrix(trgradg,1,nlstate,1,npar);    jmean=sum/k;
   } /* End age */    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   free_vector(xp,1,npar);   }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
 }  {
     
 /************ Variance of one-step probabilities  ******************/    int Ndum[20],ij=1, k, j, i, maxncov=19;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    int cptcode=0;
 {    cptcoveff=0; 
   int i, j;   
   int k=0, cptcode;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   double **dnewm,**doldm;    for (k=1; k<=7; k++) ncodemax[k]=0;
   double *xp;  
   double *gp, *gm;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   double **gradg, **trgradg;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   double age,agelim, cov[NCOVMAX];                                 modality*/ 
   int theta;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   char fileresprob[FILENAMELENGTH];        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   strcpy(fileresprob,"prob");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   strcat(fileresprob,fileres);                                         Tvar[j]. If V=sex and male is 0 and 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {                                         female is 1, then  cptcode=1.*/
     printf("Problem with resultfile: %s\n", fileresprob);      }
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for (i=0; i<=cptcode; i++) {
          if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       }
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      ij=1; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1; i<=ncodemax[j]; i++) {
          for (k=0; k<= maxncov; k++) {
   cov[1]=1;          if (Ndum[k] != 0) {
   for (age=bage; age<=fage; age ++){            nbcode[Tvar[j]][ij]=k; 
     cov[2]=age;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     gradg=matrix(1,npar,1,9);            
     trgradg=matrix(1,9,1,npar);            ij++;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          if (ij > ncodemax[j]) break; 
            }  
     for(theta=1; theta <=npar; theta++){      } 
       for(i=1; i<=npar; i++)    }  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
         for (k=0; k< maxncov; k++) Ndum[k]=0;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       for (i=1; i<=ncovmodel-2; i++) { 
       k=0;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       for(i=1; i<= (nlstate+ndeath); i++){     ij=Tvar[i];
         for(j=1; j<=(nlstate+ndeath);j++){     Ndum[ij]++;
            k=k+1;   }
           gp[k]=pmmij[i][j];  
         }   ij=1;
       }   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
       for(i=1; i<=npar; i++)       Tvaraff[ij]=i; /*For printing */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       ij++;
         }
    }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);   
       k=0;   cptcoveff=ij-1; /*Number of simple covariates*/
       for(i=1; i<=(nlstate+ndeath); i++){  }
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;  /*********** Health Expectancies ****************/
           gm[k]=pmmij[i][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 )
       }  
        {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    /* Health expectancies */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     }    double age, agelim, hf;
     double ***p3mat,***varhe;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double **dnewm,**doldm;
       for(theta=1; theta <=npar; theta++)    double *xp;
       trgradg[j][theta]=gradg[theta][j];    double **gp, **gm;
      double ***gradg, ***trgradg;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    int theta;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      pmij(pmmij,cov,ncovmodel,x,nlstate);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
      k=0;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      for(i=1; i<=(nlstate+ndeath); i++){    
        for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficreseij,"# Health expectancies\n");
          k=k+1;    fprintf(ficreseij,"# Age");
          gm[k]=pmmij[i][j];    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=nlstate;j++)
      }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
          fprintf(ficreseij,"\n");
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
     }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    else  hstepm=estepm;   
      }*/    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   fprintf(ficresprob,"\n%d ",(int)age);     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){     * progression in between and thus overestimating or underestimating according
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);     * to the curvature of the survival function. If, for the same date, we 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   }     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));     * curvature will be obtained if estepm is as small as stepm. */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* For example we decided to compute the life expectancy with the smallest unit */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* 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 
  free_vector(xp,1,npar);       nstepm is the number of stepm from age to agelin. 
 fclose(ficresprob);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
 }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
 /******************* Printing html file ***********/       means that if the survival funtion is printed only each two years of age and if
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  int lastpass, int stepm, int weightopt, char model[],\       results. So we changed our mind and took the option of the best precision.
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    */
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  char version[], int popforecast, int estepm ){  
   int jj1, k1, i1, cpt;    agelim=AGESUP;
   FILE *fichtm;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /*char optionfilehtm[FILENAMELENGTH];*/      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   strcpy(optionfilehtm,optionfile);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcat(optionfilehtm,".htm");      /* if (stepm >= YEARM) hstepm=1;*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("Problem with %s \n",optionfilehtm), exit(0);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       gp=matrix(0,nhstepm,1,nlstate*nlstate);
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      gm=matrix(0,nhstepm,1,nlstate*nlstate);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  
 \n      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 Total number of observations=%d <br>\n         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 <hr  size=\"2\" color=\"#EC5E5E\">   
  <ul><li>Outputs files<br>\n  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n  
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      /* Computing Variances of health expectancies */
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n       for(theta=1; theta <=npar; theta++){
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  fprintf(fichtm,"\n        }
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        cptj=0;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
  if(popforecast==1) fprintf(fichtm,"\n            cptj=cptj+1;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         <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," <li>Graphs</li><p>");       
        
  m=cptcoveff;        for(i=1; i<=npar; i++) 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  jj1=0;        
  for(k1=1; k1<=m;k1++){        cptj=0;
    for(i1=1; i1<=ncodemax[k1];i1++){        for(j=1; j<= nlstate; j++){
        jj1++;          for(i=1;i<=nlstate;i++){
        if (cptcovn > 0) {            cptj=cptj+1;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
          for (cpt=1; cpt<=cptcoveff;cpt++)              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          }
        }        }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        for(j=1; j<= nlstate*nlstate; j++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              for(h=0; h<=nhstepm-1; h++){
        for(cpt=1; cpt<nlstate;cpt++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          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(cpt=1; cpt<=nlstate;cpt++) {  /* End theta */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }       for(h=0; h<=nhstepm-1; h++)
      for(cpt=1; cpt<=nlstate;cpt++) {        for(j=1; j<=nlstate*nlstate;j++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          for(theta=1; theta <=npar; theta++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            trgradg[h][j][theta]=gradg[h][theta][j];
      }       
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>       for(i=1;i<=nlstate*nlstate;i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(j=1;j<=nlstate*nlstate;j++)
 fprintf(fichtm,"\n</body>");          varhe[i][j][(int)age] =0.;
    }  
    }       printf("%d|",(int)age);fflush(stdout);
 fclose(fichtm);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 }       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
 /******************* Gnuplot file **************/          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   strcpy(optionfilegnuplot,optionfilefiname);        }
   strcat(optionfilegnuplot,".gp.txt");      }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      /* Computing expectancies */
     printf("Problem with file %s",optionfilegnuplot);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 #ifdef windows            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fprintf(ficgp,"cd \"%s\" \n",pathc);            
 #endif  /* 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]);*/
 m=pow(2,cptcoveff);  
            }
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(ficreseij,"%3.0f",age );
    for (k1=1; k1<= m ; k1 ++) {      cptj=0;
       for(i=1; i<=nlstate;i++)
 #ifdef windows        for(j=1; j<=nlstate;j++){
     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);          cptj++;
 #endif          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 #ifdef unix        }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      fprintf(ficreseij,"\n");
 #endif     
       free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 for (i=1; i<= nlstate ; i ++) {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
     for (i=1; i<= nlstate ; i ++) {    printf("\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficlog,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    free_vector(xp,1,npar);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      for (i=1; i<= nlstate ; i ++) {    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  /************ Variance ******************/
 #ifdef unix  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)
 fprintf(ficgp,"\nset ter gif small size 400,300");  {
 #endif    /* Variance of health expectancies */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    }    /* double **newm;*/
   }    double **dnewm,**doldm;
   /*2 eme*/    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
   for (k1=1; k1<= m ; k1 ++) {    int k, cptcode;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    double *xp;
        double **gp, **gm;  /* for var eij */
     for (i=1; i<= nlstate+1 ; i ++) {    double ***gradg, ***trgradg; /*for var eij */
       k=2*i;    double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double *gpp, *gmp; /* for var p point j */
       for (j=1; j<= nlstate+1 ; j ++) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***p3mat;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double age,agelim, hf;
 }      double ***mobaverage;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int theta;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    char digit[4];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    char digitp[25];
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    char fileresprobmorprev[FILENAMELENGTH];
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      if(popbased==1){
       fprintf(ficgp,"\" t\"\" w l 0,");      if(mobilav!=0)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        strcpy(digitp,"-populbased-mobilav-");
       for (j=1; j<= nlstate+1 ; j ++) {      else strcpy(digitp,"-populbased-nomobil-");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    else 
 }        strcpy(digitp,"-stablbased-");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");    if (mobilav!=0) {
     }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      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);
   /*3eme*/      }
     }
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {    strcpy(fileresprobmorprev,"prmorprev"); 
       k=2+nlstate*(cpt-1);    sprintf(digit,"%-d",ij);
       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);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       for (i=1; i< nlstate ; i ++) {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         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);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       }    strcat(fileresprobmorprev,fileres);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   /* CV preval stat */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for (k1=1; k1<= m ; k1 ++) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for (cpt=1; cpt<nlstate ; cpt ++) {    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);
       k=3;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for (i=1; i< nlstate ; i ++)      for(i=1; i<=nlstate;i++)
         fprintf(ficgp,"+$%d",k+i+1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    }  
          fprintf(ficresprobmorprev,"\n");
       l=3+(nlstate+ndeath)*cpt;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       for (i=1; i< nlstate ; i ++) {      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         l=3+(nlstate+ndeath)*cpt;      exit(0);
         fprintf(ficgp,"+$%d",l+i+1);    }
       }    else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        fprintf(ficgp,"\n# Routine varevsij");
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }        printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   /* proba elementaires */      exit(0);
    for(i=1,jk=1; i <=nlstate; i++){    }
     for(k=1; k <=(nlstate+ndeath); k++){    else{
       if (k != i) {      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");
         for(j=1; j <=ncovmodel; j++){      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
            }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           jk++;  
           fprintf(ficgp,"\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
         }    fprintf(ficresvij,"# Age");
       }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
     for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    xp=vector(1,npar);
    i=1;    dnewm=matrix(1,nlstate,1,npar);
    for(k2=1; k2<=nlstate; k2++) {    doldm=matrix(1,nlstate,1,nlstate);
      k3=i;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      for(k=1; k<=(nlstate+ndeath); k++) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 ij=1;    gpp=vector(nlstate+1,nlstate+ndeath);
         for(j=3; j <=ncovmodel; j++) {    gmp=vector(nlstate+1,nlstate+ndeath);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    
             ij++;    if(estepm < stepm){
           }      printf ("Problem %d lower than %d\n",estepm, stepm);
           else    }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    else  hstepm=estepm;   
         }    /* For example we decided to compute the life expectancy with the smallest unit */
           fprintf(ficgp,")/(1");    /* 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 
         for(k1=1; k1 <=nlstate; k1++){         nstepm is the number of stepm from age to agelin. 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       Look at hpijx to understand the reason of that which relies in memory size
 ij=1;       and note for a fixed period like k years */
           for(j=3; j <=ncovmodel; j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       survival function given by stepm (the optimization length). Unfortunately it
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       means that if the survival funtion is printed every two years of age and if
             ij++;       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.
           else    */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }    agelim = AGESUP;
           fprintf(ficgp,")");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         i=i+ncovmodel;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        }      gp=matrix(0,nhstepm,1,nlstate);
      }      gm=matrix(0,nhstepm,1,nlstate);
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   fclose(ficgp);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 }  /* end gnuplot */        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        if (popbased==1) {
           if(mobilav ==0){
   int i, cpt, cptcod;            for(i=1; i<=nlstate;i++)
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)              prlim[i][i]=probs[(int)age][i][ij];
       for (i=1; i<=nlstate;i++)          }else{ /* mobilav */ 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            for(i=1; i<=nlstate;i++)
           mobaverage[(int)agedeb][i][cptcod]=0.;              prlim[i][i]=mobaverage[(int)age][i][ij];
              }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        }
       for (i=1; i<=nlstate;i++){    
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(j=1; j<= nlstate; j++){
           for (cpt=0;cpt<=4;cpt++){          for(h=0; h<=nhstepm; h++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          }
         }        }
       }        /* This for computing probability of death (h=1 means
     }           computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
 }        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
 /************** Forecasting ******************/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 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){        }    
          /* end probability of death */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double *popeffectif,*popcount;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double ***p3mat;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char fileresf[FILENAMELENGTH];   
         if (popbased==1) {
  agelim=AGESUP;          if(mobilav ==0){
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   strcpy(fileresf,"f");          }
   strcat(fileresf,fileres);        }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          }
         }
   if (mobilav==1) {        /* This for computing probability of death (h=1 means
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);           computed over hstepm matrices product = hstepm*stepm months) 
     movingaverage(agedeb, fage, ageminpar, mobaverage);           as a weighted average of prlim.
   }        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   if (stepm<=12) stepsize=1;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   agelim=AGESUP;        /* end probability of death */
    
   hstepm=1;        for(j=1; j<= nlstate; j++) /* vareij */
   hstepm=hstepm/stepm;          for(h=0; h<=nhstepm; h++){
   yp1=modf(dateintmean,&yp);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   anprojmean=yp;          }
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   yp1=modf((yp2*30.5),&yp);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   jprojmean=yp;        }
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;      } /* End theta */
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   for(cptcov=1;cptcov<=i2;cptcov++){      for(h=0; h<=nhstepm; h++) /* veij */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(j=1; j<=nlstate;j++)
       k=k+1;          for(theta=1; theta <=npar; theta++)
       fprintf(ficresf,"\n#******");            trgradg[h][j][theta]=gradg[h][theta][j];
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       }        for(theta=1; theta <=npar; theta++)
       fprintf(ficresf,"******\n");          trgradgp[j][theta]=gradgp[theta][j];
       fprintf(ficresf,"# StartingAge FinalAge");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
            hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
            for(i=1;i<=nlstate;i++)
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        for(j=1;j<=nlstate;j++)
         fprintf(ficresf,"\n");          vareij[i][j][(int)age] =0.;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
       for(h=0;h<=nhstepm;h++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(k=0;k<=nhstepm;k++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           nhstepm = nhstepm/hstepm;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                    for(i=1;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1;j<=nlstate;j++)
           oldm=oldms;savm=savms;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
              }
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {      /* pptj */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      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=1; j<=nlstate+ndeath;j++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
               kk1=0.;kk2=0;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
               for(i=1; i<=nlstate;i++) {                        varppt[j][i]=doldmp[j][i];
                 if (mobilav==1)      /* end ppptj */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      /*  x centered again */
                 else {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                 }   
                      if (popbased==1) {
               }        if(mobilav ==0){
               if (h==(int)(calagedate+12*cpt)){          for(i=1; i<=nlstate;i++)
                 fprintf(ficresf," %.3f", kk1);            prlim[i][i]=probs[(int)age][i][ij];
                                }else{ /* mobilav */ 
               }          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=mobaverage[(int)age][i][ij];
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
         }               
       }      /* This for computing probability of death (h=1 means
     }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
              */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   fclose(ficresf);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
 }      }    
 /************** Forecasting ******************/      /* end probability of death */
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   int *popage;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        for(i=1; i<=nlstate;i++){
   double *popeffectif,*popcount;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];      } 
       fprintf(ficresprobmorprev,"\n");
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresvij,"%.0f ",age );
   agelim=AGESUP;      for(i=1; i<=nlstate;i++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        for(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
        fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
   strcpy(filerespop,"pop");      free_matrix(gm,0,nhstepm,1,nlstate);
   strcat(filerespop,fileres);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     printf("Problem with forecast resultfile: %s\n", filerespop);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    } /* End age */
   printf("Computing forecasting: result on file '%s' \n", filerespop);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (mobilav==1) {    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   if (stepm<=12) stepsize=1;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   agelim=AGESUP;    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);
   hstepm=1;    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);
   hstepm=hstepm/stepm;    /*  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);
    */
   if (popforecast==1) {    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,nlstate);
     popage=ivector(0,AGESUP);    free_matrix(dnewm,1,nlstate,1,npar);
     popeffectif=vector(0,AGESUP);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     popcount=vector(0,AGESUP);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
        free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     i=1;      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    fclose(ficresprobmorprev);
        fclose(ficgp);
     imx=i;    fclose(fichtm);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  }  
   }  
   /************ Variance of prevlim ******************/
   for(cptcov=1;cptcov<=i2;cptcov++){  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)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  {
       k=k+1;    /* Variance of prevalence limit */
       fprintf(ficrespop,"\n#******");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       for(j=1;j<=cptcoveff;j++) {    double **newm;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **dnewm,**doldm;
       }    int i, j, nhstepm, hstepm;
       fprintf(ficrespop,"******\n");    int k, cptcode;
       fprintf(ficrespop,"# Age");    double *xp;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double *gp, *gm;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    double **gradg, **trgradg;
          double age,agelim;
       for (cpt=0; cpt<=0;cpt++) {    int theta;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       
            fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresvpl,"# Age");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for(i=1; i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;        fprintf(ficresvpl," %1d-%1d",i,i);
              fprintf(ficresvpl,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    xp=vector(1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      dnewm=matrix(1,nlstate,1,npar);
            doldm=matrix(1,nlstate,1,nlstate);
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {    hstepm=1*YEARM; /* Every year of age */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
             }    agelim = AGESUP;
             for(j=1; j<=nlstate+ndeath;j++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
               kk1=0.;kk2=0;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               for(i=1; i<=nlstate;i++) {                    if (stepm >= YEARM) hstepm=1;
                 if (mobilav==1)      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      gradg=matrix(1,npar,1,nlstate);
                 else {      gp=vector(1,nlstate);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      gm=vector(1,nlstate);
                 }  
               }      for(theta=1; theta <=npar; theta++){
               if (h==(int)(calagedate+12*cpt)){        for(i=1; i<=npar; i++){ /* Computes gradient */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   /*fprintf(ficrespop," %.3f", kk1);        }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               }        for(i=1;i<=nlstate;i++)
             }          gp[i] = prlim[i][i];
             for(i=1; i<=nlstate;i++){      
               kk1=0.;        for(i=1; i<=npar; i++) /* Computes gradient */
                 for(j=1; j<=nlstate;j++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 }        for(i=1;i<=nlstate;i++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          gm[i] = prlim[i][i];
             }  
         for(i=1;i<=nlstate;i++)
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      } /* End theta */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      trgradg =matrix(1,nlstate,1,npar);
         }  
       }      for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
   /******/          trgradg[j][theta]=gradg[theta][j];
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      for(i=1;i<=nlstate;i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          varpl[i][(int)age] =0.;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           nhstepm = nhstepm/hstepm;      for(i=1;i<=nlstate;i++)
                  varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      fprintf(ficresvpl,"%.0f ",age );
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficresvpl,"\n");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      free_vector(gp,1,nlstate);
             }      free_vector(gm,1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {      free_matrix(gradg,1,npar,1,nlstate);
               kk1=0.;kk2=0;      free_matrix(trgradg,1,nlstate,1,npar);
               for(i=1; i<=nlstate;i++) {                  } /* End age */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }    free_vector(xp,1,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    free_matrix(doldm,1,nlstate,1,npar);
             }    free_matrix(dnewm,1,nlstate,1,nlstate);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
         }  
       }  /************ 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 i, j=0,  i1, k1, l1, t, tj;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   if (popforecast==1) {    int first=1, first1;
     free_ivector(popage,0,AGESUP);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     free_vector(popeffectif,0,AGESUP);    double **dnewm,**doldm;
     free_vector(popcount,0,AGESUP);    double *xp;
   }    double *gp, *gm;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **gradg, **trgradg;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **mu;
   fclose(ficrespop);    double age,agelim, cov[NCOVMAX];
 }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
 /***********************************************/    char fileresprob[FILENAMELENGTH];
 /**************** Main Program *****************/    char fileresprobcov[FILENAMELENGTH];
 /***********************************************/    char fileresprobcor[FILENAMELENGTH];
   
 int main(int argc, char *argv[])    double ***varpij;
 {  
     strcpy(fileresprob,"prob"); 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    strcat(fileresprob,fileres);
   double agedeb, agefin,hf;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   double fret;    }
   double **xi,tmp,delta;    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
   double dum; /* Dummy variable */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   double ***p3mat;      printf("Problem with resultfile: %s\n", fileresprobcov);
   int *indx;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   char line[MAXLINE], linepar[MAXLINE];    }
   char title[MAXLINE];    strcpy(fileresprobcor,"probcor"); 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    strcat(fileresprobcor,fileres);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   char filerest[FILENAMELENGTH];    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   char fileregp[FILENAMELENGTH];    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   char popfile[FILENAMELENGTH];    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   int firstobs=1, lastobs=10;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   int c,  h , cpt,l;    
   int ju,jl, mi;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    fprintf(ficresprob,"# Age");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   int mobilav=0,popforecast=0;    fprintf(ficresprobcov,"# Age");
   int hstepm, nhstepm;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    fprintf(ficresprobcov,"# Age");
   
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;    for(i=1; i<=nlstate;i++)
   double **prlim;      for(j=1; j<=(nlstate+ndeath);j++){
   double *severity;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   double ***param; /* Matrix of parameters */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   double  *p;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   double **matcov; /* Matrix of covariance */      }  
   double ***delti3; /* Scale */   /* fprintf(ficresprob,"\n");
   double *delti; /* Scale */    fprintf(ficresprobcov,"\n");
   double ***eij, ***vareij;    fprintf(ficresprobcor,"\n");
   double **varpl; /* Variances of prevalence limits by age */   */
   double *epj, vepp;   xp=vector(1,npar);
   double kk1, kk2;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";    first=1;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   char z[1]="c", occ;      exit(0);
 #include <sys/time.h>    }
 #include <time.h>    else{
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      fprintf(ficgp,"\n# Routine varprob");
      }
   /* long total_usecs;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   struct timeval start_time, end_time;      printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      exit(0);
   getcwd(pathcd, size);    }
     else{
   printf("\n%s",version);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   if(argc <=1){      fprintf(fichtm,"\n");
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   }      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   else{      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");
     strcpy(pathtot,argv[1]);  
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);    cov[1]=1;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    tj=cptcoveff;
   /* cutv(path,optionfile,pathtot,'\\');*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    for(t=1; t<=tj;t++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      for(i1=1; i1<=ncodemax[t];i1++){ 
   chdir(path);        j1++;
   replace(pathc,path);        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
 /*-------- arguments in the command line --------*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
   strcpy(fileres,"r");          fprintf(ficresprobcov, "\n#********** Variable "); 
   strcat(fileres, optionfilefiname);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(fileres,".txt");    /* Other files have txt extension */          fprintf(ficresprobcov, "**********\n#\n");
           
   /*---------arguments file --------*/          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          fprintf(ficgp, "**********\n#\n");
     printf("Problem with optionfile %s\n",optionfile);          
     goto end;          
   }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcpy(filereso,"o");          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcat(filereso,fileres);          
   if((ficparo=fopen(filereso,"w"))==NULL) {          fprintf(ficresprobcor, "\n#********** Variable ");    
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcor, "**********\n#");    
         }
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);          cov[2]=age;
     fgets(line, MAXLINE, ficpar);          for (k=1; k<=cptcovn;k++) {
     puts(line);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fputs(line,ficparo);          }
   }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   ungetc(c,ficpar);          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]]];
   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);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   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);          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);
                
   covar=matrix(0,NCOVMAX,1,n);            k=0;
   cptcovn=0;            for(i=1; i<= (nlstate); i++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   ncovmodel=2+cptcovn;                gp[k]=pmmij[i][j];
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              }
              }
   /* Read guess parameters */            
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=npar; i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     puts(line);            k=0;
     fputs(line,ficparo);            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);                k=k+1;
                  gm[k]=pmmij[i][j];
   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);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       fprintf(ficparo,"%1d%1d",i1,j1);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       printf("%1d%1d",i,j);          }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         printf(" %lf",param[i][j][k]);            for(theta=1; theta <=npar; theta++)
         fprintf(ficparo," %lf",param[i][j][k]);              trgradg[j][theta]=gradg[theta][j];
       }          
       fscanf(ficpar,"\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       printf("\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       fprintf(ficparo,"\n");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
   p=param[1][1];          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   /* Reads comments: lines beginning with '#' */          k=0;
   while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1; i<=(nlstate); i++){
     ungetc(c,ficpar);            for(j=1; j<=(nlstate+ndeath);j++){
     fgets(line, MAXLINE, ficpar);              k=k+1;
     puts(line);              mu[k][(int) age]=pmmij[i][j];
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              varpij[i][j][(int)age] = doldm[i][j];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){          /*printf("\n%d ",(int)age);
     for(j=1; j <=nlstate+ndeath-1; j++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       printf("%1d%1d",i,j);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficparo,"%1d%1d",i1,j1);            }*/
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);          fprintf(ficresprob,"\n%d ",(int)age);
         printf(" %le",delti3[i][j][k]);          fprintf(ficresprobcov,"\n%d ",(int)age);
         fprintf(ficparo," %le",delti3[i][j][k]);          fprintf(ficresprobcor,"\n%d ",(int)age);
       }  
       fscanf(ficpar,"\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       printf("\n");            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       fprintf(ficparo,"\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   delti=delti3[1][1];          }
            i=0;
   /* Reads comments: lines beginning with '#' */          for (k=1; k<=(nlstate);k++){
   while((c=getc(ficpar))=='#' && c!= EOF){            for (l=1; l<=(nlstate+ndeath);l++){ 
     ungetc(c,ficpar);              i=i++;
     fgets(line, MAXLINE, ficpar);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     puts(line);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     fputs(line,ficparo);              for (j=1; j<=i;j++){
   }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   ungetc(c,ficpar);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                }
   matcov=matrix(1,npar,1,npar);            }
   for(i=1; i <=npar; i++){          }/* end of loop for state */
     fscanf(ficpar,"%s",&str);        } /* end of loop for age */
     printf("%s",str);  
     fprintf(ficparo,"%s",str);        /* Confidence intervalle of pij  */
     for(j=1; j <=i; j++){        /*
       fscanf(ficpar," %le",&matcov[i][j]);          fprintf(ficgp,"\nset noparametric;unset label");
       printf(" %.5le",matcov[i][j]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       fprintf(ficparo," %.5le",matcov[i][j]);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     }          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     fscanf(ficpar,"\n");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     printf("\n");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     fprintf(ficparo,"\n");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   }        */
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       matcov[i][j]=matcov[j][i];        first1=1;
            for (k2=1; k2<=(nlstate);k2++){
   printf("\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
     /*-------- Rewriting paramater file ----------*/            for (k1=1; k1<=(nlstate);k1++){
      strcpy(rfileres,"r");    /* "Rparameterfile */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                if(l1==k1) continue;
      strcat(rfileres,".");    /* */                i=(k1-1)*(nlstate+ndeath)+l1;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                if(i<=j) continue;
     if((ficres =fopen(rfileres,"w"))==NULL) {                for (age=bage; age<=fage; age ++){ 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                  if ((int)age %5==0){
     }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     fprintf(ficres,"#%s\n",version);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                        cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     /*-------- data file ----------*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
     if((fic=fopen(datafile,"r"))==NULL)    {                    mu2=mu[j][(int) age]/stepm*YEARM;
       printf("Problem with datafile: %s\n", datafile);goto end;                    c12=cv12/sqrt(v1*v2);
     }                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     n= lastobs;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     severity = vector(1,maxwav);                    /* Eigen vectors */
     outcome=imatrix(1,maxwav+1,1,n);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     num=ivector(1,n);                    /*v21=sqrt(1.-v11*v11); *//* error */
     moisnais=vector(1,n);                    v21=(lc1-v1)/cv12*v11;
     annais=vector(1,n);                    v12=-v21;
     moisdc=vector(1,n);                    v22=v11;
     andc=vector(1,n);                    tnalp=v21/v11;
     agedc=vector(1,n);                    if(first1==1){
     cod=ivector(1,n);                      first1=0;
     weight=vector(1,n);                      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);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                    }
     mint=matrix(1,maxwav,1,n);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     anint=matrix(1,maxwav,1,n);                    /*printf(fignu*/
     s=imatrix(1,maxwav+1,1,n);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     adl=imatrix(1,maxwav+1,1,n);                        /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     tab=ivector(1,NCOVMAX);                    if(first==1){
     ncodemax=ivector(1,8);                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
     i=1;                      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);
     while (fgets(line, MAXLINE, fic) != NULL)    {                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       if ((i >= firstobs) && (i <=lastobs)) {                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                              fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
         for (j=maxwav;j>=1;j--){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           strcpy(line,stra);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      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));
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    }else{
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                      first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for (j=ncovcol;j>=1;j--){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    }/* if first */
         }                  } /* age mod 5 */
         num[i]=atol(stra);                } /* end loop age */
                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                first=1;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/              } /*l12 */
             } /* k12 */
         i=i+1;          } /*l1 */
       }        }/* k1 */
     }      } /* loop covariates */
     /* printf("ii=%d", ij);    }
        scanf("%d",i);*/    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   imx=i-1; /* Number of individuals */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
   /* for (i=1; i<=imx; i++){    fclose(ficresprob);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    fclose(ficresprobcov);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    fclose(ficresprobcor);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    fclose(ficgp);
     }*/    fclose(fichtm);
    }
   /* 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]));}  /******************* Printing html file ***********/
   */  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                      int lastpass, int stepm, int weightopt, char model[],\
   /* Calculation of the number of parameter from char model*/                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   Tvar=ivector(1,15);                    int popforecast, int estepm ,\
   Tprod=ivector(1,15);                    double jprev1, double mprev1,double anprev1, \
   Tvaraff=ivector(1,15);                    double jprev2, double mprev2,double anprev2){
   Tvard=imatrix(1,15,1,2);    int jj1, k1, i1, cpt;
   Tage=ivector(1,15);          /*char optionfilehtm[FILENAMELENGTH];*/
        if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   if (strlen(model) >1){      printf("Problem with %s \n",optionfilehtm), exit(0);
     j=0, j1=0, k1=1, k2=1;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     j=nbocc(model,'+');    }
     j1=nbocc(model,'*');  
     cptcovn=j+1;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
     cptcovprod=j1;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
       - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     strcpy(modelsav,model);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){   - Life expectancies by age and initial health status (estepm=%2d months): 
       printf("Error. Non available option model=%s ",model);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
       goto end;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     }  
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');   m=cptcoveff;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/   jj1=0;
       if (strchr(strb,'*')) {   for(k1=1; k1<=m;k1++){
         cutv(strd,strc,strb,'*');     for(i1=1; i1<=ncodemax[k1];i1++){
         if (strcmp(strc,"age")==0) {       jj1++;
           cptcovprod--;       if (cptcovn > 0) {
           cutv(strb,stre,strd,'V');         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           Tvar[i]=atoi(stre);         for (cpt=1; cpt<=cptcoveff;cpt++) 
           cptcovage++;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             Tage[cptcovage]=i;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             /*printf("stre=%s ", stre);*/       }
         }       /* Pij */
         else if (strcmp(strd,"age")==0) {       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>
           cptcovprod--;  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           cutv(strb,stre,strc,'V');       /* Quasi-incidences */
           Tvar[i]=atoi(stre);       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>
           cptcovage++;  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           Tage[cptcovage]=i;         /* Stable prevalence in each health state */
         }         for(cpt=1; cpt<nlstate;cpt++){
         else {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
           cutv(strb,stre,strc,'V');  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           Tvar[i]=ncovcol+k1;         }
           cutv(strb,strc,strd,'V');       for(cpt=1; cpt<=nlstate;cpt++) {
           Tprod[k1]=i;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
           Tvard[k1][1]=atoi(strc);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           Tvard[k1][2]=atoi(stre);       }
           Tvar[cptcovn+k2]=Tvard[k1][1];       fprintf(fichtm,"\n<br>- Total life expectancy by age and
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  health expectancies in states (1) and (2): e%s%d.png<br>
           for (k=1; k<=lastobs;k++)  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     } /* end i1 */
           k1++;   }/* End k1 */
           k2=k2+2;   fprintf(fichtm,"</ul>");
         }  
       }  
       else {   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
        /*  scanf("%d",i);*/   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
       cutv(strd,strc,strb,'V');   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
       Tvar[i]=atoi(strc);   - 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 
       strcpy(modelsav,stra);     - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);   - 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);
         scanf("%d",i);*/  
     }   if(popforecast==1) fprintf(fichtm,"\n
 }   - 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
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          <br>",fileres,fileres,fileres,fileres);
   printf("cptcovprod=%d ", cptcovprod);   else 
   scanf("%d ",i);*/     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);
     fclose(fic);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
     /*  if(mle==1){*/   m=cptcoveff;
     if (weightopt != 1) { /* Maximisation without weights*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }   jj1=0;
     /*-calculation of age at interview from date of interview and age at death -*/   for(k1=1; k1<=m;k1++){
     agev=matrix(1,maxwav,1,imx);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
     for (i=1; i<=imx; i++) {       if (cptcovn > 0) {
       for(m=2; (m<= maxwav); m++) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         for (cpt=1; cpt<=cptcoveff;cpt++) 
          anint[m][i]=9999;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          s[m][i]=-1;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }       }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;       for(cpt=1; cpt<=nlstate;cpt++) {
       }         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     }  interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     for (i=1; i<=imx; i++)  {       }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);     } /* end i1 */
       for(m=1; (m<= maxwav); m++){   }/* End k1 */
         if(s[m][i] >0){   fprintf(fichtm,"</ul>");
           if (s[m][i] >= nlstate+1) {  fclose(fichtm);
             if(agedc[i]>0)  }
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];  /******************* Gnuplot file **************/
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
            else {  
               if (andc[i]!=9999){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int ng;
               agev[m][i]=-1;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               }      printf("Problem with file %s",optionfilegnuplot);
             }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /*#ifdef windows */
             if(mint[m][i]==99 || anint[m][i]==9999)      fprintf(ficgp,"cd \"%s\" \n",pathc);
               agev[m][i]=1;      /*#endif */
             else if(agev[m][i] <agemin){  m=pow(2,cptcoveff);
               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);*/   /* 1eme*/
             }    for (cpt=1; cpt<= nlstate ; cpt ++) {
             else if(agev[m][i] >agemax){     for (k1=1; k1<= m ; k1 ++) {
               agemax=agev[m][i];       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       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);
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/       for (i=1; i<= nlstate ; i ++) {
             /*   agev[m][i] = age[i]+2*m;*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           else { /* =9 */       }
             agev[m][i]=1;       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);
             s[m][i]=-1;       for (i=1; i<= nlstate ; i ++) {
           }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         }         else fprintf(ficgp," \%%*lf (\%%*lf)");
         else /*= 0 Unknown */       } 
           agev[m][i]=1;       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
       }       for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for (i=1; i<=imx; i++)  {       }  
       for(m=1; (m<= maxwav); m++){       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         if (s[m][i] > (nlstate+ndeath)) {     }
           printf("Error: Wrong value in nlstate or ndeath\n");      }
           goto end;    /*2 eme*/
         }    
       }    for (k1=1; k1<= m ; k1 ++) { 
     }      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      
       for (i=1; i<= nlstate+1 ; i ++) {
     free_vector(severity,1,maxwav);        k=2*i;
     free_imatrix(outcome,1,maxwav+1,1,n);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     free_vector(moisnais,1,n);        for (j=1; j<= nlstate+1 ; j ++) {
     free_vector(annais,1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     /* free_matrix(mint,1,maxwav,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
        free_matrix(anint,1,maxwav,1,n);*/        }   
     free_vector(moisdc,1,n);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     free_vector(andc,1,n);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
            for (j=1; j<= nlstate+1 ; j ++) {
     wav=ivector(1,imx);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        }   
            fprintf(ficgp,"\" t\"\" w l 0,");
     /* Concatenates waves */        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
       Tcode=ivector(1,100);        }   
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       ncodemax[1]=1;        else fprintf(ficgp,"\" t\"\" w l 0,");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      }
          }
    codtab=imatrix(1,100,1,10);    
    h=0;    /*3eme*/
    m=pow(2,cptcoveff);    
      for (k1=1; k1<= m ; k1 ++) { 
    for(k=1;k<=cptcoveff; k++){      for (cpt=1; cpt<= nlstate ; cpt ++) {
      for(i=1; i <=(m/pow(2,k));i++){        k=2+nlstate*(2*cpt-2);
        for(j=1; j <= ncodemax[k]; j++){        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
            h++;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
          }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
        }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
      }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    }          
    /* 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< nlstate ; i ++) {
    /* for(i=1; i <=m ;i++){          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
       for(k=1; k <=cptcovn; k++){          
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        } 
       }      }
       printf("\n");    }
       }    
       scanf("%d",i);*/    /* CV preval stat */
        for (k1=1; k1<= m ; k1 ++) { 
    /* Calculates basic frequencies. Computes observed prevalence at single age      for (cpt=1; cpt<nlstate ; cpt ++) {
        and prints on file fileres'p'. */        k=3;
         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);
            
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i< nlstate ; i ++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"+$%d",k+i+1);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        l=3+(nlstate+ndeath)*cpt;
              fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     /* For Powell, parameters are in a vector p[] starting at p[1]        for (i=1; i< nlstate ; i ++) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          l=3+(nlstate+ndeath)*cpt;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          fprintf(ficgp,"+$%d",l+i+1);
         }
     if(mle==1){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      } 
     }    }  
        
     /*--------- results files --------------*/    /* proba elementaires */
     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);    for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
    jk=1;          for(j=1; j <=ncovmodel; j++){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            jk++; 
    for(i=1,jk=1; i <=nlstate; i++){            fprintf(ficgp,"\n");
      for(k=1; k <=(nlstate+ndeath); k++){          }
        if (k != i)        }
          {      }
            printf("%d%d ",i,k);     }
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
              printf("%f ",p[jk]);       for(jk=1; jk <=m; jk++) {
              fprintf(ficres,"%f ",p[jk]);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
              jk++;         if (ng==2)
            }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
            printf("\n");         else
            fprintf(ficres,"\n");           fprintf(ficgp,"\nset title \"Probability\"\n");
          }         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
      }         i=1;
    }         for(k2=1; k2<=nlstate; k2++) {
  if(mle==1){           k3=i;
     /* Computing hessian and covariance matrix */           for(k=1; k<=(nlstate+ndeath); k++) {
     ftolhess=ftol; /* Usually correct */             if (k != k2){
     hesscov(matcov, p, npar, delti, ftolhess, func);               if(ng==2)
  }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");               else
     printf("# Scales (for hessian or gradient estimation)\n");                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
      for(i=1,jk=1; i <=nlstate; i++){               ij=1;
       for(j=1; j <=nlstate+ndeath; j++){               for(j=3; j <=ncovmodel; j++) {
         if (j!=i) {                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           fprintf(ficres,"%1d%1d",i,j);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           printf("%1d%1d",i,j);                   ij++;
           for(k=1; k<=ncovmodel;k++){                 }
             printf(" %.5e",delti[jk]);                 else
             fprintf(ficres," %.5e",delti[jk]);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             jk++;               }
           }               fprintf(ficgp,")/(1");
           printf("\n");               
           fprintf(ficres,"\n");               for(k1=1; k1 <=nlstate; k1++){   
         }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       }                 ij=1;
      }                 for(j=3; j <=ncovmodel; j++){
                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     k=1;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     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");                     ij++;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");                   }
     for(i=1;i<=npar;i++){                   else
       /*  if (k>nlstate) k=1;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       i1=(i-1)/(ncovmodel*nlstate)+1;                 }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                 fprintf(ficgp,")");
       printf("%s%d%d",alph[k],i1,tab[i]);*/               }
       fprintf(ficres,"%3d",i);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       printf("%3d",i);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       for(j=1; j<=i;j++){               i=i+ncovmodel;
         fprintf(ficres," %.5e",matcov[i][j]);             }
         printf(" %.5e",matcov[i][j]);           } /* end k */
       }         } /* end k2 */
       fprintf(ficres,"\n");       } /* end jk */
       printf("\n");     } /* end ng */
       k++;     fclose(ficgp); 
     }  }  /* end gnuplot */
      
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  /*************** Moving average **************/
       fgets(line, MAXLINE, ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       puts(line);  
       fputs(line,ficparo);    int i, cpt, cptcod;
     }    int modcovmax =1;
     ungetc(c,ficpar);    int mobilavrange, mob;
     estepm=0;    double age;
     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;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     if (fage <= 2) {                             a covariate has 2 modalities */
       bage = ageminpar;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       fage = agemaxpar;  
     }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
          if(mobilav==1) mobilavrange=5; /* default */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      else mobilavrange=mobilav;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      for (age=bage; age<=fage; age++)
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=modcovmax;cptcod++)
     while((c=getc(ficpar))=='#' && c!= EOF){            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     ungetc(c,ficpar);      /* We keep the original values on the extreme ages bage, fage and for 
     fgets(line, MAXLINE, ficpar);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     puts(line);         we use a 5 terms etc. until the borders are no more concerned. 
     fputs(line,ficparo);      */ 
   }      for (mob=3;mob <=mobilavrange;mob=mob+2){
   ungetc(c,ficpar);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (i=1; i<=nlstate;i++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                        mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   while((c=getc(ficpar))=='#' && c!= EOF){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     ungetc(c,ficpar);                }
     fgets(line, MAXLINE, ficpar);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     puts(line);            }
     fputs(line,ficparo);          }
   }        }/* end age */
   ungetc(c,ficpar);      }/* end mob */
      }else return -1;
     return 0;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  }/* End movingaverage */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);  /************** Forecasting ******************/
   fprintf(ficparo,"pop_based=%d\n",popbased);    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){
   fprintf(ficres,"pop_based=%d\n",popbased);      /* proj1, year, month, day of starting projection 
         agemin, agemax range of age
   while((c=getc(ficpar))=='#' && c!= EOF){       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).
     fgets(line, MAXLINE, ficpar);    */
     puts(line);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     fputs(line,ficparo);    int *popage;
   }    double agec; /* generic age */
   ungetc(c,ficpar);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
   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);    double ***p3mat;
 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);    double ***mobaverage;
 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);    char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
 while((c=getc(ficpar))=='#' && c!= EOF){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     ungetc(c,ficpar);   
     fgets(line, MAXLINE, ficpar);    strcpy(fileresf,"f"); 
     puts(line);    strcat(fileresf,fileres);
     fputs(line,ficparo);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", fileresf);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    printf("Computing forecasting: result on file '%s' \n", fileresf);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
     if (mobilav!=0) {
 /*------------ gnuplot -------------*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 /*------------ free_vector  -------------*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  chdir(path);      }
      }
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    stepsize=(int) (stepm+YEARM-1)/YEARM;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      if (stepm<=12) stepsize=1;
  free_ivector(num,1,n);    if(estepm < stepm){
  free_vector(agedc,1,n);      printf ("Problem %d lower than %d\n",estepm, stepm);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    }
  fclose(ficparo);    else  hstepm=estepm;   
  fclose(ficres);  
     hstepm=hstepm/stepm; 
 /*--------- index.htm --------*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    anprojmean=yp;
     yp2=modf((yp1*12),&yp);
      mprojmean=yp;
   /*--------------- Prevalence limit --------------*/    yp1=modf((yp2*30.5),&yp);
      jprojmean=yp;
   strcpy(filerespl,"pl");    if(jprojmean==0) jprojmean=1;
   strcat(filerespl,fileres);    if(mprojmean==0) jprojmean=1;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    i1=cptcoveff;
   }    if (cptcovn < 1){i1=1;}
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   fprintf(ficrespl,"#Age ");    
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   fprintf(ficrespl,"\n");  
      for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   prlim=matrix(1,nlstate,1,nlstate);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k=k+1;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresf,"\n#******");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1;j<=cptcoveff;j++) {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          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]]);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        }
   k=0;        fprintf(ficresf,"******\n");
   agebase=ageminpar;        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   agelim=agemaxpar;        for(j=1; j<=nlstate+ndeath;j++){ 
   ftolpl=1.e-10;          for(i=1; i<=nlstate;i++)              
   i1=cptcoveff;            fprintf(ficresf," p%d%d",i,j);
   if (cptcovn < 1){i1=1;}          fprintf(ficresf," p.%d",j);
         }
   for(cptcov=1;cptcov<=i1;cptcov++){        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresf,"\n");
         k=k+1;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         for(j=1;j<=cptcoveff;j++)            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm = nhstepm/hstepm; 
         fprintf(ficrespl,"******\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    oldm=oldms;savm=savms;
         for (age=agebase; age<=agelim; age++){            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          
           fprintf(ficrespl,"%.0f",age );            for (h=0; h<=nhstepm; h++){
           for(i=1; i<=nlstate;i++)              if (h==(int) (YEARM*yearp)) {
           fprintf(ficrespl," %.5f", prlim[i][i]);                fprintf(ficresf,"\n");
           fprintf(ficrespl,"\n");                for(j=1;j<=cptcoveff;j++) 
         }                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     }              } 
   fclose(ficrespl);              for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
   /*------------- h Pij x at various ages ------------*/                for(i=1; i<=nlstate;i++) {
                    if (mobilav==1) 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                  else {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   }                  }
   printf("Computing pij: result on file '%s' \n", filerespij);                  if (h==(int)(YEARM*yearp))
                      fprintf(ficresf," %.3f", p3mat[i][j][h]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                }
   /*if (stepm<=24) stepsize=2;*/                if (h==(int)(YEARM*yearp)){
                   fprintf(ficresf," %.3f", ppij);
   agelim=AGESUP;                }
   hstepm=stepsize*YEARM; /* Every year of age */              }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;    }
         fprintf(ficrespij,"\n#****** ");         
         for(j=1;j<=cptcoveff;j++)    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    fclose(ficresf);
          }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /************** Forecasting *****not tested NB*************/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  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){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int *popage;
           fprintf(ficrespij,"# Age");    double calagedatem, agelim, kk1, kk2;
           for(i=1; i<=nlstate;i++)    double *popeffectif,*popcount;
             for(j=1; j<=nlstate+ndeath;j++)    double ***p3mat,***tabpop,***tabpopprev;
               fprintf(ficrespij," %1d-%1d",i,j);    double ***mobaverage;
           fprintf(ficrespij,"\n");    char filerespop[FILENAMELENGTH];
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             for(i=1; i<=nlstate;i++)    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               for(j=1; j<=nlstate+ndeath;j++)    agelim=AGESUP;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
             fprintf(ficrespij,"\n");    
           }    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           fprintf(ficrespij,"\n");    
         }    strcpy(filerespop,"pop"); 
     }    strcat(filerespop,fileres);
   }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
   fclose(ficrespij);    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
   /*---------- Forecasting ------------------*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    if (mobilav!=0) {
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_matrix(mint,1,maxwav,1,n);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     free_vector(weight,1,n);}        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   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);  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
     
   /*---------- Health expectancies and variances ------------*/    agelim=AGESUP;
     
   strcpy(filerest,"t");    hstepm=1;
   strcat(filerest,fileres);    hstepm=hstepm/stepm; 
   if((ficrest=fopen(filerest,"w"))==NULL) {    
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if (popforecast==1) {
   }      if((ficpop=fopen(popfile,"r"))==NULL) {
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
   strcpy(filerese,"e");      popage=ivector(0,AGESUP);
   strcat(filerese,fileres);      popeffectif=vector(0,AGESUP);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      popcount=vector(0,AGESUP);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      
   }      i=1;   
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
  strcpy(fileresv,"v");      imx=i;
   strcat(fileresv,fileres);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
   k=0;        fprintf(ficrespop,"\n#******");
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=1;j<=cptcoveff;j++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       k=k+1;        }
       fprintf(ficrest,"\n#****** ");        fprintf(ficrespop,"******\n");
       for(j=1;j<=cptcoveff;j++)        fprintf(ficrespop,"# Age");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       fprintf(ficrest,"******\n");        if (popforecast==1)  fprintf(ficrespop," [Population]");
         
       fprintf(ficreseij,"\n#****** ");        for (cpt=0; cpt<=0;cpt++) { 
       for(j=1;j<=cptcoveff;j++)          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
       fprintf(ficreseij,"******\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       fprintf(ficresvij,"\n#****** ");            nhstepm = nhstepm/hstepm; 
       for(j=1;j<=cptcoveff;j++)            
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresvij,"******\n");            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          
       oldm=oldms;savm=savms;            for (h=0; h<=nhstepm; h++){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);                if (h==(int) (calagedatem+YEARM*cpt)) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       oldm=oldms;savm=savms;              } 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);              for(j=1; j<=nlstate+ndeath;j++) {
                    kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                    if (mobilav==1) 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                  else {
       fprintf(ficrest,"\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
       epj=vector(1,nlstate+1);                }
       for(age=bage; age <=fage ;age++){                if (h==(int)(calagedatem+12*cpt)){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
         if (popbased==1) {                    /*fprintf(ficrespop," %.3f", kk1);
           for(i=1; i<=nlstate;i++)                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
             prlim[i][i]=probs[(int)age][i][k];                }
         }              }
                      for(i=1; i<=nlstate;i++){
         fprintf(ficrest," %4.0f",age);                kk1=0.;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                  for(j=1; j<=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                  }
           }                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
           epj[nlstate+1] +=epj[j];              }
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
           for(j=1;j <=nlstate;j++)                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             vepp += vareij[i][j][(int)age];            }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1;j <=nlstate;j++){          }
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        }
         }   
         fprintf(ficrest,"\n");    /******/
       }  
     }        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   }          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   fclose(ficreseij);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fclose(ficresvij);            nhstepm = nhstepm/hstepm; 
   fclose(ficrest);            
   fclose(ficpar);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_vector(epj,1,nlstate+1);            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   /*------- Variance limit prevalence------*/              for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
   strcpy(fileresvpl,"vpl");                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   strcat(fileresvpl,fileres);              } 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              for(j=1; j<=nlstate+ndeath;j++) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                kk1=0.;kk2=0;
     exit(0);                for(i=1; i<=nlstate;i++) {              
   }                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   k=0;              }
   for(cptcov=1;cptcov<=i1;cptcov++){            }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       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");   
          if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    if (popforecast==1) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      free_ivector(popage,0,AGESUP);
     }      free_vector(popeffectif,0,AGESUP);
  }      free_vector(popcount,0,AGESUP);
     }
   fclose(ficresvpl);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*---------- End : free ----------------*/    fclose(ficrespop);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  }
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  /***********************************************/
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  /**************** Main Program *****************/
    /***********************************************/
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  int main(int argc, char *argv[])
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
      double agedeb, agefin,hf;
   free_matrix(matcov,1,npar,1,npar);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    double fret;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double **xi,tmp,delta;
   
   if(erreur >0)    double dum; /* Dummy variable */
     printf("End of Imach with error or warning %d\n",erreur);    double ***p3mat;
   else   printf("End of Imach\n");    double ***mobaverage;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int *indx;
      char line[MAXLINE], linepar[MAXLINE];
   /* 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);*/    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   /*printf("Total time was %d uSec.\n", total_usecs);*/    int firstobs=1, lastobs=10;
   /*------ End -----------*/    int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
  end:    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
 #ifdef windows    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   /* chdir(pathcd);*/    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
 #endif    int mobilav=0,popforecast=0;
  /*system("wgnuplot graph.plt");*/    int hstepm, nhstepm;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
  /*system("cd ../gp37mgw");*/    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    double bage, fage, age, agelim, agebase;
  strcat(plotcmd," ");    double ftolpl=FTOL;
  strcat(plotcmd,optionfilegnuplot);    double **prlim;
  system(plotcmd);    double *severity;
     double ***param; /* Matrix of parameters */
 #ifdef windows    double  *p;
   while (z[0] != 'q') {    double **matcov; /* Matrix of covariance */
     /* chdir(path); */    double ***delti3; /* Scale */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    double *delti; /* Scale */
     scanf("%s",z);    double ***eij, ***vareij;
     if (z[0] == 'c') system("./imach");    double **varpl; /* Variances of prevalence limits by age */
     else if (z[0] == 'e') system(optionfilehtm);    double *epj, vepp;
     else if (z[0] == 'g') system(plotcmd);    double kk1, kk2;
     else if (z[0] == 'q') exit(0);    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   }  
 #endif    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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