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version 1.41.2.2, 2003/06/13 07:45:28 version 1.65, 2002/12/11 16:58:19
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
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month or quarter trimester,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is model 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 .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
   #define windows
 /*#define windows*/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
   #define NINTERVMAX 8
 #define NINTERVMAX 8  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define MAXN 20000
 #define MAXN 20000  #define YEARM 12. /* Number of months per year */
 #define YEARM 12. /* Number of months per year */  #define AGESUP 130
 #define AGESUP 130  #define AGEBASE 40
 #define AGEBASE 40  #ifdef windows
   #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 int erreur; /* Error number */  #else
 int nvar;  #define DIRSEPARATOR '/'
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define ODIRSEPARATOR '\\'
 int npar=NPARMAX;  #endif
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */  char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int erreur; /* Error number */
 int popbased=0;  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int *wav; /* Number of waves for this individuual 0 is possible */  int npar=NPARMAX;
 int maxwav; /* Maxim number of waves */  int nlstate=2; /* Number of live states */
 int jmin, jmax; /* min, max spacing between 2 waves */  int ndeath=1; /* Number of dead states */
 int mle, weightopt;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int popbased=0;
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int maxwav; /* Maxim number of waves */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int mle, weightopt;
 FILE *ficgp,*ficresprob,*ficpop;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 FILE *ficreseij;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   char filerese[FILENAMELENGTH];  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
  FILE  *ficresvij;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   char fileresv[FILENAMELENGTH];  double jmean; /* Mean space between 2 waves */
  FILE  *ficresvpl;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   char fileresvpl[FILENAMELENGTH];  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define NR_END 1  FILE *ficlog;
 #define FREE_ARG char*  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define FTOL 1.0e-10  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 #define NRANSI  FILE *ficreseij;
 #define ITMAX 200  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 #define TOL 2.0e-4  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 #define CGOLD 0.3819660  char fileresvpl[FILENAMELENGTH];
 #define ZEPS 1.0e-10  char title[MAXLINE];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GOLD 1.618034  
 #define GLIMIT 100.0  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define TINY 1.0e-20  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 static double maxarg1,maxarg2;  char fileregp[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
    char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)  #define NR_END 1
   #define FREE_ARG char*
 static double sqrarg;  #define FTOL 1.0e-10
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define NRANSI 
   #define ITMAX 200 
 int imx;  
 int stepm;  #define TOL 2.0e-4 
 /* Stepm, step in month: minimum step interpolation*/  
   #define CGOLD 0.3819660 
 int estepm;  #define ZEPS 1.0e-10 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 int m,nb;  #define GOLD 1.618034 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GLIMIT 100.0 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define TINY 1.0e-20 
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double *weight;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 int **s; /* Status */    
 double *agedc, **covar, idx;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define rint(a) floor(a+0.5)
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  static double sqrarg;
 double ftolhess; /* Tolerance for computing hessian */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int imx; 
 {  int stepm;
    char *s;                             /* pointer */  /* Stepm, step in month: minimum step interpolation*/
    int  l1, l2;                         /* length counters */  
   int estepm;
    l1 = strlen( path );                 /* length of path */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  int m,nb;
    s = strrchr( path, '\\' );           /* find last / */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 #else  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    s = strrchr( path, '/' );            /* find last / */  double **pmmij, ***probs;
 #endif  double dateintmean=0;
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  double *weight;
       extern char       *getwd( );  int **s; /* Status */
   double *agedc, **covar, idx;
       if ( getwd( dirc ) == NULL ) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 #else  
       extern char       *getcwd( );  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  /**************** split *************************/
          return( GLOCK_ERROR_GETCWD );  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       }  {
       strcpy( name, path );             /* we've got it */    char  *ss;                            /* pointer */
    } else {                             /* strip direcotry from path */    int   l1, l2;                         /* length counters */
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    l1 = strlen(path );                   /* length of path */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, s );                /* save file name */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    if ( ss == NULL ) {                   /* no directory, so use current */
       dirc[l1-l2] = 0;                  /* add zero */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
    }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
    l1 = strlen( dirc );                 /* length of directory */  #if     defined(__bsd__)                /* get current working directory */
 #ifdef windows      extern char *getwd( );
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else      if ( getwd( dirc ) == NULL ) {
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #else
 #endif      extern char *getcwd( );
    s = strrchr( name, '.' );            /* find last / */  
    s++;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    strcpy(ext,s);                       /* save extension */  #endif
    l1= strlen( name);        return( GLOCK_ERROR_GETCWD );
    l2= strlen( s)+1;      }
    strncpy( finame, name, l1-l2);      strcpy( name, path );               /* we've got it */
    finame[l1-l2]= 0;    } else {                              /* strip direcotry from path */
    return( 0 );                         /* we're done */      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 /******************************************/      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 void replace(char *s, char*t)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   int i;  #ifdef windows
   int lg=20;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   i=0;  #else
   lg=strlen(t);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   for(i=0; i<= lg; i++) {  #endif
     (s[i] = t[i]);    ss = strrchr( name, '.' );            /* find last / */
     if (t[i]== '\\') s[i]='/';    ss++;
   }    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 int nbocc(char *s, char occ)    strncpy( finame, name, l1-l2);
 {    finame[l1-l2]= 0;
   int i,j=0;    return( 0 );                          /* we're done */
   int lg=20;  }
   i=0;  
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  /******************************************/
   if  (s[i] == occ ) j++;  
   }  void replace(char *s, char*t)
   return j;  {
 }    int i;
     int lg=20;
 void cutv(char *u,char *v, char*t, char occ)    i=0;
 {    lg=strlen(t);
   int i,lg,j,p=0;    for(i=0; i<= lg; i++) {
   i=0;      (s[i] = t[i]);
   for(j=0; j<=strlen(t)-1; j++) {      if (t[i]== '\\') s[i]='/';
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    }
   }  }
   
   lg=strlen(t);  int nbocc(char *s, char occ)
   for(j=0; j<p; j++) {  {
     (u[j] = t[j]);    int i,j=0;
   }    int lg=20;
      u[p]='\0';    i=0;
     lg=strlen(s);
    for(j=0; j<= lg; j++) {    for(i=0; i<= lg; i++) {
     if (j>=(p+1))(v[j-p-1] = t[j]);    if  (s[i] == occ ) j++;
   }    }
 }    return j;
   }
 /********************** nrerror ********************/  
   void cutv(char *u,char *v, char*t, char occ)
 void nrerror(char error_text[])  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   fprintf(stderr,"ERREUR ...\n");       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   fprintf(stderr,"%s\n",error_text);       gives u="abcedf" and v="ghi2j" */
   exit(1);    int i,lg,j,p=0;
 }    i=0;
 /*********************** vector *******************/    for(j=0; j<=strlen(t)-1; j++) {
 double *vector(int nl, int nh)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!v) nrerror("allocation failure in vector");    for(j=0; j<p; j++) {
   return v-nl+NR_END;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG)(v+nl-NR_END));    }
 }  }
   
 /************************ivector *******************************/  /********************** nrerror ********************/
 int *ivector(long nl,long nh)  
 {  void nrerror(char error_text[])
   int *v;  {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    fprintf(stderr,"ERREUR ...\n");
   if (!v) nrerror("allocation failure in ivector");    fprintf(stderr,"%s\n",error_text);
   return v-nl+NR_END;    exit(EXIT_FAILURE);
 }  }
   /*********************** vector *******************/
 /******************free ivector **************************/  double *vector(int nl, int nh)
 void free_ivector(int *v, long nl, long nh)  {
 {    double *v;
   free((FREE_ARG)(v+nl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /******************* imatrix *******************************/  }
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  {
   int **m;    free((FREE_ARG)(v+nl-NR_END));
    }
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  /************************ivector *******************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  int *ivector(long nl,long nh)
   m += NR_END;  {
   m -= nrl;    int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
   /* allocate rows and set pointers to them */    return v-nl+NR_END;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /******************free ivector **************************/
   m[nrl] -= ncl;  void free_ivector(int *v, long nl, long nh)
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    free((FREE_ARG)(v+nl-NR_END));
    }
   /* return pointer to array of pointers to rows */  
   return m;  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /****************** free_imatrix *************************/  { 
 void free_imatrix(m,nrl,nrh,ncl,nch)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       int **m;    int **m; 
       long nch,ncl,nrh,nrl;    
      /* free an int matrix allocated by imatrix() */    /* allocate pointers to rows */ 
 {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()"); 
   free((FREE_ARG) (m+nrl-NR_END));    m += NR_END; 
 }    m -= nrl; 
     
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    /* allocate rows and set pointers to them */ 
 {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double **m;    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m += NR_END;    
   m -= nrl;    /* return pointer to array of pointers to rows */ 
     return m; 
   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;  /****************** free_imatrix *************************/
   m[nrl] -= ncl;  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;        long nch,ncl,nrh,nrl; 
   return m;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 /*************************free matrix ************************/    free((FREE_ARG) (m+nrl-NR_END)); 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  } 
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /******************* matrix *******************************/
   free((FREE_ARG)(m+nrl-NR_END));  double **matrix(long nrl, long nrh, long ncl, long nch)
 }  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 /******************* ma3x *******************************/    double **m;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    if (!m) nrerror("allocation failure 1 in matrix()");
   double ***m;    m += NR_END;
     m -= nrl;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m += NR_END;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   m -= nrl;    m[nrl] += NR_END;
     m[nrl] -= ncl;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   m[nrl] += NR_END;    return m;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(m+nrl-NR_END));
   m[nrl][ncl] -= nll;  }
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  /******************* ma3x *******************************/
    double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (i=nrl+1; i<=nrh; i++) {  {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for (j=ncl+1; j<=nch; j++)    double ***m;
       m[i][j]=m[i][j-1]+nlay;  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   return m;    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl] += NR_END;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] -= ncl;
   free((FREE_ARG)(m+nrl-NR_END));  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 /***************** f1dim *************************/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 extern int ncom;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 extern double *pcom,*xicom;    m[nrl][ncl] += NR_END;
 extern double (*nrfunc)(double []);    m[nrl][ncl] -= nll;
      for (j=ncl+1; j<=nch; j++) 
 double f1dim(double x)      m[nrl][j]=m[nrl][j-1]+nlay;
 {    
   int j;    for (i=nrl+1; i<=nrh; i++) {
   double f;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double *xt;      for (j=ncl+1; j<=nch; j++) 
          m[i][j]=m[i][j-1]+nlay;
   xt=vector(1,ncom);    }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    return m;
   f=(*nrfunc)(xt);  }
   free_vector(xt,1,ncom);  
   return f;  /*************************free ma3x ************************/
 }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 /*****************brent *************************/    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /***************** f1dim *************************/
   double ftemp;  extern int ncom; 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern double *pcom,*xicom;
   double e=0.0;  extern double (*nrfunc)(double []); 
     
   a=(ax < cx ? ax : cx);  double f1dim(double x) 
   b=(ax > cx ? ax : cx);  { 
   x=w=v=bx;    int j; 
   fw=fv=fx=(*f)(x);    double f;
   for (iter=1;iter<=ITMAX;iter++) {    double *xt; 
     xm=0.5*(a+b);   
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    xt=vector(1,ncom); 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     printf(".");fflush(stdout);    f=(*nrfunc)(xt); 
 #ifdef DEBUG    free_vector(xt,1,ncom); 
     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);    return f; 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  } 
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /*****************brent *************************/
       *xmin=x;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       return fx;  { 
     }    int iter; 
     ftemp=fu;    double a,b,d,etemp;
     if (fabs(e) > tol1) {    double fu,fv,fw,fx;
       r=(x-w)*(fx-fv);    double ftemp;
       q=(x-v)*(fx-fw);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       p=(x-v)*q-(x-w)*r;    double e=0.0; 
       q=2.0*(q-r);   
       if (q > 0.0) p = -p;    a=(ax < cx ? ax : cx); 
       q=fabs(q);    b=(ax > cx ? ax : cx); 
       etemp=e;    x=w=v=bx; 
       e=d;    fw=fv=fx=(*f)(x); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    for (iter=1;iter<=ITMAX;iter++) { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      xm=0.5*(a+b); 
       else {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         d=p/q;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         u=x+d;      printf(".");fflush(stdout);
         if (u-a < tol2 || b-u < tol2)      fprintf(ficlog,".");fflush(ficlog);
           d=SIGN(tol1,xm-x);  #ifdef DEBUG
       }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     } else {      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);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     }  #endif
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     fu=(*f)(u);        *xmin=x; 
     if (fu <= fx) {        return fx; 
       if (u >= x) a=x; else b=x;      } 
       SHFT(v,w,x,u)      ftemp=fu;
         SHFT(fv,fw,fx,fu)      if (fabs(e) > tol1) { 
         } else {        r=(x-w)*(fx-fv); 
           if (u < x) a=u; else b=u;        q=(x-v)*(fx-fw); 
           if (fu <= fw || w == x) {        p=(x-v)*q-(x-w)*r; 
             v=w;        q=2.0*(q-r); 
             w=u;        if (q > 0.0) p = -p; 
             fv=fw;        q=fabs(q); 
             fw=fu;        etemp=e; 
           } else if (fu <= fv || v == x || v == w) {        e=d; 
             v=u;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
             fv=fu;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           }        else { 
         }          d=p/q; 
   }          u=x+d; 
   nrerror("Too many iterations in brent");          if (u-a < tol2 || b-u < tol2) 
   *xmin=x;            d=SIGN(tol1,xm-x); 
   return fx;        } 
 }      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 /****************** mnbrak ***********************/      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      fu=(*f)(u); 
             double (*func)(double))      if (fu <= fx) { 
 {        if (u >= x) a=x; else b=x; 
   double ulim,u,r,q, dum;        SHFT(v,w,x,u) 
   double fu;          SHFT(fv,fw,fx,fu) 
            } else { 
   *fa=(*func)(*ax);            if (u < x) a=u; else b=u; 
   *fb=(*func)(*bx);            if (fu <= fw || w == x) { 
   if (*fb > *fa) {              v=w; 
     SHFT(dum,*ax,*bx,dum)              w=u; 
       SHFT(dum,*fb,*fa,dum)              fv=fw; 
       }              fw=fu; 
   *cx=(*bx)+GOLD*(*bx-*ax);            } else if (fu <= fv || v == x || v == w) { 
   *fc=(*func)(*cx);              v=u; 
   while (*fb > *fc) {              fv=fu; 
     r=(*bx-*ax)*(*fb-*fc);            } 
     q=(*bx-*cx)*(*fb-*fa);          } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    nrerror("Too many iterations in brent"); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    *xmin=x; 
     if ((*bx-u)*(u-*cx) > 0.0) {    return fx; 
       fu=(*func)(u);  } 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /****************** mnbrak ***********************/
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           SHFT(*fb,*fc,fu,(*func)(u))              double (*func)(double)) 
           }  { 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    double ulim,u,r,q, dum;
       u=ulim;    double fu; 
       fu=(*func)(u);   
     } else {    *fa=(*func)(*ax); 
       u=(*cx)+GOLD*(*cx-*bx);    *fb=(*func)(*bx); 
       fu=(*func)(u);    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     SHFT(*ax,*bx,*cx,u)        SHFT(dum,*fb,*fa,dum) 
       SHFT(*fa,*fb,*fc,fu)        } 
       }    *cx=(*bx)+GOLD*(*bx-*ax); 
 }    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 /*************** linmin ************************/      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 int ncom;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 double *pcom,*xicom;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 double (*nrfunc)(double []);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
        if ((*bx-u)*(u-*cx) > 0.0) { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        fu=(*func)(u); 
 {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double brent(double ax, double bx, double cx,        fu=(*func)(u); 
                double (*f)(double), double tol, double *xmin);        if (fu < *fc) { 
   double f1dim(double x);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,            SHFT(*fb,*fc,fu,(*func)(u)) 
               double *fc, double (*func)(double));            } 
   int j;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double xx,xmin,bx,ax;        u=ulim; 
   double fx,fb,fa;        fu=(*func)(u); 
        } else { 
   ncom=n;        u=(*cx)+GOLD*(*cx-*bx); 
   pcom=vector(1,n);        fu=(*func)(u); 
   xicom=vector(1,n);      } 
   nrfunc=func;      SHFT(*ax,*bx,*cx,u) 
   for (j=1;j<=n;j++) {        SHFT(*fa,*fb,*fc,fu) 
     pcom[j]=p[j];        } 
     xicom[j]=xi[j];  } 
   }  
   ax=0.0;  /*************** linmin ************************/
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int ncom; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double *pcom,*xicom;
 #ifdef DEBUG  double (*nrfunc)(double []); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);   
 #endif  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   for (j=1;j<=n;j++) {  { 
     xi[j] *= xmin;    double brent(double ax, double bx, double cx, 
     p[j] += xi[j];                 double (*f)(double), double tol, double *xmin); 
   }    double f1dim(double x); 
   free_vector(xicom,1,n);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   free_vector(pcom,1,n);                double *fc, double (*func)(double)); 
 }    int j; 
     double xx,xmin,bx,ax; 
 /*************** powell ************************/    double fx,fb,fa;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   
             double (*func)(double []))    ncom=n; 
 {    pcom=vector(1,n); 
   void linmin(double p[], double xi[], int n, double *fret,    xicom=vector(1,n); 
               double (*func)(double []));    nrfunc=func; 
   int i,ibig,j;    for (j=1;j<=n;j++) { 
   double del,t,*pt,*ptt,*xit;      pcom[j]=p[j]; 
   double fp,fptt;      xicom[j]=xi[j]; 
   double *xits;    } 
   pt=vector(1,n);    ax=0.0; 
   ptt=vector(1,n);    xx=1.0; 
   xit=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   xits=vector(1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   *fret=(*func)(p);  #ifdef DEBUG
   for (j=1;j<=n;j++) pt[j]=p[j];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (*iter=1;;++(*iter)) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fp=(*fret);  #endif
     ibig=0;    for (j=1;j<=n;j++) { 
     del=0.0;      xi[j] *= xmin; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      p[j] += xi[j]; 
     for (i=1;i<=n;i++)    } 
       printf(" %d %.12f",i, p[i]);    free_vector(xicom,1,n); 
     printf("\n");    free_vector(pcom,1,n); 
     for (i=1;i<=n;i++) {  } 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /*************** powell ************************/
 #ifdef DEBUG  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       printf("fret=%lf \n",*fret);              double (*func)(double [])) 
 #endif  { 
       printf("%d",i);fflush(stdout);    void linmin(double p[], double xi[], int n, double *fret, 
       linmin(p,xit,n,fret,func);                double (*func)(double [])); 
       if (fabs(fptt-(*fret)) > del) {    int i,ibig,j; 
         del=fabs(fptt-(*fret));    double del,t,*pt,*ptt,*xit;
         ibig=i;    double fp,fptt;
       }    double *xits;
 #ifdef DEBUG    pt=vector(1,n); 
       printf("%d %.12e",i,(*fret));    ptt=vector(1,n); 
       for (j=1;j<=n;j++) {    xit=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xits=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for(j=1;j<=n;j++)    for (*iter=1;;++(*iter)) { 
         printf(" p=%.12e",p[j]);      fp=(*fret); 
       printf("\n");      ibig=0; 
 #endif      del=0.0; 
     }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      for (i=1;i<=n;i++) 
       int k[2],l;        printf(" %d %.12f",i, p[i]);
       k[0]=1;      fprintf(ficlog," %d %.12f",i, p[i]);
       k[1]=-1;      printf("\n");
       printf("Max: %.12e",(*func)(p));      fprintf(ficlog,"\n");
       for (j=1;j<=n;j++)      for (i=1;i<=n;i++) { 
         printf(" %.12e",p[j]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       printf("\n");        fptt=(*fret); 
       for(l=0;l<=1;l++) {  #ifdef DEBUG
         for (j=1;j<=n;j++) {        printf("fret=%lf \n",*fret);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        fprintf(ficlog,"fret=%lf \n",*fret);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #endif
         }        printf("%d",i);fflush(stdout);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
 #endif        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
           ibig=i; 
       free_vector(xit,1,n);        } 
       free_vector(xits,1,n);  #ifdef DEBUG
       free_vector(ptt,1,n);        printf("%d %.12e",i,(*fret));
       free_vector(pt,1,n);        fprintf(ficlog,"%d %.12e",i,(*fret));
       return;        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          printf(" x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=n;j++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       ptt[j]=2.0*p[j]-pt[j];        }
       xit[j]=p[j]-pt[j];        for(j=1;j<=n;j++) {
       pt[j]=p[j];          printf(" p=%.12e",p[j]);
     }          fprintf(ficlog," p=%.12e",p[j]);
     fptt=(*func)(ptt);        }
     if (fptt < fp) {        printf("\n");
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        fprintf(ficlog,"\n");
       if (t < 0.0) {  #endif
         linmin(p,xit,n,fret,func);      } 
         for (j=1;j<=n;j++) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           xi[j][ibig]=xi[j][n];  #ifdef DEBUG
           xi[j][n]=xit[j];        int k[2],l;
         }        k[0]=1;
 #ifdef DEBUG        k[1]=-1;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        printf("Max: %.12e",(*func)(p));
         for(j=1;j<=n;j++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
           printf(" %.12e",xit[j]);        for (j=1;j<=n;j++) {
         printf("\n");          printf(" %.12e",p[j]);
 #endif          fprintf(ficlog," %.12e",p[j]);
       }        }
     }        printf("\n");
   }        fprintf(ficlog,"\n");
 }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 /**** Prevalence limit ****************/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {          }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      matrix by transitions matrix until convergence is reached */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   int i, ii,j,k;  #endif
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();        free_vector(xit,1,n); 
   double **newm;        free_vector(xits,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        return; 
     for (j=1;j<=nlstate+ndeath;j++){      } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
    cov[1]=1.;        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      fptt=(*func)(ptt); 
     newm=savm;      if (fptt < fp) { 
     /* Covariates have to be included here again */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
      cov[2]=agefin;        if (t < 0.0) { 
            linmin(p,xit,n,fret,func); 
       for (k=1; k<=cptcovn;k++) {          for (j=1;j<=n;j++) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            xi[j][ibig]=xi[j][n]; 
         /*      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]]);*/            xi[j][n]=xit[j]; 
       }          }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #ifdef DEBUG
       for (k=1; k<=cptcovprod;k++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/            printf(" %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            fprintf(ficlog," %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          printf("\n");
           fprintf(ficlog,"\n");
     savm=oldm;  #endif
     oldm=newm;        }
     maxmax=0.;      } 
     for(j=1;j<=nlstate;j++){    } 
       min=1.;  } 
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /**** Prevalence limit (stable prevalence)  ****************/
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         prlim[i][j]= newm[i][j]/(1-sumnew);  {
         max=FMAX(max,prlim[i][j]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         min=FMIN(min,prlim[i][j]);       matrix by transitions matrix until convergence is reached */
       }  
       maxmin=max-min;    int i, ii,j,k;
       maxmax=FMAX(maxmax,maxmin);    double min, max, maxmin, maxmax,sumnew=0.;
     }    double **matprod2();
     if(maxmax < ftolpl){    double **out, cov[NCOVMAX], **pmij();
       return prlim;    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
   }  
 }    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
 /*************** transition probabilities ***************/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {     cov[1]=1.;
   double s1, s2;   
   /*double t34;*/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i,j,j1, nc, ii, jj;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
     for(i=1; i<= nlstate; i++){      /* Covariates have to be included here again */
     for(j=1; j<i;j++){       cov[2]=agefin;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    
         /*s2 += param[i][j][nc]*cov[nc];*/        for (k=1; k<=cptcovn;k++) {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          /*      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]]);*/
       }        }
       ps[i][j]=s2;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        for (k=1; k<=cptcovprod;k++)
     }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       ps[i][j]=s2;  
     }      savm=oldm;
   }      oldm=newm;
     /*ps[3][2]=1;*/      maxmax=0.;
       for(j=1;j<=nlstate;j++){
   for(i=1; i<= nlstate; i++){        min=1.;
      s1=0;        max=0.;
     for(j=1; j<i; j++)        for(i=1; i<=nlstate; i++) {
       s1+=exp(ps[i][j]);          sumnew=0;
     for(j=i+1; j<=nlstate+ndeath; j++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       s1+=exp(ps[i][j]);          prlim[i][j]= newm[i][j]/(1-sumnew);
     ps[i][i]=1./(s1+1.);          max=FMAX(max,prlim[i][j]);
     for(j=1; j<i; j++)          min=FMIN(min,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];        }
     for(j=i+1; j<=nlstate+ndeath; j++)        maxmin=max-min;
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmax=FMAX(maxmax,maxmin);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      }
   } /* end i */      if(maxmax < ftolpl){
         return prlim;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      }
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
       ps[ii][jj]=0;  }
       ps[ii][ii]=1;  
     }  /*************** transition probabilities ***************/ 
   }  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double s1, s2;
     for(jj=1; jj<= nlstate+ndeath; jj++){    /*double t34;*/
      printf("%lf ",ps[ii][jj]);    int i,j,j1, nc, ii, jj;
    }  
     printf("\n ");      for(i=1; i<= nlstate; i++){
     }      for(j=1; j<i;j++){
     printf("\n ");printf("%lf ",cov[2]);*/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 /*          /*s2 += param[i][j][nc]*cov[nc];*/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   goto end;*/          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     return ps;        }
 }        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 /**************** Product of 2 matrices ******************/      }
       for(j=i+1; j<=nlstate+ndeath;j++){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        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];
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        }
   /* in, b, out are matrice of pointers which should have been initialized        ps[i][j]=s2;
      before: only the contents of out is modified. The function returns      }
      a pointer to pointers identical to out */    }
   long i, j, k;      /*ps[3][2]=1;*/
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)    for(i=1; i<= nlstate; i++){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)       s1=0;
         out[i][k] +=in[i][j]*b[j][k];      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
   return out;      for(j=i+1; j<=nlstate+ndeath; j++)
 }        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
 /************* Higher Matrix Product ***************/        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        ps[i][j]= exp(ps[i][j])*ps[i][i];
 {      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    } /* end i */
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      for(jj=1; jj<= nlstate+ndeath; jj++){
      (typically every 2 years instead of every month which is too big).        ps[ii][jj]=0;
      Model is determined by parameters x and covariates have to be        ps[ii][ii]=1;
      included manually here.      }
     }
      */  
   
   int i, j, d, h, k;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double **out, cov[NCOVMAX];      for(jj=1; jj<= nlstate+ndeath; jj++){
   double **newm;       printf("%lf ",ps[ii][jj]);
      }
   /* Hstepm could be zero and should return the unit matrix */      printf("\n ");
   for (i=1;i<=nlstate+ndeath;i++)      }
     for (j=1;j<=nlstate+ndeath;j++){      printf("\n ");printf("%lf ",cov[2]);*/
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*
       po[i][j][0]=(i==j ? 1.0 : 0.0);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     }    goto end;*/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      return ps;
   for(h=1; h <=nhstepm; h++){  }
     for(d=1; d <=hstepm; d++){  
       newm=savm;  /**************** Product of 2 matrices ******************/
       /* Covariates have to be included here again */  
       cov[1]=1.;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1; k<=cptcovage;k++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* in, b, out are matrice of pointers which should have been initialized 
       for (k=1; k<=cptcovprod;k++)       before: only the contents of out is modified. The function returns
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       a pointer to pointers identical to out */
     long i, j, k;
     for(i=nrl; i<= nrh; i++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      for(k=ncolol; k<=ncoloh; k++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          out[i][k] +=in[i][j]*b[j][k];
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    return out;
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /************* Higher Matrix Product ***************/
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          */  {
       }    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
   } /* end h */       duration (i.e. until
   return po;       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
 }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big).
        Model is determined by parameters x and covariates have to be 
 /*************** log-likelihood *************/       included manually here. 
 double func( double *x)  
 {       */
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    int i, j, d, h, k;
   double **out;    double **out, cov[NCOVMAX];
   double sw; /* Sum of weights */    double **newm;
   double lli; /* Individual log likelihood */  
   int s1, s2;    /* Hstepm could be zero and should return the unit matrix */
   long ipmx;    for (i=1;i<=nlstate+ndeath;i++)
   /*extern weight */      for (j=1;j<=nlstate+ndeath;j++){
   /* We are differentiating ll according to initial status */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /*for(i=1;i<imx;i++)      }
     printf(" %d\n",s[4][i]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   */    for(h=1; h <=nhstepm; h++){
   cov[1]=1.;      for(d=1; d <=hstepm; d++){
         newm=savm;
   for(k=1; k<=nlstate; k++) ll[k]=0.;        /* Covariates have to be included here again */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        cov[1]=1.;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for(mi=1; mi<= wav[i]-1; mi++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (k=1; k<=cptcovage;k++)
         for (j=1;j<=nlstate+ndeath;j++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for (k=1; k<=cptcovprod;k++)
           savm[ii][j]=(ii==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]]];
         }  
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         for (kk=1; kk<=cptcovage;kk++) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         }        savm=oldm;
                oldm=newm;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      for(i=1; i<=nlstate+ndeath; i++)
         savm=oldm;        for(j=1;j<=nlstate+ndeath;j++) {
         oldm=newm;          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]);
                   */
       } /* end mult */        }
          } /* end h */
       s1=s[mw[mi][i]][i];    return po;
       s2=s[mw[mi+1][i]][i];  }
       if( s2 > nlstate){  
         /* i.e. if s2 is a death state and if the date of death is known then the contribution  
            to the likelihood is the probability to die between last step unit time and current  /*************** log-likelihood *************/
            step unit time, which is also the differences between probability to die before dh  double func( double *x)
            and probability to die before dh-stepm .  {
            In version up to 0.92 likelihood was computed    int i, ii, j, k, mi, d, kk;
            as if date of death was unknown. Death was treated as any other    double l, ll[NLSTATEMAX], cov[NCOVMAX];
            health state: the date of the interview describes the actual state    double **out;
            and not the date of a change in health state. The former idea was    double sw; /* Sum of weights */
            to consider that at each interview the state was recorded    double lli; /* Individual log likelihood */
            (healthy, disable or death) and IMaCh was corrected; but when we    int s1, s2;
            introduced the exact date of death then we should have modified    double bbh;
            the contribution of an exact death to the likelihood. This new    long ipmx;
            contribution is smaller and very dependent of the step unit    /*extern weight */
            stepm. It is no more the probability to die between last interview    /* We are differentiating ll according to initial status */
            and month of death but the probability to survive from last    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
            interview up to one month before death multiplied by the    /*for(i=1;i<imx;i++) 
            probability to die within a month. Thanks to Chris      printf(" %d\n",s[4][i]);
            Jackson for correcting this bug.  Former versions increased    */
            mortality artificially. The bad side is that we add another loop    cov[1]=1.;
            which slows down the processing. The difference can be up to 10%  
            lower mortality.    for(k=1; k<=nlstate; k++) ll[k]=0.;
         */  
         lli=log(out[s1][s2] - savm[s1][s2]);    if(mle==1){
       }else{      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       ipmx +=1;            for (j=1;j<=nlstate+ndeath;j++){
       sw += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/            }
     } /* end of wave */          for(d=0; d<dh[mi][i]; d++){
   } /* end of individual */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];            for (kk=1; kk<=cptcovage;kk++) {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */            }
   /*exit(0);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   return -l;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
           } /* end mult */
 /*********** Maximum Likelihood Estimation ***************/        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          /* But now since version 0.9 we anticipate for bias and large stepm.
 {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int i,j, iter;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double **xi,*delti;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double fret;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   xi=matrix(1,npar,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for (i=1;i<=npar;i++)           * probability in order to take into account the bias as a fraction of the way
     for (j=1;j<=npar;j++)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       xi[i][j]=(i==j ? 1.0 : 0.0);           * -stepm/2 to stepm/2 .
   printf("Powell\n");           * For stepm=1 the results are the same as for previous versions of Imach.
   powell(p,xi,npar,ftol,&iter,&fret,func);           * For stepm > 1 the results are less biased than in previous versions. 
            */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          s1=s[mw[mi][i]][i];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 }          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
 /**** Computes Hessian and covariance matrix ***/           */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
   double  **a,**y,*x,pd;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double **hess;          /*if(lli ==000.0)*/
   int i, j,jk;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int *indx;          ipmx +=1;
           sw += weight[i];
   double hessii(double p[], double delta, int theta, double delti[]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double hessij(double p[], double delti[], int i, int j);        } /* end of wave */
   void lubksb(double **a, int npar, int *indx, double b[]) ;      } /* end of individual */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hess=matrix(1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   printf("\nCalculation of the hessian matrix. Wait...\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++){            for (j=1;j<=nlstate+ndeath;j++){
     printf("%d",i);fflush(stdout);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     hess[i][i]=hessii(p,ftolhess,i,delti);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /*printf(" %f ",p[i]);*/            }
     /*printf(" %lf ",hess[i][i]);*/          for(d=0; d<=dh[mi][i]; d++){
   }            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (i=1;i<=npar;i++) {            for (kk=1; kk<=cptcovage;kk++) {
     for (j=1;j<=npar;j++)  {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (j>i) {            }
         printf(".%d%d",i,j);fflush(stdout);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         hess[i][j]=hessij(p,delti,i,j);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         hess[j][i]=hess[i][j];                savm=oldm;
         /*printf(" %lf ",hess[i][j]);*/            oldm=newm;
       }          } /* end mult */
     }        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   printf("\n");          /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");           * (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
   a=matrix(1,npar,1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   y=matrix(1,npar,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   x=vector(1,npar);           * probability in order to take into account the bias as a fraction of the way
   indx=ivector(1,npar);           * 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]=hess[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. 
            */
   for (j=1;j<=npar;j++) {          s1=s[mw[mi][i]][i];
     for (i=1;i<=npar;i++) x[i]=0;          s2=s[mw[mi+1][i]][i];
     x[j]=1;          bbh=(double)bh[mi][i]/(double)stepm; 
     lubksb(a,npar,indx,x);          /* bias is positive if real duration
     for (i=1;i<=npar;i++){           * is higher than the multiple of stepm and negative otherwise.
       matcov[i][j]=x[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]));*/
           /*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 */
   printf("\n#Hessian matrix#\n");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (i=1;i<=npar;i++) {          /*if(lli ==000.0)*/
     for (j=1;j<=npar;j++) {          /*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); */
       printf("%.3e ",hess[i][j]);          ipmx +=1;
     }          sw += weight[i];
     printf("\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
       } /* end of individual */
   /* Recompute Inverse */    }  else if(mle==3){  /* exponential inter-extrapolation */
   for (i=1;i<=npar;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   ludcmp(a,npar,indx,&pd);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   /*  printf("\n#Hessian matrix recomputed#\n");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=npar;j++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++) x[i]=0;            }
     x[j]=1;          for(d=0; d<dh[mi][i]; d++){
     lubksb(a,npar,indx,x);            newm=savm;
     for (i=1;i<=npar;i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       y[i][j]=x[i];            for (kk=1; kk<=cptcovage;kk++) {
       printf("%.3e ",y[i][j]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     printf("\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   */            savm=oldm;
             oldm=newm;
   free_matrix(a,1,npar,1,npar);          } /* end mult */
   free_matrix(y,1,npar,1,npar);        
   free_vector(x,1,npar);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   free_ivector(indx,1,npar);          /* But now since version 0.9 we anticipate for bias and large stepm.
   free_matrix(hess,1,npar,1,npar);           * 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
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 /*************** hessian matrix ****************/           * probability in order to take into account the bias as a fraction of the way
 double hessii( double x[], double delta, int theta, double delti[])           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 {           * -stepm/2 to stepm/2 .
   int i;           * For stepm=1 the results are the same as for previous versions of Imach.
   int l=1, lmax=20;           * For stepm > 1 the results are less biased than in previous versions. 
   double k1,k2;           */
   double p2[NPARMAX+1];          s1=s[mw[mi][i]][i];
   double res;          s2=s[mw[mi+1][i]][i];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          bbh=(double)bh[mi][i]/(double)stepm; 
   double fx;          /* bias is positive if real duration
   int k=0,kmax=10;           * is higher than the multiple of stepm and negative otherwise.
   double l1;           */
           /* 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 */
   fx=func(x);          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 */
   for (i=1;i<=npar;i++) p2[i]=x[i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for(l=0 ; l <=lmax; l++){          /*if(lli ==000.0)*/
     l1=pow(10,l);          /*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); */
     delts=delt;          ipmx +=1;
     for(k=1 ; k <kmax; k=k+1){          sw += weight[i];
       delt = delta*(l1*k);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       p2[theta]=x[theta] +delt;        } /* end of wave */
       k1=func(p2)-fx;      } /* end of individual */
       p2[theta]=x[theta]-delt;    }else{  /* ml=4 no inter-extrapolation */
       k2=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
 #ifdef DEBUG            for (j=1;j<=nlstate+ndeath;j++){
       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);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          for(d=0; d<dh[mi][i]; d++){
         k=kmax;            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            for (kk=1; kk<=cptcovage;kk++) {
         k=kmax; l=lmax*10.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          
         delts=delt;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   delti[theta]=delts;          } /* end mult */
   return res;        
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 }          ipmx +=1;
           sw += weight[i];
 double hessij( double x[], double delti[], int thetai,int thetaj)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 {        } /* end of wave */
   int i;      } /* end of individual */
   int l=1, l1, lmax=20;    } /* End of if */
   double k1,k2,k3,k4,res,fx;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double p2[NPARMAX+1];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   int k;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   fx=func(x);  }
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*********** Maximum Likelihood Estimation ***************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    int i,j, iter;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double **xi,*delti;
     k2=func(p2)-fx;    double fret;
      xi=matrix(1,npar,1,npar);
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (i=1;i<=npar;i++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for (j=1;j<=npar;j++)
     k3=func(p2)-fx;        xi[i][j]=(i==j ? 1.0 : 0.0);
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;    powell(p,xi,npar,ftol,&iter,&fret,func);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 #ifdef DEBUG    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  }
   }  
   return res;  /**** Computes Hessian and covariance matrix ***/
 }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
 /************** Inverse of matrix **************/    double  **a,**y,*x,pd;
 void ludcmp(double **a, int n, int *indx, double *d)    double **hess;
 {    int i, j,jk;
   int i,imax,j,k;    int *indx;
   double big,dum,sum,temp;  
   double *vv;    double hessii(double p[], double delta, int theta, double delti[]);
      double hessij(double p[], double delti[], int i, int j);
   vv=vector(1,n);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   *d=1.0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   for (i=1;i<=n;i++) {  
     big=0.0;    hess=matrix(1,npar,1,npar);
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;    printf("\nCalculation of the hessian matrix. Wait...\n");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     vv[i]=1.0/big;    for (i=1;i<=npar;i++){
   }      printf("%d",i);fflush(stdout);
   for (j=1;j<=n;j++) {      fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1;i<j;i++) {      hess[i][i]=hessii(p,ftolhess,i,delti);
       sum=a[i][j];      /*printf(" %f ",p[i]);*/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      /*printf(" %lf ",hess[i][i]);*/
       a[i][j]=sum;    }
     }    
     big=0.0;    for (i=1;i<=npar;i++) {
     for (i=j;i<=n;i++) {      for (j=1;j<=npar;j++)  {
       sum=a[i][j];        if (j>i) { 
       for (k=1;k<j;k++)          printf(".%d%d",i,j);fflush(stdout);
         sum -= a[i][k]*a[k][j];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       a[i][j]=sum;          hess[i][j]=hessij(p,delti,i,j);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          hess[j][i]=hess[i][j];    
         big=dum;          /*printf(" %lf ",hess[i][j]);*/
         imax=i;        }
       }      }
     }    }
     if (j != imax) {    printf("\n");
       for (k=1;k<=n;k++) {    fprintf(ficlog,"\n");
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         a[j][k]=dum;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    
       *d = -(*d);    a=matrix(1,npar,1,npar);
       vv[imax]=vv[j];    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
     indx[j]=imax;    indx=ivector(1,npar);
     if (a[j][j] == 0.0) a[j][j]=TINY;    for (i=1;i<=npar;i++)
     if (j != n) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       dum=1.0/(a[j][j]);    ludcmp(a,npar,indx,&pd);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   free_vector(vv,1,n);  /* Doesn't work */      x[j]=1;
 ;      lubksb(a,npar,indx,x);
 }      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
 void lubksb(double **a, int n, int *indx, double b[])      }
 {    }
   int i,ii=0,ip,j;  
   double sum;    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   for (i=1;i<=n;i++) {    for (i=1;i<=npar;i++) { 
     ip=indx[i];      for (j=1;j<=npar;j++) { 
     sum=b[ip];        printf("%.3e ",hess[i][j]);
     b[ip]=b[i];        fprintf(ficlog,"%.3e ",hess[i][j]);
     if (ii)      }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      printf("\n");
     else if (sum) ii=i;      fprintf(ficlog,"\n");
     b[i]=sum;    }
   }  
   for (i=n;i>=1;i--) {    /* Recompute Inverse */
     sum=b[i];    for (i=1;i<=npar;i++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     b[i]=sum/a[i][i];    ludcmp(a,npar,indx,&pd);
   }  
 }    /*  printf("\n#Hessian matrix recomputed#\n");
   
 /************ Frequencies ********************/    for (j=1;j<=npar;j++) {
 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)      for (i=1;i<=npar;i++) x[i]=0;
 {  /* Some frequencies */      x[j]=1;
        lubksb(a,npar,indx,x);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      for (i=1;i<=npar;i++){ 
   double ***freq; /* Frequencies */        y[i][j]=x[i];
   double *pp;        printf("%.3e ",y[i][j]);
   double pos, k2, dateintsum=0,k2cpt=0;        fprintf(ficlog,"%.3e ",y[i][j]);
   FILE *ficresp;      }
   char fileresp[FILENAMELENGTH];      printf("\n");
        fprintf(ficlog,"\n");
   pp=vector(1,nlstate);    }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    */
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);    free_matrix(a,1,npar,1,npar);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    free_matrix(y,1,npar,1,npar);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    free_vector(x,1,npar);
     exit(0);    free_ivector(indx,1,npar);
   }    free_matrix(hess,1,npar,1,npar);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  
    }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*************** hessian matrix ****************/
    double hessii( double x[], double delta, int theta, double delti[])
   for(k1=1; k1<=j;k1++){  {
     for(i1=1; i1<=ncodemax[k1];i1++){    int i;
       j1++;    int l=1, lmax=20;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double k1,k2;
         scanf("%d", i);*/    double p2[NPARMAX+1];
       for (i=-1; i<=nlstate+ndeath; i++)      double res;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           for(m=agemin; m <= agemax+3; m++)    double fx;
             freq[i][jk][m]=0;    int k=0,kmax=10;
          double l1;
       dateintsum=0;  
       k2cpt=0;    fx=func(x);
       for (i=1; i<=imx; i++) {    for (i=1;i<=npar;i++) p2[i]=x[i];
         bool=1;    for(l=0 ; l <=lmax; l++){
         if  (cptcovn>0) {      l1=pow(10,l);
           for (z1=1; z1<=cptcoveff; z1++)      delts=delt;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for(k=1 ; k <kmax; k=k+1){
               bool=0;        delt = delta*(l1*k);
         }        p2[theta]=x[theta] +delt;
         if (bool==1) {        k1=func(p2)-fx;
           for(m=firstpass; m<=lastpass; m++){        p2[theta]=x[theta]-delt;
             k2=anint[m][i]+(mint[m][i]/12.);        k2=func(p2)-fx;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        /*res= (k1-2.0*fx+k2)/delt/delt; */
               if(agev[m][i]==0) agev[m][i]=agemax+1;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        
               if (m<lastpass) {  #ifdef DEBUG
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        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);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
               }  #endif
                      /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                 dateintsum=dateintsum+k2;          k=kmax;
                 k2cpt++;        }
               }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             }          k=kmax; l=lmax*10.;
           }        }
         }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       }          delts=delt;
                }
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
     }
       if  (cptcovn>0) {    delti[theta]=delts;
         fprintf(ficresp, "\n#********** Variable ");    return res; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(ficresp, "**********\n#");  }
       }  
       for(i=1; i<=nlstate;i++)  double hessij( double x[], double delti[], int thetai,int thetaj)
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
       fprintf(ficresp, "\n");    int i;
          int l=1, l1, lmax=20;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    double k1,k2,k3,k4,res,fx;
         if(i==(int)agemax+3)    double p2[NPARMAX+1];
           printf("Total");    int k;
         else  
           printf("Age %d", i);    fx=func(x);
         for(jk=1; jk <=nlstate ; jk++){    for (k=1; k<=2; k++) {
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1;i<=npar;i++) p2[i]=x[i];
             pp[jk] += freq[jk][m][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(jk=1; jk <=nlstate ; jk++){      k1=func(p2)-fx;
           for(m=-1, pos=0; m <=0 ; m++)    
             pos += freq[jk][m][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
           if(pp[jk]>=1.e-10)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      k2=func(p2)-fx;
           else    
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
         for(jk=1; jk <=nlstate ; jk++){    
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      p2[thetai]=x[thetai]-delti[thetai]/k;
             pp[jk] += freq[jk][m][i];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      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,pos=0; jk <=nlstate ; jk++)  #ifdef DEBUG
           pos += pp[jk];      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(jk=1; jk <=nlstate ; jk++){      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);
           if(pos>=1.e-5)  #endif
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    }
           else    return res;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  }
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  /************** Inverse of matrix **************/
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  void ludcmp(double **a, int n, int *indx, double *d) 
               probs[i][jk][j1]= pp[jk]/pos;  { 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    int i,imax,j,k; 
             }    double big,dum,sum,temp; 
             else    double *vv; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);   
           }    vv=vector(1,n); 
         }    *d=1.0; 
            for (i=1;i<=n;i++) { 
         for(jk=-1; jk <=nlstate+ndeath; jk++)      big=0.0; 
           for(m=-1; m <=nlstate+ndeath; m++)      for (j=1;j<=n;j++) 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        if ((temp=fabs(a[i][j])) > big) big=temp; 
         if(i <= (int) agemax)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           fprintf(ficresp,"\n");      vv[i]=1.0/big; 
         printf("\n");    } 
       }    for (j=1;j<=n;j++) { 
     }      for (i=1;i<j;i++) { 
   }        sum=a[i][j]; 
   dateintmean=dateintsum/k2cpt;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
   fclose(ficresp);      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      big=0.0; 
   free_vector(pp,1,nlstate);      for (i=j;i<=n;i++) { 
          sum=a[i][j]; 
   /* End of Freq */        for (k=1;k<j;k++) 
 }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
 /************ Prevalence ********************/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 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)          big=dum; 
 {  /* Some frequencies */          imax=i; 
          } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      } 
   double ***freq; /* Frequencies */      if (j != imax) { 
   double *pp;        for (k=1;k<=n;k++) { 
   double pos, k2;          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
   pp=vector(1,nlstate);          a[j][k]=dum; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        } 
          *d = -(*d); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        vv[imax]=vv[j]; 
   j1=0;      } 
        indx[j]=imax; 
   j=cptcoveff;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      if (j != n) { 
          dum=1.0/(a[j][j]); 
  for(k1=1; k1<=j;k1++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     for(i1=1; i1<=ncodemax[k1];i1++){      } 
       j1++;    } 
      free_vector(vv,1,n);  /* Doesn't work */
       for (i=-1; i<=nlstate+ndeath; i++)    ;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    } 
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  void lubksb(double **a, int n, int *indx, double b[]) 
        { 
       for (i=1; i<=imx; i++) {    int i,ii=0,ip,j; 
         bool=1;    double sum; 
         if  (cptcovn>0) {   
           for (z1=1; z1<=cptcoveff; z1++)    for (i=1;i<=n;i++) { 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      ip=indx[i]; 
               bool=0;      sum=b[ip]; 
         }      b[ip]=b[i]; 
         if (bool==1) {      if (ii) 
           for(m=firstpass; m<=lastpass; m++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
             k2=anint[m][i]+(mint[m][i]/12.);      else if (sum) ii=i; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      b[i]=sum; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=n;i>=1;i--) { 
               if (m<lastpass)      sum=b[i]; 
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
               else      b[i]=sum/a[i][i]; 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    } 
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  } 
             }  
           }  /************ Frequencies ********************/
         }  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
       }  {  /* Some frequencies */
         for(i=(int)agemin; i <= (int)agemax+3; i++){    
           for(jk=1; jk <=nlstate ; jk++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int first;
               pp[jk] += freq[jk][m][i];    double ***freq; /* Frequencies */
           }    double *pp;
           for(jk=1; jk <=nlstate ; jk++){    double pos, k2, dateintsum=0,k2cpt=0;
             for(m=-1, pos=0; m <=0 ; m++)    FILE *ficresp;
             pos += freq[jk][m][i];    char fileresp[FILENAMELENGTH];
         }    
            pp=vector(1,nlstate);
          for(jk=1; jk <=nlstate ; jk++){    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    strcpy(fileresp,"p");
              pp[jk] += freq[jk][m][i];    strcat(fileresp,fileres);
          }    if((ficresp=fopen(fileresp,"w"))==NULL) {
                printf("Problem with prevalence resultfile: %s\n", fileresp);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
          for(jk=1; jk <=nlstate ; jk++){              }
            if( i <= (int) agemax){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
              if(pos>=1.e-5){    j1=0;
                probs[i][jk][j1]= pp[jk]/pos;    
              }    j=cptcoveff;
            }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          }  
              first=1;
         }  
     }    for(k1=1; k1<=j;k1++){
   }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          scanf("%d", i);*/
   free_vector(pp,1,nlstate);        for (i=-1; i<=nlstate+ndeath; i++)  
            for (jk=-1; jk<=nlstate+ndeath; jk++)  
 }  /* End of Freq */            for(m=agemin; m <= agemax+3; m++)
               freq[i][jk][m]=0;
 /************* Waves Concatenation ***************/        
         dateintsum=0;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        k2cpt=0;
 {        for (i=1; i<=imx; i++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          bool=1;
      Death is a valid wave (if date is known).          if  (cptcovn>0) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            for (z1=1; z1<=cptcoveff; z1++) 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      and mw[mi+1][i]. dh depends on stepm.                bool=0;
      */          }
           if (bool==1){
   int i, mi, m;            for(m=firstpass; m<=lastpass; m++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              k2=anint[m][i]+(mint[m][i]/12.);
      double sum=0., jmean=0.;*/              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
   int j, k=0,jk, ju, jl;                if(agev[m][i]==1) agev[m][i]=agemax+2;
   double sum=0.;                if (m<lastpass) {
   jmin=1e+5;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   jmax=-1;                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
   jmean=0.;                }
   for(i=1; i<=imx; i++){                
     mi=0;                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
     m=firstpass;                  dateintsum=dateintsum+k2;
     while(s[m][i] <= nlstate){                  k2cpt++;
       if(s[m][i]>=1)                }
         mw[++mi][i]=m;              }
       if(m >=lastpass)            }
         break;          }
       else        }
         m++;         
     }/* end while */        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */        if  (cptcovn>0) {
       /* if(mi==0)  never been interviewed correctly before death */          fprintf(ficresp, "\n#********** Variable "); 
          /* Only death is a correct wave */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       mw[mi][i]=m;          fprintf(ficresp, "**********\n#");
     }        }
         for(i=1; i<=nlstate;i++) 
     wav[i]=mi;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     if(mi==0)        fprintf(ficresp, "\n");
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        
   }        for(i=(int)agemin; i <= (int)agemax+3; i++){
           if(i==(int)agemax+3){
   for(i=1; i<=imx; i++){            fprintf(ficlog,"Total");
     for(mi=1; mi<wav[i];mi++){          }else{
       if (stepm <=0)            if(first==1){
         dh[mi][i]=1;              first=0;
       else{              printf("See log file for details...\n");
         if (s[mw[mi+1][i]][i] > nlstate) {            }
           if (agedc[i] < 2*AGESUP) {            fprintf(ficlog,"Age %d", i);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          }
           if(j==0) j=1;  /* Survives at least one month after exam */          for(jk=1; jk <=nlstate ; jk++){
           k=k+1;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           if (j >= jmax) jmax=j;              pp[jk] += freq[jk][m][i]; 
           if (j <= jmin) jmin=j;          }
           sum=sum+j;          for(jk=1; jk <=nlstate ; jk++){
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            for(m=-1, pos=0; m <=0 ; m++)
           }              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
         else{              if(first==1){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           k=k+1;              }
           if (j >= jmax) jmax=j;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           else if (j <= jmin)jmin=j;            }else{
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */              if(first==1)
           sum=sum+j;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         jk= j/stepm;            }
         jl= j -jk*stepm;          }
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)          for(jk=1; jk <=nlstate ; jk++){
           dh[mi][i]=jk;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         else              pp[jk] += freq[jk][m][i];
           dh[mi][i]=jk+1;          }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */          for(jk=1,pos=0; jk <=nlstate ; jk++)
       }            pos += pp[jk];
     }          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
   jmean=sum/k;              if(first==1)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /*********** Tricode ****************************/            }else{
 void tricode(int *Tvar, int **nbcode, int imx)              if(first==1)
 {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int Ndum[20],ij=1, k, j, i;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int cptcode=0;            }
   cptcoveff=0;            if( i <= (int) agemax){
                if(pos>=1.e-5){
   for (k=0; k<19; k++) Ndum[k]=0;                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
   for (k=1; k<=7; k++) ncodemax[k]=0;                probs[i][jk][j1]= pp[jk]/pos;
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              }
     for (i=1; i<=imx; i++) {              else
       ij=(int)(covar[Tvar[j]][i]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
       Ndum[ij]++;            }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          }
       if (ij > cptcode) cptcode=ij;          
     }          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
     for (i=0; i<=cptcode; i++) {              if(freq[jk][m][i] !=0 ) {
       if(Ndum[i]!=0) ncodemax[j]++;              if(first==1)
     }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     ij=1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
           if(i <= (int) agemax)
     for (i=1; i<=ncodemax[j]; i++) {            fprintf(ficresp,"\n");
       for (k=0; k<=19; k++) {          if(first==1)
         if (Ndum[k] != 0) {            printf("Others in log...\n");
           nbcode[Tvar[j]][ij]=k;          fprintf(ficlog,"\n");
                  }
           ij++;      }
         }    }
         if (ij > ncodemax[j]) break;    dateintmean=dateintsum/k2cpt; 
       }     
     }    fclose(ficresp);
   }      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
  for (k=0; k<19; k++) Ndum[k]=0;    
     /* End of Freq */
  for (i=1; i<=ncovmodel-2; i++) {  }
       ij=Tvar[i];  
       Ndum[ij]++;  /************ 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)
   {  /* Some frequencies */
  ij=1;   
  for (i=1; i<=10; i++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    if((Ndum[i]!=0) && (i<=ncovcol)){    double ***freq; /* Frequencies */
      Tvaraff[ij]=i;    double *pp;
      ij++;    double pos, k2;
    }  
  }    pp=vector(1,nlstate);
      
     cptcoveff=ij-1;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 }    j1=0;
     
 /*********** Health Expectancies ****************/    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 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(k1=1; k1<=j;k1++){
 {      for(i1=1; i1<=ncodemax[k1];i1++){
   /* Health expectancies */        j1++;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        
   double age, agelim, hf;        for (i=-1; i<=nlstate+ndeath; i++)  
   double ***p3mat,***varhe;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   double **dnewm,**doldm;            for(m=agemin; m <= agemax+3; m++)
   double *xp;              freq[i][jk][m]=0;
   double **gp, **gm;       
   double ***gradg, ***trgradg;        for (i=1; i<=imx; i++) {
   int theta;          bool=1;
           if  (cptcovn>0) {
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            for (z1=1; z1<=cptcoveff; z1++) 
   xp=vector(1,npar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   dnewm=matrix(1,nlstate*2,1,npar);                bool=0;
   doldm=matrix(1,nlstate*2,1,nlstate*2);          } 
            if (bool==1) { 
   fprintf(ficreseij,"# Health expectancies\n");            for(m=firstpass; m<=lastpass; m++){
   fprintf(ficreseij,"# Age");              k2=anint[m][i]+(mint[m][i]/12.);
   for(i=1; i<=nlstate;i++)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     for(j=1; j<=nlstate;j++)                if(agev[m][i]==0) agev[m][i]=agemax+1;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);                if(agev[m][i]==1) agev[m][i]=agemax+2;
   fprintf(ficreseij,"\n");                if (m<lastpass) {
                   if (calagedate>0) 
   if(estepm < stepm){                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
     printf ("Problem %d lower than %d\n",estepm, stepm);                  else
   }                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   else  hstepm=estepm;                    freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
   /* We compute the life expectancy from trapezoids spaced every estepm months                }
    * 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            }
    * we are calculating an estimate of the Life Expectancy assuming a linear          }
    * progression inbetween and thus overestimating or underestimating according        }
    * to the curvature of the survival function. If, for the same date, we        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
    * 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, pp[jk]=0; m <=nlstate+ndeath ; m++)
    * hypothesis. A more precise result, taking into account a more precise              pp[jk] += freq[jk][m][i]; 
    * curvature will be obtained if estepm is as small as stepm. */          }
           for(jk=1; jk <=nlstate ; jk++){
   /* For example we decided to compute the life expectancy with the smallest unit */            for(m=-1, pos=0; m <=0 ; m++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              pos += freq[jk][m][i];
      nhstepm is the number of hstepm from age to agelim          }
      nstepm is the number of stepm from age to agelin.          
      Look at hpijx to understand the reason of that which relies in memory size          for(jk=1; jk <=nlstate ; jk++){
      and note for a fixed period like estepm months */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              pp[jk] += freq[jk][m][i];
      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          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
      results. So we changed our mind and took the option of the best precision.          
   */          for(jk=1; jk <=nlstate ; jk++){    
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            if( i <= (int) agemax){
               if(pos>=1.e-5){
   agelim=AGESUP;                probs[i][jk][j1]= pp[jk]/pos;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              }
     /* nhstepm age range expressed in number of stepm */            }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          }/* end jk */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        }/* end i */
     /* if (stepm >= YEARM) hstepm=1;*/      } /* end i1 */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    } /* end k1 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    
     gp=matrix(0,nhstepm,1,nlstate*2);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     gm=matrix(0,nhstepm,1,nlstate*2);    free_vector(pp,1,nlstate);
     
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  }  /* End of Freq */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    /************* Waves Concatenation ***************/
    
   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. */  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     /* Computing Variances of health expectancies */       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(theta=1; theta <=npar; theta++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(i=1; i<=npar; i++){       and mw[mi+1][i]. dh depends on stepm.
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       */
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, mi, m;
      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       cptj=0;       double sum=0., jmean=0.;*/
       for(j=1; j<= nlstate; j++){    int first;
         for(i=1; i<=nlstate; i++){    int j, k=0,jk, ju, jl;
           cptj=cptj+1;    double sum=0.;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    first=0;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    jmin=1e+5;
           }    jmax=-1;
         }    jmean=0.;
       }    for(i=1; i<=imx; i++){
            mi=0;
            m=firstpass;
       for(i=1; i<=npar; i++)      while(s[m][i] <= nlstate){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if(s[m][i]>=1)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            mw[++mi][i]=m;
              if(m >=lastpass)
       cptj=0;          break;
       for(j=1; j<= nlstate; j++){        else
         for(i=1;i<=nlstate;i++){          m++;
           cptj=cptj+1;      }/* end while */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      if (s[m][i] > nlstate){
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        mi++;     /* Death is another wave */
           }        /* if(mi==0)  never been interviewed correctly before death */
         }           /* Only death is a correct wave */
       }        mw[mi][i]=m;
            }
      
       wav[i]=mi;
       for(j=1; j<= nlstate*2; j++)      if(mi==0){
         for(h=0; h<=nhstepm-1; h++){        if(first==0){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
         }          first=1;
         }
      }        if(first==1){
              fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
 /* End theta */        }
       } /* end mi==0 */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    }
   
      for(h=0; h<=nhstepm-1; h++)    for(i=1; i<=imx; i++){
       for(j=1; j<=nlstate*2;j++)      for(mi=1; mi<wav[i];mi++){
         for(theta=1; theta <=npar; theta++)        if (stepm <=0)
         trgradg[h][j][theta]=gradg[h][theta][j];          dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) {
      for(i=1;i<=nlstate*2;i++)            if (agedc[i] < 2*AGESUP) {
       for(j=1;j<=nlstate*2;j++)            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         varhe[i][j][(int)age] =0.;            if(j==0) j=1;  /* Survives at least one month after exam */
             k=k+1;
     for(h=0;h<=nhstepm-1;h++){            if (j >= jmax) jmax=j;
       for(k=0;k<=nhstepm-1;k++){            if (j <= jmin) jmin=j;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);            sum=sum+j;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
         for(i=1;i<=nlstate*2;i++)            }
           for(j=1;j<=nlstate*2;j++)          }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     }            k=k+1;
             if (j >= jmax) jmax=j;
                  else if (j <= jmin)jmin=j;
     /* Computing expectancies */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for(i=1; i<=nlstate;i++)            sum=sum+j;
       for(j=1; j<=nlstate;j++)          }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          jk= j/stepm;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          jl= j -jk*stepm;
                    ju= j -(jk+1)*stepm;
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          if(mle <=1){ 
             if(jl==0){
         }              dh[mi][i]=jk;
               bh[mi][i]=0;
     fprintf(ficreseij,"%3.0f",age );            }else{ /* We want a negative bias in order to only have interpolation ie
     cptj=0;                    * at the price of an extra matrix product in likelihood */
     for(i=1; i<=nlstate;i++)              dh[mi][i]=jk+1;
       for(j=1; j<=nlstate;j++){              bh[mi][i]=ju;
         cptj++;            }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          }else{
       }            if(jl <= -ju){
     fprintf(ficreseij,"\n");              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
     free_matrix(gm,0,nhstepm,1,nlstate*2);                                   * is higher than the multiple of stepm and negative otherwise.
     free_matrix(gp,0,nhstepm,1,nlstate*2);                                   */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);            }
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);            else{
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
   free_vector(xp,1,npar);            }
   free_matrix(dnewm,1,nlstate*2,1,npar);            if(dh[mi][i]==0){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);              dh[mi][i]=1; /* At least one step */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);              bh[mi][i]=ju; /* At least one step */
 }              printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
             }
 /************ Variance ******************/            if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
 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)          }
 {        } /* end if mle */
   /* Variance of health expectancies */      } /* end wave */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   double **newm;    jmean=sum/k;
   double **dnewm,**doldm;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   int i, j, nhstepm, hstepm, h, nstepm ;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   int k, cptcode;   }
   double *xp;  
   double **gp, **gm;  /*********** Tricode ****************************/
   double ***gradg, ***trgradg;  void tricode(int *Tvar, int **nbcode, int imx)
   double ***p3mat;  {
   double age,agelim, hf;    
   int theta;    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    cptcoveff=0; 
   fprintf(ficresvij,"# Age");   
   for(i=1; i<=nlstate;i++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for(j=1; j<=nlstate;j++)    for (k=1; k<=7; k++) ncodemax[k]=0;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   xp=vector(1,npar);                                 modality*/ 
   dnewm=matrix(1,nlstate,1,npar);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   doldm=matrix(1,nlstate,1,nlstate);        Ndum[ij]++; /*store the modality */
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   if(estepm < stepm){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     printf ("Problem %d lower than %d\n",estepm, stepm);                                         Tvar[j]. If V=sex and male is 0 and 
   }                                         female is 1, then  cptcode=1.*/
   else  hstepm=estepm;        }
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=0; i<=cptcode; i++) {
      nhstepm is the number of hstepm from age to agelim        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 */
      nstepm is the number of stepm from age to agelin.      }
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */      ij=1; 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for (i=1; i<=ncodemax[j]; i++) {
      survival function given by stepm (the optimization length). Unfortunately it        for (k=0; k<= maxncov; k++) {
      means that if the survival funtion is printed only each two years of age and if          if (Ndum[k] != 0) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            nbcode[Tvar[j]][ij]=k; 
      results. So we changed our mind and took the option of the best precision.            /* 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; */
   */            
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            ij++;
   agelim = AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          if (ij > ncodemax[j]) break; 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      } 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     gm=matrix(0,nhstepm,1,nlstate);  
    for (i=1; i<=ncovmodel-2; i++) { 
     for(theta=1; theta <=npar; theta++){     /* 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<=npar; i++){ /* Computes gradient */     ij=Tvar[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);     Ndum[ij]++;
       }   }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   ij=1;
    for (i=1; i<= maxncov; i++) {
       if (popbased==1) {     if((Ndum[i]!=0) && (i<=ncovcol)){
         for(i=1; i<=nlstate;i++)       Tvaraff[ij]=i; /*For printing */
           prlim[i][i]=probs[(int)age][i][ij];       ij++;
       }     }
     }
       for(j=1; j<= nlstate; j++){   
         for(h=0; h<=nhstepm; h++){   cptcoveff=ij-1; /*Number of simple covariates*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  /*********** Health Expectancies ****************/
       }  
      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<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Health expectancies */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
      double age, agelim, hf;
       if (popbased==1) {    double ***p3mat,***varhe;
         for(i=1; i<=nlstate;i++)    double **dnewm,**doldm;
           prlim[i][i]=probs[(int)age][i][ij];    double *xp;
       }    double **gp, **gm;
     double ***gradg, ***trgradg;
       for(j=1; j<= nlstate; j++){    int theta;
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate*2,1,npar);
       }    doldm=matrix(1,nlstate*2,1,nlstate*2);
     
       for(j=1; j<= nlstate; j++)    fprintf(ficreseij,"# Health expectancies\n");
         for(h=0; h<=nhstepm; h++){    fprintf(ficreseij,"# Age");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=nlstate;j++)
     } /* End theta */        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
     if(estepm < stepm){
     for(h=0; h<=nhstepm; h++)      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(j=1; j<=nlstate;j++)    }
         for(theta=1; theta <=npar; theta++)    else  hstepm=estepm;   
           trgradg[h][j][theta]=gradg[h][theta][j];    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */     * if stepm=24 months pijx are given only every 2 years and by summing them
     for(i=1;i<=nlstate;i++)     * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(j=1;j<=nlstate;j++)     * progression inbetween and thus overestimating or underestimating according
         vareij[i][j][(int)age] =0.;     * 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(h=0;h<=nhstepm;h++){     * to compare the new estimate of Life expectancy with the same linear 
       for(k=0;k<=nhstepm;k++){     * hypothesis. A more precise result, taking into account a more precise
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);     * curvature will be obtained if estepm is as small as stepm. */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)    /* For example we decided to compute the life expectancy with the smallest unit */
           for(j=1;j<=nlstate;j++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;       nhstepm is the number of hstepm from age to agelim 
       }       nstepm is the number of stepm from age to agelin. 
     }       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     fprintf(ficresvij,"%.0f ",age );    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(i=1; i<=nlstate;i++)       survival function given by stepm (the optimization length). Unfortunately it
       for(j=1; j<=nlstate;j++){       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);       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.
     fprintf(ficresvij,"\n");    */
     free_matrix(gp,0,nhstepm,1,nlstate);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    agelim=AGESUP;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* nhstepm age range expressed in number of stepm */
   } /* End age */      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   free_vector(xp,1,npar);      /* if (stepm >= YEARM) hstepm=1;*/
   free_matrix(doldm,1,nlstate,1,npar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   free_matrix(dnewm,1,nlstate,1,nlstate);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
 }      gp=matrix(0,nhstepm,1,nlstate*2);
       gm=matrix(0,nhstepm,1,nlstate*2);
 /************ 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)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   /* Variance of prevalence limit */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/   
   double **newm;  
   double **dnewm,**doldm;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int i, j, nhstepm, hstepm;  
   int k, cptcode;      /* Computing Variances of health expectancies */
   double *xp;  
   double *gp, *gm;       for(theta=1; theta <=npar; theta++){
   double **gradg, **trgradg;        for(i=1; i<=npar; i++){ 
   double age,agelim;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int theta;        }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    
   fprintf(ficresvpl,"# Age");        cptj=0;
   for(i=1; i<=nlstate;i++)        for(j=1; j<= nlstate; j++){
       fprintf(ficresvpl," %1d-%1d",i,i);          for(i=1; i<=nlstate; i++){
   fprintf(ficresvpl,"\n");            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   xp=vector(1,npar);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          }
          }
   hstepm=1*YEARM; /* Every year of age */       
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       
   agelim = AGESUP;        for(i=1; i<=npar; i++) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     if (stepm >= YEARM) hstepm=1;        
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        cptj=0;
     gradg=matrix(1,npar,1,nlstate);        for(j=1; j<= nlstate; j++){
     gp=vector(1,nlstate);          for(i=1;i<=nlstate;i++){
     gm=vector(1,nlstate);            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     for(theta=1; theta <=npar; theta++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(j=1; j<= nlstate*2; j++)
       for(i=1;i<=nlstate;i++)          for(h=0; h<=nhstepm-1; h++){
         gp[i] = prlim[i][i];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
              }
       for(i=1; i<=npar; i++) /* Computes gradient */       } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);     
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /* End theta */
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   
       for(i=1;i<=nlstate;i++)       for(h=0; h<=nhstepm-1; h++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for(j=1; j<=nlstate*2;j++)
     } /* End theta */          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
     trgradg =matrix(1,nlstate,1,npar);       
   
     for(j=1; j<=nlstate;j++)       for(i=1;i<=nlstate*2;i++)
       for(theta=1; theta <=npar; theta++)        for(j=1;j<=nlstate*2;j++)
         trgradg[j][theta]=gradg[theta][j];          varhe[i][j][(int)age] =0.;
   
     for(i=1;i<=nlstate;i++)       printf("%d|",(int)age);fflush(stdout);
       varpl[i][(int)age] =0.;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       for(h=0;h<=nhstepm-1;h++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for(k=0;k<=nhstepm-1;k++){
     for(i=1;i<=nlstate;i++)          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
           for(i=1;i<=nlstate*2;i++)
     fprintf(ficresvpl,"%.0f ",age );            for(j=1;j<=nlstate*2;j++)
     for(i=1; i<=nlstate;i++)              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        }
     fprintf(ficresvpl,"\n");      }
     free_vector(gp,1,nlstate);      /* Computing expectancies */
     free_vector(gm,1,nlstate);      for(i=1; i<=nlstate;i++)
     free_matrix(gradg,1,npar,1,nlstate);        for(j=1; j<=nlstate;j++)
     free_matrix(trgradg,1,nlstate,1,npar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   } /* End age */            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
   free_vector(xp,1,npar);  /* 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]);*/
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
   
 }      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
 /************ Variance of one-step probabilities  ******************/      for(i=1; i<=nlstate;i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        for(j=1; j<=nlstate;j++){
 {          cptj++;
   int i, j, i1, k1, j1, z1;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   int k=0, cptcode;        }
   double **dnewm,**doldm;      fprintf(ficreseij,"\n");
   double *xp;     
   double *gp, *gm;      free_matrix(gm,0,nhstepm,1,nlstate*2);
   double **gradg, **trgradg;      free_matrix(gp,0,nhstepm,1,nlstate*2);
   double age,agelim, cov[NCOVMAX];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
   int theta;      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
   char fileresprob[FILENAMELENGTH];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   strcpy(fileresprob,"prob");    printf("\n");
   strcat(fileresprob,fileres);    fprintf(ficlog,"\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);    free_vector(xp,1,npar);
   }    free_matrix(dnewm,1,nlstate*2,1,npar);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
      free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");  }
   fprintf(ficresprob,"# Age");  
   for(i=1; i<=nlstate;i++)  /************ Variance ******************/
     for(j=1; j<=(nlstate+ndeath);j++)  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   fprintf(ficresprob,"\n");    /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   xp=vector(1,npar);    int i, j, nhstepm, hstepm, h, nstepm ;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int k, cptcode;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double *xp;
      double **gp, **gm;  /* for var eij */
   cov[1]=1;    double ***gradg, ***trgradg; /*for var eij */
   j=cptcoveff;    double **gradgp, **trgradgp; /* for var p point j */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double *gpp, *gmp; /* for var p point j */
   j1=0;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   for(k1=1; k1<=1;k1++){    double ***p3mat;
     for(i1=1; i1<=ncodemax[k1];i1++){    double age,agelim, hf;
     j1++;    double ***mobaverage;
     int theta;
     if  (cptcovn>0) {    char digit[4];
       fprintf(ficresprob, "\n#********** Variable ");    char digitp[25];
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficresprob, "**********\n#");    char fileresprobmorprev[FILENAMELENGTH];
     }  
        if(popbased==1){
       for (age=bage; age<=fage; age ++){      if(mobilav!=0)
         cov[2]=age;        strcpy(digitp,"-populbased-mobilav-");
         for (k=1; k<=cptcovn;k++) {      else strcpy(digitp,"-populbased-nomobil-");
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    }
              else 
         }      strcpy(digitp,"-stablbased-");
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
         for (k=1; k<=cptcovprod;k++)    if (mobilav!=0) {
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         gradg=matrix(1,npar,1,9);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         trgradg=matrix(1,9,1,npar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    }
      
         for(theta=1; theta <=npar; theta++){    strcpy(fileresprobmorprev,"prmorprev"); 
           for(i=1; i<=npar; i++)    sprintf(digit,"%-d",ij);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
              strcat(fileresprobmorprev,digit); /* Tvar to be done */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
              strcat(fileresprobmorprev,fileres);
           k=0;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           for(i=1; i<= (nlstate+ndeath); i++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               k=k+1;    }
               gp[k]=pmmij[i][j];    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           }    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
              fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           for(i=1; i<=npar; i++)    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      fprintf(ficresprobmorprev," p.%-d SE",j);
          for(i=1; i<=nlstate;i++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           k=0;    }  
           for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficresprobmorprev,"\n");
             for(j=1; j<=(nlstate+ndeath);j++){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               k=k+1;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
               gm[k]=pmmij[i][j];      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
             }      exit(0);
           }    }
          else{
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      fprintf(ficgp,"\n# Routine varevsij");
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      }
         }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           for(theta=1; theta <=npar; theta++)      exit(0);
             trgradg[j][theta]=gradg[theta][j];    }
            else{
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
            }
         pmij(pmmij,cov,ncovmodel,x,nlstate);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          
         k=0;    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");
         for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficresvij,"# Age");
           for(j=1; j<=(nlstate+ndeath);j++){    for(i=1; i<=nlstate;i++)
             k=k+1;      for(j=1; j<=nlstate;j++)
             gm[k]=pmmij[i][j];        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
           }    fprintf(ficresvij,"\n");
         }  
          xp=vector(1,npar);
      /*printf("\n%d ",(int)age);    dnewm=matrix(1,nlstate,1,npar);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    doldm=matrix(1,nlstate,1,nlstate);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      }*/    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
         fprintf(ficresprob,"\n%d ",(int)age);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    gmp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      
       }    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    else  hstepm=estepm;   
     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 k years */
 }    /* 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 ){    agelim = AGESUP;
   int jj1, k1, i1, cpt;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   FILE *fichtm;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /*char optionfilehtm[FILENAMELENGTH];*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(optionfilehtm,optionfile);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   strcat(optionfilehtm,".htm");      gp=matrix(0,nhstepm,1,nlstate);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      gm=matrix(0,nhstepm,1,nlstate);
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }  
       for(theta=1; theta <=npar; theta++){
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        for(i=1; i<=npar; i++){ /* Computes gradient */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 \n        }
 Total number of observations=%d <br>\n        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Outputs files<br>\n        if (popbased==1) {
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          if(mobilav ==0){
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n            for(i=1; i<=nlstate;i++)
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              prlim[i][i]=probs[(int)age][i][ij];
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          }else{ /* mobilav */ 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n            for(i=1; i<=nlstate;i++)
  - 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);              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
  fprintf(fichtm,"\n        }
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        for(j=1; j<= nlstate; j++){
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n          for(h=0; h<=nhstepm; h++){
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
  if(popforecast==1) fprintf(fichtm,"\n        }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        /* This for computing forces of mortality (h=1)as a weighted average */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
         <br>",fileres,fileres,fileres,fileres);          for(i=1; i<= nlstate; i++)
  else            gpp[j] += prlim[i][i]*p3mat[i][j][1];
    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>");        /* end force of mortality */
   
  m=cptcoveff;        for(i=1; i<=npar; i++) /* Computes gradient */
  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;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  for(k1=1; k1<=m;k1++){   
    for(i1=1; i1<=ncodemax[k1];i1++){        if (popbased==1) {
        jj1++;          if(mobilav ==0){
        if (cptcovn > 0) {            for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              prlim[i][i]=probs[(int)age][i][ij];
          for (cpt=1; cpt<=cptcoveff;cpt++)          }else{ /* mobilav */ 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            for(i=1; i<=nlstate;i++)
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              prlim[i][i]=mobaverage[(int)age][i][ij];
        }          }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      
        for(cpt=1; cpt<nlstate;cpt++){        for(j=1; j<= nlstate; j++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          for(h=0; h<=nhstepm; h++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
        }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        }
 interval) in state (%d): v%s%d%d.gif <br>        /* This for computing force of mortality (h=1)as a weighted average */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
      }          for(i=1; i<= nlstate; i++)
      for(cpt=1; cpt<=nlstate;cpt++) {            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        }    
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        /* end force of mortality */
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(j=1; j<= nlstate; j++) /* vareij */
 health expectancies in states (1) and (2): e%s%d.gif<br>          for(h=0; h<=nhstepm; h++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 fprintf(fichtm,"\n</body>");          }
    }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 fclose(fichtm);        }
 }  
       } /* End theta */
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   strcpy(optionfilegnuplot,optionfilefiname);          for(theta=1; theta <=npar; theta++)
   strcat(optionfilegnuplot,".gp.txt");            trgradg[h][j][theta]=gradg[h][theta][j];
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   }        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 #endif      for(i=1;i<=nlstate;i++)
 m=pow(2,cptcoveff);        for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {      for(h=0;h<=nhstepm;h++){
    for (k1=1; k1<= m ; k1 ++) {        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      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);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {            for(j=1;j<=nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }      }
     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 ++) {      /* pptj */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
 }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
      for (i=1; i<= nlstate ; i ++) {          varppt[j][i]=doldmp[j][i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* end ppptj */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 }        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));   
       if (popbased==1) {
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if(mobilav ==0){
    }          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=probs[(int)age][i][ij];
   /*2 eme*/        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);        }
          }
     for (i=1; i<= nlstate+1 ; i ++) {      
       k=2*i;      /* This for computing force of mortality (h=1)as a weighted average */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1; i<= nlstate; i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }    
 }        /* end force of mortality */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for (j=1; j<= nlstate+1 ; j ++) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1; i<=nlstate;i++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 }          }
       fprintf(ficgp,"\" t\"\" w l 0,");      } 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficresprobmorprev,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresvij,"%.0f ",age );
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }          for(j=1; j<=nlstate;j++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       else fprintf(ficgp,"\" t\"\" w l 0,");        }
     }      fprintf(ficresvij,"\n");
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      free_matrix(gp,0,nhstepm,1,nlstate);
   }      free_matrix(gm,0,nhstepm,1,nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /*3eme*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for (k1=1; k1<= m ; k1 ++) {    } /* End age */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
       k=2+nlstate*(2*cpt-2);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
 */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
       for (i=1; i< nlstate ; i ++) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
       }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
   /* CV preval stat */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for (k1=1; k1<= m ; k1 ++) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     for (cpt=1; cpt<nlstate ; cpt ++) {    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       k=3;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficgp,"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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    fclose(ficresprobmorprev);
     fclose(ficgp);
       for (i=1; i< nlstate ; i ++)    fclose(fichtm);
         fprintf(ficgp,"+$%d",k+i+1);  }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
        /************ Variance of prevlim ******************/
       l=3+(nlstate+ndeath)*cpt;  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)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  {
       for (i=1; i< nlstate ; i ++) {    /* Variance of prevalence limit */
         l=3+(nlstate+ndeath)*cpt;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         fprintf(ficgp,"+$%d",l+i+1);    double **newm;
       }    double **dnewm,**doldm;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int i, j, nhstepm, hstepm;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int k, cptcode;
     }    double *xp;
   }      double *gp, *gm;
      double **gradg, **trgradg;
   /* proba elementaires */    double age,agelim;
    for(i=1,jk=1; i <=nlstate; i++){    int theta;
     for(k=1; k <=(nlstate+ndeath); k++){     
       if (k != i) {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         for(j=1; j <=ncovmodel; j++){    fprintf(ficresvpl,"# Age");
            for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        fprintf(ficresvpl," %1d-%1d",i,i);
           jk++;    fprintf(ficresvpl,"\n");
           fprintf(ficgp,"\n");  
         }    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     }    
     hstepm=1*YEARM; /* Every year of age */
     for(jk=1; jk <=m; jk++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    agelim = AGESUP;
    i=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    for(k2=1; k2<=nlstate; k2++) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      k3=i;      if (stepm >= YEARM) hstepm=1;
      for(k=1; k<=(nlstate+ndeath); k++) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        if (k != k2){      gradg=matrix(1,npar,1,nlstate);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      gp=vector(1,nlstate);
 ij=1;      gm=vector(1,nlstate);
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(theta=1; theta <=npar; theta++){
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=1; i<=npar; i++){ /* Computes gradient */
             ij++;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           }        }
           else        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(i=1;i<=nlstate;i++)
         }          gp[i] = prlim[i][i];
           fprintf(ficgp,")/(1");      
                for(i=1; i<=npar; i++) /* Computes gradient */
         for(k1=1; k1 <=nlstate; k1++){            xp[i] = x[i] - (i==theta ?delti[theta]:0);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 ij=1;        for(i=1;i<=nlstate;i++)
           for(j=3; j <=ncovmodel; j++){          gm[i] = prlim[i][i];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=1;i<=nlstate;i++)
             ij++;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           }      } /* End theta */
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      trgradg =matrix(1,nlstate,1,npar);
           }  
           fprintf(ficgp,")");      for(j=1; j<=nlstate;j++)
         }        for(theta=1; theta <=npar; theta++)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          trgradg[j][theta]=gradg[theta][j];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;      for(i=1;i<=nlstate;i++)
        }        varpl[i][(int)age] =0.;
      }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
    }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for(i=1;i<=nlstate;i++)
    }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
   fclose(ficgp);      fprintf(ficresvpl,"%.0f ",age );
 }  /* end gnuplot */      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
 /*************** Moving average **************/      free_vector(gp,1,nlstate);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
   int i, cpt, cptcod;      free_matrix(trgradg,1,nlstate,1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    } /* End age */
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    free_vector(xp,1,npar);
           mobaverage[(int)agedeb][i][cptcod]=0.;    free_matrix(doldm,1,nlstate,1,npar);
        free_matrix(dnewm,1,nlstate,1,nlstate);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){  }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){  /************ Variance of one-step probabilities  ******************/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           }  {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int i, j=0,  i1, k1, l1, t, tj;
         }    int k2, l2, j1,  z1;
       }    int k=0,l, cptcode;
     }    int first=1, first1;
        double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 }    double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
 /************** Forecasting ******************/    double **gradg, **trgradg;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    double **mu;
      double age,agelim, cov[NCOVMAX];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int *popage;    int theta;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    char fileresprob[FILENAMELENGTH];
   double *popeffectif,*popcount;    char fileresprobcov[FILENAMELENGTH];
   double ***p3mat;    char fileresprobcor[FILENAMELENGTH];
   char fileresf[FILENAMELENGTH];  
     double ***varpij;
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   strcpy(fileresf,"f");    }
   strcat(fileresf,fileres);    strcpy(fileresprobcov,"probcov"); 
   if((ficresf=fopen(fileresf,"w"))==NULL) {    strcat(fileresprobcov,fileres);
     printf("Problem with forecast resultfile: %s\n", fileresf);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   printf("Computing forecasting: result on file '%s' \n", fileresf);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
   if (mobilav==1) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobcor);
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   if (stepm<=12) stepsize=1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   agelim=AGESUP;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   hstepm=1;    
   hstepm=hstepm/stepm;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   yp1=modf(dateintmean,&yp);    fprintf(ficresprob,"# Age");
   anprojmean=yp;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   yp2=modf((yp1*12),&yp);    fprintf(ficresprobcov,"# Age");
   mprojmean=yp;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   yp1=modf((yp2*30.5),&yp);    fprintf(ficresprobcov,"# Age");
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
   for(cptcov=1;cptcov<=i2;cptcov++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }  
       k=k+1;    fprintf(ficresprob,"\n");
       fprintf(ficresf,"\n#******");    fprintf(ficresprobcov,"\n");
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficresprobcor,"\n");
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    xp=vector(1,npar);
       }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fprintf(ficresf,"******\n");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       fprintf(ficresf,"# StartingAge FinalAge");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
          first=1;
          if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         fprintf(ficresf,"\n");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        exit(0);
     }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    else{
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      fprintf(ficgp,"\n# Routine varprob");
           nhstepm = nhstepm/hstepm;    }
              if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("Problem with html file: %s\n", optionfilehtm);
           oldm=oldms;savm=savms;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        exit(0);
            }
           for (h=0; h<=nhstepm; h++){    else{
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      fprintf(fichtm,"\n");
             }  
             for(j=1; j<=nlstate+ndeath;j++) {      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
               kk1=0.;kk2=0;      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");
               for(i=1; i<=nlstate;i++) {                    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");
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    cov[1]=1;
                 }    tj=cptcoveff;
                    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
               }    j1=0;
               if (h==(int)(calagedate+12*cpt)){    for(t=1; t<=tj;t++){
                 fprintf(ficresf," %.3f", kk1);      for(i1=1; i1<=ncodemax[t];i1++){ 
                                j1++;
               }        if  (cptcovn>0) {
             }          fprintf(ficresprob, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprob, "**********\n#");
         }          fprintf(ficresprobcov, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprobcov, "**********\n#");
   }          
                  fprintf(ficgp, "\n#********** Variable "); 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#");
   fclose(ficresf);          
 }          
 /************** Forecasting ******************/          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          
   int *popage;          fprintf(ficresprobcor, "\n#********** Variable ");    
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *popeffectif,*popcount;          fprintf(ficgp, "**********\n#");    
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];        
         for (age=bage; age<=fage; age ++){ 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          cov[2]=age;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (k=1; k<=cptcovn;k++) {
   agelim=AGESUP;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          }
            for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          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]]];
            
   strcpy(filerespop,"pop");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   strcat(filerespop,fileres);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
     printf("Problem with forecast resultfile: %s\n", filerespop);          gm=vector(1,(nlstate)*(nlstate+ndeath));
   }      
   printf("Computing forecasting: result on file '%s' \n", filerespop);          for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
             
   if (mobilav==1) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            
     movingaverage(agedeb, fage, ageminpar, mobaverage);            k=0;
   }            for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;                k=k+1;
   if (stepm<=12) stepsize=1;                gp[k]=pmmij[i][j];
                }
   agelim=AGESUP;            }
              
   hstepm=1;            for(i=1; i<=npar; i++)
   hstepm=hstepm/stepm;              xp[i] = x[i] - (i==theta ?delti[theta]:0);
        
   if (popforecast==1) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     if((ficpop=fopen(popfile,"r"))==NULL) {            k=0;
       printf("Problem with population file : %s\n",popfile);exit(0);            for(i=1; i<=(nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
     popage=ivector(0,AGESUP);                k=k+1;
     popeffectif=vector(0,AGESUP);                gm[k]=pmmij[i][j];
     popcount=vector(0,AGESUP);              }
                }
     i=1;         
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                  gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
     imx=i;          }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
   for(cptcov=1;cptcov<=i2;cptcov++){              trgradg[j][theta]=gradg[theta][j];
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          
       k=k+1;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       fprintf(ficrespop,"\n#******");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for(j=1;j<=cptcoveff;j++) {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficrespop,"******\n");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          pmij(pmmij,cov,ncovmodel,x,nlstate);
       if (popforecast==1)  fprintf(ficrespop," [Population]");          
                k=0;
       for (cpt=0; cpt<=0;cpt++) {          for(i=1; i<=(nlstate); i++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              for(j=1; j<=(nlstate+ndeath);j++){
                      k=k+1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              mu[k][(int) age]=pmmij[i][j];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;          }
                    for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           oldm=oldms;savm=savms;              varpij[i][j][(int)age] = doldm[i][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                  /*printf("\n%d ",(int)age);
           for (h=0; h<=nhstepm; h++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             if (h==(int) (calagedate+YEARM*cpt)) {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }            }*/
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;          fprintf(ficresprob,"\n%d ",(int)age);
               for(i=1; i<=nlstate;i++) {                        fprintf(ficresprobcov,"\n%d ",(int)age);
                 if (mobilav==1)          fprintf(ficresprobcor,"\n%d ",(int)age);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                 }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
               if (h==(int)(calagedate+12*cpt)){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          }
                   /*fprintf(ficrespop," %.3f", kk1);          i=0;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          for (k=1; k<=(nlstate);k++){
               }            for (l=1; l<=(nlstate+ndeath);l++){ 
             }              i=i++;
             for(i=1; i<=nlstate;i++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               kk1=0.;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                 for(j=1; j<=nlstate;j++){              for (j=1; j<=i;j++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              }
             }            }
           }/* end of loop for state */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        } /* end of loop for age */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }        /* Confidence intervalle of pij  */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*
         }          fprintf(ficgp,"\nset noparametric;unset label");
       }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   /******/          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                  first1=1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k2=1; k2<=(nlstate);k2++){
           oldm=oldms;savm=savms;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              if(l2==k2) continue;
           for (h=0; h<=nhstepm; h++){            j=(k2-1)*(nlstate+ndeath)+l2;
             if (h==(int) (calagedate+YEARM*cpt)) {            for (k1=1; k1<=(nlstate);k1++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
             }                if(l1==k1) continue;
             for(j=1; j<=nlstate+ndeath;j++) {                i=(k1-1)*(nlstate+ndeath)+l1;
               kk1=0.;kk2=0;                if(i<=j) continue;
               for(i=1; i<=nlstate;i++) {                              for (age=bage; age<=fage; age ++){ 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                      if ((int)age %5==0){
               }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
             }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           }                    mu1=mu[i][(int) age]/stepm*YEARM ;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    mu2=mu[j][(int) age]/stepm*YEARM;
         }                    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.;
   }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                      /* Eigen vectors */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
   if (popforecast==1) {                    v21=(lc1-v1)/cv12*v11;
     free_ivector(popage,0,AGESUP);                    v12=-v21;
     free_vector(popeffectif,0,AGESUP);                    v22=v11;
     free_vector(popcount,0,AGESUP);                    tnalp=v21/v11;
   }                    if(first1==1){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      first1=0;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      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);
   fclose(ficrespop);                    }
 }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
 /***********************************************/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
 /**************** Main Program *****************/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
 /***********************************************/                    if(first==1){
                       first=0;
 int main(int argc, char *argv[])                      fprintf(ficgp,"\nset parametric;unset label");
 {                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                      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);
   double agedeb, agefin,hf;                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   double fret;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double **xi,tmp,delta;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   double dum; /* Dummy variable */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double ***p3mat;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   int *indx;                    }else{
   char line[MAXLINE], linepar[MAXLINE];                      first=0;
   char title[MAXLINE];                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                      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",\
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   char filerest[FILENAMELENGTH];                    }/* if first */
   char fileregp[FILENAMELENGTH];                  } /* age mod 5 */
   char popfile[FILENAMELENGTH];                } /* end loop age */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   int firstobs=1, lastobs=10;                first=1;
   int sdeb, sfin; /* Status at beginning and end */              } /*l12 */
   int c,  h , cpt,l;            } /* k12 */
   int ju,jl, mi;          } /*l1 */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        }/* k1 */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      } /* loop covariates */
   int mobilav=0,popforecast=0;    }
   int hstepm, nhstepm;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
   double bage, fage, age, agelim, agebase;    fclose(ficresprob);
   double ftolpl=FTOL;    fclose(ficresprobcov);
   double **prlim;    fclose(ficresprobcor);
   double *severity;    fclose(ficgp);
   double ***param; /* Matrix of parameters */    fclose(fichtm);
   double  *p;  }
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  
   double *delti; /* Scale */  /******************* Printing html file ***********/
   double ***eij, ***vareij;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   double **varpl; /* Variances of prevalence limits by age */                    int lastpass, int stepm, int weightopt, char model[],\
   double *epj, vepp;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   double kk1, kk2;                    int popforecast, int estepm ,\
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                    double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";    /*char optionfilehtm[FILENAMELENGTH];*/
   char *alph[]={"a","a","b","c","d","e"}, str[4];    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   char z[1]="c", occ;    }
 #include <sys/time.h>  
 #include <time.h>     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];   - 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
   /* long total_usecs;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   struct timeval start_time, end_time;   - Life expectancies by age and initial health status (estepm=%2d months): 
       <a href=\"e%s\">e%s</a> <br>\n</li>", \
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   getcwd(pathcd, size);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   printf("\n%s",version);  
   if(argc <=1){   m=cptcoveff;
     printf("\nEnter the parameter file name: ");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     scanf("%s",pathtot);  
   }   jj1=0;
   else{   for(k1=1; k1<=m;k1++){
     strcpy(pathtot,argv[1]);     for(i1=1; i1<=ncodemax[k1];i1++){
   }       jj1++;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/       if (cptcovn > 0) {
   /*cygwin_split_path(pathtot,path,optionfile);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
   /* cutv(path,optionfile,pathtot,'\\');*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);       }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       /* Pij */
   chdir(path);       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>
   replace(pathc,path);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
 /*-------- arguments in the command line --------*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   strcpy(fileres,"r");         /* Stable prevalence in each health state */
   strcat(fileres, optionfilefiname);         for(cpt=1; cpt<nlstate;cpt++){
   strcat(fileres,".txt");    /* Other files have txt extension */           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   /*---------arguments file --------*/         }
        for(cpt=1; cpt<=nlstate;cpt++) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     printf("Problem with optionfile %s\n",optionfile);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     goto end;       }
   }       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   strcpy(filereso,"o");  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   strcat(filereso,fileres);     } /* end i1 */
   if((ficparo=fopen(filereso,"w"))==NULL) {   }/* End k1 */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;   fprintf(fichtm,"</ul>");
   }  
   
   /* Reads comments: lines beginning with '#' */   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   while((c=getc(ficpar))=='#' && c!= EOF){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     ungetc(c,ficpar);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     fgets(line, MAXLINE, ficpar);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     puts(line);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     fputs(line,ficparo);   - Variances and covariances 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 (no covariance): <a href=\"t%s\">t%s</a> <br>\n
   ungetc(c,ficpar);   - 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);
   
   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);   if(popforecast==1) fprintf(fichtm,"\n
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   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);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
 while((c=getc(ficpar))=='#' && c!= EOF){          <br>",fileres,fileres,fileres,fileres);
     ungetc(c,ficpar);   else 
     fgets(line, MAXLINE, ficpar);     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);
     puts(line);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     fputs(line,ficparo);  
   }   m=cptcoveff;
   ungetc(c,ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
       jj1=0;
   covar=matrix(0,NCOVMAX,1,n);   for(k1=1; k1<=m;k1++){
   cptcovn=0;     for(i1=1; i1<=ncodemax[k1];i1++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       jj1++;
        if (cptcovn > 0) {
   ncovmodel=2+cptcovn;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /* Read guess parameters */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /* Reads comments: lines beginning with '#' */       }
   while((c=getc(ficpar))=='#' && c!= EOF){       for(cpt=1; cpt<=nlstate;cpt++) {
     ungetc(c,ficpar);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     fgets(line, MAXLINE, ficpar);  interval) in state (%d): v%s%d%d.png <br>
     puts(line);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     fputs(line,ficparo);       }
   }     } /* end i1 */
   ungetc(c,ficpar);   }/* End k1 */
     fprintf(fichtm,"</ul>");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  fclose(fichtm);
     for(i=1; i <=nlstate; i++)  }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  /******************* Gnuplot file **************/
       fprintf(ficparo,"%1d%1d",i1,j1);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         fscanf(ficpar," %lf",&param[i][j][k]);    int ng;
         printf(" %lf",param[i][j][k]);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         fprintf(ficparo," %lf",param[i][j][k]);      printf("Problem with file %s",optionfilegnuplot);
       }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
       fscanf(ficpar,"\n");    }
       printf("\n");  
       fprintf(ficparo,"\n");    /*#ifdef windows */
     }      fprintf(ficgp,"cd \"%s\" \n",pathc);
        /*#endif */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  m=pow(2,cptcoveff);
     
   p=param[1][1];   /* 1eme*/
      for (cpt=1; cpt<= nlstate ; cpt ++) {
   /* Reads comments: lines beginning with '#' */     for (k1=1; k1<= m ; k1 ++) {
   while((c=getc(ficpar))=='#' && c!= EOF){       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     ungetc(c,ficpar);       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);
     fgets(line, MAXLINE, ficpar);  
     puts(line);       for (i=1; i<= nlstate ; i ++) {
     fputs(line,ficparo);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
   ungetc(c,ficpar);       }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       for (i=1; i<= nlstate ; i ++) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   for(i=1; i <=nlstate; i++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(j=1; j <=nlstate+ndeath-1; j++){       } 
       fscanf(ficpar,"%1d%1d",&i1,&j1);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
       printf("%1d%1d",i,j);       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficparo,"%1d%1d",i1,j1);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       for(k=1; k<=ncovmodel;k++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
         fscanf(ficpar,"%le",&delti3[i][j][k]);       }  
         printf(" %le",delti3[i][j][k]);       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         fprintf(ficparo," %le",delti3[i][j][k]);     }
       }    }
       fscanf(ficpar,"\n");    /*2 eme*/
       printf("\n");    
       fprintf(ficparo,"\n");    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);
   delti=delti3[1][1];      
        for (i=1; i<= nlstate+1 ; i ++) {
   /* Reads comments: lines beginning with '#' */        k=2*i;
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     ungetc(c,ficpar);        for (j=1; j<= nlstate+1 ; j ++) {
     fgets(line, MAXLINE, ficpar);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     puts(line);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fputs(line,ficparo);        }   
   }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   ungetc(c,ficpar);        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);
   matcov=matrix(1,npar,1,npar);        for (j=1; j<= nlstate+1 ; j ++) {
   for(i=1; i <=npar; i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fscanf(ficpar,"%s",&str);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("%s",str);        }   
     fprintf(ficparo,"%s",str);        fprintf(ficgp,"\" t\"\" w l 0,");
     for(j=1; j <=i; j++){        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       fscanf(ficpar," %le",&matcov[i][j]);        for (j=1; j<= nlstate+1 ; j ++) {
       printf(" %.5le",matcov[i][j]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficparo," %.5le",matcov[i][j]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
     fscanf(ficpar,"\n");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     printf("\n");        else fprintf(ficgp,"\" t\"\" w l 0,");
     fprintf(ficparo,"\n");      }
   }    }
   for(i=1; i <=npar; i++)    
     for(j=i+1;j<=npar;j++)    /*3eme*/
       matcov[i][j]=matcov[j][i];    
        for (k1=1; k1<= m ; k1 ++) { 
   printf("\n");      for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     /*-------- Rewriting paramater file ----------*/        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
      strcpy(rfileres,"r");    /* "Rparameterfile */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
      strcat(rfileres,".");    /* */          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     if((ficres =fopen(rfileres,"w"))==NULL) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     }          
     fprintf(ficres,"#%s\n",version);        */
            for (i=1; i< nlstate ; i ++) {
     /*-------- data file ----------*/          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);
     if((fic=fopen(datafile,"r"))==NULL)    {          
       printf("Problem with datafile: %s\n", datafile);goto end;        } 
     }      }
     }
     n= lastobs;    
     severity = vector(1,maxwav);    /* CV preval stat */
     outcome=imatrix(1,maxwav+1,1,n);    for (k1=1; k1<= m ; k1 ++) { 
     num=ivector(1,n);      for (cpt=1; cpt<nlstate ; cpt ++) {
     moisnais=vector(1,n);        k=3;
     annais=vector(1,n);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     moisdc=vector(1,n);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     andc=vector(1,n);        
     agedc=vector(1,n);        for (i=1; i< nlstate ; i ++)
     cod=ivector(1,n);          fprintf(ficgp,"+$%d",k+i+1);
     weight=vector(1,n);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        
     mint=matrix(1,maxwav,1,n);        l=3+(nlstate+ndeath)*cpt;
     anint=matrix(1,maxwav,1,n);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     s=imatrix(1,maxwav+1,1,n);        for (i=1; i< nlstate ; i ++) {
     adl=imatrix(1,maxwav+1,1,n);              l=3+(nlstate+ndeath)*cpt;
     tab=ivector(1,NCOVMAX);          fprintf(ficgp,"+$%d",l+i+1);
     ncodemax=ivector(1,8);        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     i=1;      } 
     while (fgets(line, MAXLINE, fic) != NULL)    {    }  
       if ((i >= firstobs) && (i <=lastobs)) {    
            /* proba elementaires */
         for (j=maxwav;j>=1;j--){    for(i=1,jk=1; i <=nlstate; i++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(k=1; k <=(nlstate+ndeath); k++){
           strcpy(line,stra);        if (k != i) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(j=1; j <=ncovmodel; j++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         }            jk++; 
                    fprintf(ficgp,"\n");
         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);  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       for(jk=1; jk <=m; jk++) {
         for (j=ncovcol;j>=1;j--){         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);         if (ng==2)
         }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         num[i]=atol(stra);         else
                   fprintf(ficgp,"\nset title \"Probability\"\n");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           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=1;
          for(k2=1; k2<=nlstate; k2++) {
         i=i+1;           k3=i;
       }           for(k=1; k<=(nlstate+ndeath); k++) {
     }             if (k != k2){
     /* printf("ii=%d", ij);               if(ng==2)
        scanf("%d",i);*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   imx=i-1; /* Number of individuals */               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   /* for (i=1; i<=imx; i++){               ij=1;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;               for(j=3; j <=ncovmodel; j++) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     }*/                   ij++;
    /*  for (i=1; i<=imx; i++){                 }
      if (s[4][i]==9)  s[4][i]=-1;                 else
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
                 fprintf(ficgp,")/(1");
   /* Calculation of the number of parameter from char model*/               
   Tvar=ivector(1,15);               for(k1=1; k1 <=nlstate; k1++){   
   Tprod=ivector(1,15);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   Tvaraff=ivector(1,15);                 ij=1;
   Tvard=imatrix(1,15,1,2);                 for(j=3; j <=ncovmodel; j++){
   Tage=ivector(1,15);                         if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                         fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   if (strlen(model) >1){                     ij++;
     j=0, j1=0, k1=1, k2=1;                   }
     j=nbocc(model,'+');                   else
     j1=nbocc(model,'*');                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     cptcovn=j+1;                 }
     cptcovprod=j1;                 fprintf(ficgp,")");
                   }
     strcpy(modelsav,model);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       printf("Error. Non available option model=%s ",model);               i=i+ncovmodel;
       goto end;             }
     }           } /* end k */
             } /* end k2 */
     for(i=(j+1); i>=1;i--){       } /* end jk */
       cutv(stra,strb,modelsav,'+');     } /* end ng */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);     fclose(ficgp); 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  }  /* end gnuplot */
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');  /*************** Moving average **************/
         if (strcmp(strc,"age")==0) {  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    int i, cpt, cptcod;
           Tvar[i]=atoi(stre);    int modcovmax =1;
           cptcovage++;    int mobilavrange, mob;
             Tage[cptcovage]=i;    double age;
             /*printf("stre=%s ", stre);*/  
         }    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
         else if (strcmp(strd,"age")==0) {                             a covariate has 2 modalities */
           cptcovprod--;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
           cptcovage++;      if(mobilav==1) mobilavrange=5; /* default */
           Tage[cptcovage]=i;      else mobilavrange=mobilav;
         }      for (age=bage; age<=fage; age++)
         else {        for (i=1; i<=nlstate;i++)
           cutv(strb,stre,strc,'V');          for (cptcod=1;cptcod<=modcovmax;cptcod++)
           Tvar[i]=ncovcol+k1;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
           cutv(strb,strc,strd,'V');      /* We keep the original values on the extreme ages bage, fage and for 
           Tprod[k1]=i;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           Tvard[k1][1]=atoi(strc);         we use a 5 terms etc. until the borders are no more concerned. 
           Tvard[k1][2]=atoi(stre);      */ 
           Tvar[cptcovn+k2]=Tvard[k1][1];      for (mob=3;mob <=mobilavrange;mob=mob+2){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (k=1; k<=lastobs;k++)          for (i=1; i<=nlstate;i++){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            for (cptcod=1;cptcod<=modcovmax;cptcod++){
           k1++;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
           k2=k2+2;                for (cpt=1;cpt<=(mob-1)/2;cpt++){
         }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
       else {                }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
        /*  scanf("%d",i);*/            }
       cutv(strd,strc,strb,'V');          }
       Tvar[i]=atoi(strc);        }/* end age */
       }      }/* end mob */
       strcpy(modelsav,stra);      }else return -1;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    return 0;
         scanf("%d",i);*/  }/* End movingaverage */
     }  
 }  
    /************** Forecasting ******************/
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[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){
   printf("cptcovprod=%d ", cptcovprod);    
   scanf("%d ",i);*/    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     fclose(fic);    int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     /*  if(mle==1){*/    double *popeffectif,*popcount;
     if (weightopt != 1) { /* Maximisation without weights*/    double ***p3mat;
       for(i=1;i<=n;i++) weight[i]=1.0;    double ***mobaverage;
     }    char fileresf[FILENAMELENGTH];
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);   agelim=AGESUP;
    calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){   
          anint[m][i]=9999;   
          s[m][i]=-1;    strcpy(fileresf,"f"); 
        }    strcat(fileresf,fileres);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    if((ficresf=fopen(fileresf,"w"))==NULL) {
       }      printf("Problem with forecast resultfile: %s\n", fileresf);
     }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     for (i=1; i<=imx; i++)  {    printf("Computing forecasting: result on file '%s' \n", fileresf);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)    if (mobilav!=0) {
               if(moisdc[i]!=99 && andc[i]!=9999)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 agev[m][i]=agedc[i];      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            else {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               if (andc[i]!=9999){      }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    }
               agev[m][i]=-1;  
               }    stepsize=(int) (stepm+YEARM-1)/YEARM;
             }    if (stepm<=12) stepsize=1;
           }    
           else if(s[m][i] !=9){ /* Should no more exist */    agelim=AGESUP;
             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)    hstepm=1;
               agev[m][i]=1;    hstepm=hstepm/stepm; 
             else if(agev[m][i] <agemin){    yp1=modf(dateintmean,&yp);
               agemin=agev[m][i];    anprojmean=yp;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    yp2=modf((yp1*12),&yp);
             }    mprojmean=yp;
             else if(agev[m][i] >agemax){    yp1=modf((yp2*30.5),&yp);
               agemax=agev[m][i];    jprojmean=yp;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    if(jprojmean==0) jprojmean=1;
             }    if(mprojmean==0) jprojmean=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/    
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
           }    
           else { /* =9 */    for(cptcov=1;cptcov<=i2;cptcov++){
             agev[m][i]=1;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
             s[m][i]=-1;        k=k+1;
           }        fprintf(ficresf,"\n#******");
         }        for(j=1;j<=cptcoveff;j++) {
         else /*= 0 Unknown */          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           agev[m][i]=1;        }
       }        fprintf(ficresf,"******\n");
            fprintf(ficresf,"# StartingAge FinalAge");
     }        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
     for (i=1; i<=imx; i++)  {        
       for(m=1; (m<= maxwav); m++){        
         if (s[m][i] > (nlstate+ndeath)) {        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficresf,"\n");
           goto end;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
         }  
       }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(severity,1,maxwav);            oldm=oldms;savm=savms;
     free_imatrix(outcome,1,maxwav+1,1,n);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     free_vector(moisnais,1,n);          
     free_vector(annais,1,n);            for (h=0; h<=nhstepm; h++){
     /* free_matrix(mint,1,maxwav,1,n);              if (h==(int) (calagedate+YEARM*cpt)) {
        free_matrix(anint,1,maxwav,1,n);*/                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
     free_vector(moisdc,1,n);              } 
     free_vector(andc,1,n);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                    for(i=1; i<=nlstate;i++) {              
     wav=ivector(1,imx);                  if (mobilav==1) 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                  else {
                        kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     /* Concatenates waves */                  }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                  
                 }
                 if (h==(int)(calagedate+12*cpt)){
       Tcode=ivector(1,100);                  fprintf(ficresf," %.3f", kk1);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                          
       ncodemax[1]=1;                }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              }
                  }
    codtab=imatrix(1,100,1,10);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    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++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;    fclose(ficresf);
            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]);*/  /************** Forecasting ******************/
          }  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
        }    
      }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
    }    int *popage;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    double calagedate, agelim, kk1, kk2;
       codtab[1][2]=1;codtab[2][2]=2; */    double *popeffectif,*popcount;
    /* for(i=1; i <=m ;i++){    double ***p3mat,***tabpop,***tabpopprev;
       for(k=1; k <=cptcovn; k++){    double ***mobaverage;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    char filerespop[FILENAMELENGTH];
       }  
       printf("\n");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       scanf("%d",i);*/    agelim=AGESUP;
        calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
    /* Calculates basic frequencies. Computes observed prevalence at single age    
        and prints on file fileres'p'. */    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     
        
        strcpy(filerespop,"pop"); 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcat(filerespop,fileres);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with forecast resultfile: %s\n", filerespop);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    }
          printf("Computing forecasting: result on file '%s' \n", filerespop);
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
        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 (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if(mle==1){    if (mobilav!=0) {
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     /*--------- results files --------------*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     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;    stepsize=(int) (stepm+YEARM-1)/YEARM;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if (stepm<=12) stepsize=1;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    for(i=1,jk=1; i <=nlstate; i++){    agelim=AGESUP;
      for(k=1; k <=(nlstate+ndeath); k++){    
        if (k != i)    hstepm=1;
          {    hstepm=hstepm/stepm; 
            printf("%d%d ",i,k);    
            fprintf(ficres,"%1d%1d ",i,k);    if (popforecast==1) {
            for(j=1; j <=ncovmodel; j++){      if((ficpop=fopen(popfile,"r"))==NULL) {
              printf("%f ",p[jk]);        printf("Problem with population file : %s\n",popfile);exit(0);
              fprintf(ficres,"%f ",p[jk]);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
              jk++;      } 
            }      popage=ivector(0,AGESUP);
            printf("\n");      popeffectif=vector(0,AGESUP);
            fprintf(ficres,"\n");      popcount=vector(0,AGESUP);
          }      
      }      i=1;   
    }      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
  if(mle==1){     
     /* Computing hessian and covariance matrix */      imx=i;
     ftolhess=ftol; /* Usually correct */      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     hesscov(matcov, p, npar, delti, ftolhess, func);    }
  }  
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    for(cptcov=1;cptcov<=i2;cptcov++){
     printf("# Scales (for hessian or gradient estimation)\n");     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
      for(i=1,jk=1; i <=nlstate; i++){        k=k+1;
       for(j=1; j <=nlstate+ndeath; j++){        fprintf(ficrespop,"\n#******");
         if (j!=i) {        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficres,"%1d%1d",i,j);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf("%1d%1d",i,j);        }
           for(k=1; k<=ncovmodel;k++){        fprintf(ficrespop,"******\n");
             printf(" %.5e",delti[jk]);        fprintf(ficrespop,"# Age");
             fprintf(ficres," %.5e",delti[jk]);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
             jk++;        if (popforecast==1)  fprintf(ficrespop," [Population]");
           }        
           printf("\n");        for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficres,"\n");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         }          
       }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
      }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                nhstepm = nhstepm/hstepm; 
     k=1;            
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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");            oldm=oldms;savm=savms;
     for(i=1;i<=npar;i++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       /*  if (k>nlstate) k=1;          
       i1=(i-1)/(ncovmodel*nlstate)+1;            for (h=0; h<=nhstepm; h++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              if (h==(int) (calagedate+YEARM*cpt)) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       fprintf(ficres,"%3d",i);              } 
       printf("%3d",i);              for(j=1; j<=nlstate+ndeath;j++) {
       for(j=1; j<=i;j++){                kk1=0.;kk2=0;
         fprintf(ficres," %.5e",matcov[i][j]);                for(i=1; i<=nlstate;i++) {              
         printf(" %.5e",matcov[i][j]);                  if (mobilav==1) 
       }                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
       fprintf(ficres,"\n");                  else {
       printf("\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       k++;                  }
     }                }
                    if (h==(int)(calagedate+12*cpt)){
     while((c=getc(ficpar))=='#' && c!= EOF){                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
       ungetc(c,ficpar);                    /*fprintf(ficrespop," %.3f", kk1);
       fgets(line, MAXLINE, ficpar);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
       puts(line);                }
       fputs(line,ficparo);              }
     }              for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);                kk1=0.;
     estepm=0;                  for(j=1; j<=nlstate;j++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     if (estepm==0 || estepm < stepm) estepm=stepm;                  }
     if (fage <= 2) {                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
       bage = ageminpar;              }
       fage = agemaxpar;  
     }              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
                    fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
     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);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     fputs(line,ficparo);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   ungetc(c,ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            oldm=oldms;savm=savms;
                  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   while((c=getc(ficpar))=='#' && c!= EOF){            for (h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);              if (h==(int) (calagedate+YEARM*cpt)) {
     fgets(line, MAXLINE, ficpar);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     puts(line);              } 
     fputs(line,ficparo);              for(j=1; j<=nlstate+ndeath;j++) {
   }                kk1=0.;kk2=0;
   ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {              
                    kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              }
             }
   fscanf(ficpar,"pop_based=%d\n",&popbased);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     puts(line);  
     fputs(line,ficparo);    if (popforecast==1) {
   }      free_ivector(popage,0,AGESUP);
   ungetc(c,ficpar);      free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
   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);    }
 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);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 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);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /***********************************************/
     fgets(line, MAXLINE, ficpar);  /**************** Main Program *****************/
     puts(line);  /***********************************************/
     fputs(line,ficparo);  
   }  int main(int argc, char *argv[])
   ungetc(c,ficpar);  {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double agedeb, agefin,hf;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double fret;
     double **xi,tmp,delta;
 /*------------ gnuplot -------------*/  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    double dum; /* Dummy variable */
      double ***p3mat;
 /*------------ free_vector  -------------*/    double ***mobaverage;
  chdir(path);    int *indx;
      char line[MAXLINE], linepar[MAXLINE];
  free_ivector(wav,1,imx);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int firstobs=1, lastobs=10;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      int sdeb, sfin; /* Status at beginning and end */
  free_ivector(num,1,n);    int c,  h , cpt,l;
  free_vector(agedc,1,n);    int ju,jl, mi;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
  fclose(ficparo);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
  fclose(ficres);    int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
 /*--------- index.htm --------*/    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
      double **prlim;
   /*--------------- Prevalence limit --------------*/    double *severity;
      double ***param; /* Matrix of parameters */
   strcpy(filerespl,"pl");    double  *p;
   strcat(filerespl,fileres);    double **matcov; /* Matrix of covariance */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double ***delti3; /* Scale */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double *delti; /* Scale */
   }    double ***eij, ***vareij;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **varpl; /* Variances of prevalence limits by age */
   fprintf(ficrespl,"#Prevalence limit\n");    double *epj, vepp;
   fprintf(ficrespl,"#Age ");    double kk1, kk2;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   fprintf(ficrespl,"\n");  
      char *alph[]={"a","a","b","c","d","e"}, str[4];
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char z[1]="c", occ;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  #include <sys/time.h>
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  #include <time.h>
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   k=0;   
   agebase=ageminpar;    /* long total_usecs;
   agelim=agemaxpar;       struct timeval start_time, end_time;
   ftolpl=1.e-10;    
   i1=cptcoveff;       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   if (cptcovn < 1){i1=1;}    getcwd(pathcd, size);
   
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("\n%s",version);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if(argc <=1){
         k=k+1;      printf("\nEnter the parameter file name: ");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      scanf("%s",pathtot);
         fprintf(ficrespl,"\n#******");    }
         for(j=1;j<=cptcoveff;j++)    else{
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      strcpy(pathtot,argv[1]);
         fprintf(ficrespl,"******\n");    }
            /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
         for (age=agebase; age<=agelim; age++){    /*cygwin_split_path(pathtot,path,optionfile);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
           fprintf(ficrespl,"%.0f",age );    /* cutv(path,optionfile,pathtot,'\\');*/
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
           fprintf(ficrespl,"\n");    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
         }    chdir(path);
       }    replace(pathc,path);
     }  
   fclose(ficrespl);    /*-------- arguments in the command line --------*/
   
   /*------------- h Pij x at various ages ------------*/    /* Log file */
      strcat(filelog, optionfilefiname);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    strcat(filelog,".log");    /* */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if((ficlog=fopen(filelog,"w"))==NULL)    {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      printf("Problem with logfile %s\n",filelog);
   }      goto end;
   printf("Computing pij: result on file '%s' \n", filerespij);    }
      fprintf(ficlog,"Log filename:%s\n",filelog);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficlog,"\n%s",version);
   /*if (stepm<=24) stepsize=2;*/    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);
   agelim=AGESUP;    fflush(ficlog);
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    /* */
      strcpy(fileres,"r");
   k=0;    strcat(fileres, optionfilefiname);
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileres,".txt");    /* Other files have txt extension */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    /*---------arguments file --------*/
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)    if((ficpar=fopen(optionfile,"r"))==NULL)    {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with optionfile %s\n",optionfile);
         fprintf(ficrespij,"******\n");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
              goto end;
         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 */    strcpy(filereso,"o");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(filereso,fileres);
           oldm=oldms;savm=savms;    if((ficparo=fopen(filereso,"w"))==NULL) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf("Problem with Output resultfile: %s\n", filereso);
           fprintf(ficrespij,"# Age");      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
           for(i=1; i<=nlstate;i++)      goto end;
             for(j=1; j<=nlstate+ndeath;j++)    }
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");    /* Reads comments: lines beginning with '#' */
            for (h=0; h<=nhstepm; h++){    while((c=getc(ficpar))=='#' && c!= EOF){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      ungetc(c,ficpar);
             for(i=1; i<=nlstate;i++)      fgets(line, MAXLINE, ficpar);
               for(j=1; j<=nlstate+ndeath;j++)      puts(line);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      fputs(line,ficparo);
             fprintf(ficrespij,"\n");    }
              }    ungetc(c,ficpar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d 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);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      fgets(line, MAXLINE, ficpar);
       puts(line);
   fclose(ficrespij);      fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   /*---------- Forecasting ------------------*/    
   if((stepm == 1) && (strcmp(model,".")==0)){     
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    covar=matrix(0,NCOVMAX,1,n); 
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   }    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   else{  
     erreur=108;    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     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);    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   }    
      /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
   /*---------- Health expectancies and variances ------------*/    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
   strcpy(filerest,"t");      fgets(line, MAXLINE, ficpar);
   strcat(filerest,fileres);      puts(line);
   if((ficrest=fopen(filerest,"w"))==NULL) {      fputs(line,ficparo);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    }
   }    ungetc(c,ficpar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
   strcpy(filerese,"e");      for(j=1; j <=nlstate+ndeath-1; j++){
   strcat(filerese,fileres);        fscanf(ficpar,"%1d%1d",&i1,&j1);
   if((ficreseij=fopen(filerese,"w"))==NULL) {        fprintf(ficparo,"%1d%1d",i1,j1);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        if(mle==1)
   }          printf("%1d%1d",i,j);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
  strcpy(fileresv,"v");          fscanf(ficpar," %lf",&param[i][j][k]);
   strcat(fileresv,fileres);          if(mle==1){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            printf(" %lf",param[i][j][k]);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            fprintf(ficlog," %lf",param[i][j][k]);
   }          }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          else
   calagedate=-1;            fprintf(ficlog," %lf",param[i][j][k]);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          fprintf(ficparo," %lf",param[i][j][k]);
         }
   k=0;        fscanf(ficpar,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){        if(mle==1)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          printf("\n");
       k=k+1;        fprintf(ficlog,"\n");
       fprintf(ficrest,"\n#****** ");        fprintf(ficparo,"\n");
       for(j=1;j<=cptcoveff;j++)      }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficrest,"******\n");    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
       fprintf(ficreseij,"\n#****** ");    p=param[1][1];
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Reads comments: lines beginning with '#' */
       fprintf(ficreseij,"******\n");    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fprintf(ficresvij,"\n#****** ");      fgets(line, MAXLINE, ficpar);
       for(j=1;j<=cptcoveff;j++)      puts(line);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fputs(line,ficparo);
       fprintf(ficresvij,"******\n");    }
     ungetc(c,ficpar);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
      for(i=1; i <=nlstate; i++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(j=1; j <=nlstate+ndeath-1; j++){
       oldm=oldms;savm=savms;        fscanf(ficpar,"%1d%1d",&i1,&j1);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        printf("%1d%1d",i,j);
            fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar,"%le",&delti3[i][j][k]);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          printf(" %le",delti3[i][j][k]);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          fprintf(ficparo," %le",delti3[i][j][k]);
       fprintf(ficrest,"\n");        }
         fscanf(ficpar,"\n");
       epj=vector(1,nlstate+1);        printf("\n");
       for(age=bage; age <=fage ;age++){        fprintf(ficparo,"\n");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }
         if (popbased==1) {    }
           for(i=1; i<=nlstate;i++)    delti=delti3[1][1];
             prlim[i][i]=probs[(int)age][i][k];    
         }    /* Reads comments: lines beginning with '#' */
            while((c=getc(ficpar))=='#' && c!= EOF){
         fprintf(ficrest," %4.0f",age);      ungetc(c,ficpar);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      fgets(line, MAXLINE, ficpar);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      puts(line);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      fputs(line,ficparo);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    }
           }    ungetc(c,ficpar);
           epj[nlstate+1] +=epj[j];    
         }    matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
         for(i=1, vepp=0.;i <=nlstate;i++)      fscanf(ficpar,"%s",&str);
           for(j=1;j <=nlstate;j++)      if(mle==1)
             vepp += vareij[i][j][(int)age];        printf("%s",str);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      fprintf(ficlog,"%s",str);
         for(j=1;j <=nlstate;j++){      fprintf(ficparo,"%s",str);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      for(j=1; j <=i; j++){
         }        fscanf(ficpar," %le",&matcov[i][j]);
         fprintf(ficrest,"\n");        if(mle==1){
       }          printf(" %.5le",matcov[i][j]);
     }          fprintf(ficlog," %.5le",matcov[i][j]);
   }        }
 free_matrix(mint,1,maxwav,1,n);        else
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficlog," %.5le",matcov[i][j]);
     free_vector(weight,1,n);        fprintf(ficparo," %.5le",matcov[i][j]);
   fclose(ficreseij);      }
   fclose(ficresvij);      fscanf(ficpar,"\n");
   fclose(ficrest);      if(mle==1)
   fclose(ficpar);        printf("\n");
   free_vector(epj,1,nlstate+1);      fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
   /*------- Variance limit prevalence------*/      }
     for(i=1; i <=npar; i++)
   strcpy(fileresvpl,"vpl");      for(j=i+1;j<=npar;j++)
   strcat(fileresvpl,fileres);        matcov[i][j]=matcov[j][i];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    if(mle==1)
     exit(0);      printf("\n");
   }    fprintf(ficlog,"\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
   
   k=0;    /*-------- Rewriting paramater file ----------*/
   for(cptcov=1;cptcov<=i1;cptcov++){    strcpy(rfileres,"r");    /* "Rparameterfile */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       k=k+1;    strcat(rfileres,".");    /* */
       fprintf(ficresvpl,"\n#****** ");    strcat(rfileres,optionfilext);    /* Other files have txt extension */
       for(j=1;j<=cptcoveff;j++)    if((ficres =fopen(rfileres,"w"))==NULL) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficresvpl,"******\n");      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
          }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(ficres,"#%s\n",version);
       oldm=oldms;savm=savms;      
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /*-------- 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;
   fclose(ficresvpl);    }
   
   /*---------- End : free ----------------*/    n= lastobs;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    severity = vector(1,maxwav);
      outcome=imatrix(1,maxwav+1,1,n);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    num=ivector(1,n);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    moisnais=vector(1,n);
      annais=vector(1,n);
      moisdc=vector(1,n);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    andc=vector(1,n);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    agedc=vector(1,n);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    cod=ivector(1,n);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    weight=vector(1,n);
      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   free_matrix(matcov,1,npar,1,npar);    mint=matrix(1,maxwav,1,n);
   free_vector(delti,1,npar);    anint=matrix(1,maxwav,1,n);
   free_matrix(agev,1,maxwav,1,imx);    s=imatrix(1,maxwav+1,1,n);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   if(erreur >0)  
     printf("End of Imach with error or warning %d\n",erreur);    i=1;
   else   printf("End of Imach\n");    while (fgets(line, MAXLINE, fic) != NULL)    {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      if ((i >= firstobs) && (i <=lastobs)) {
            
   /* 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);*/        for (j=maxwav;j>=1;j--){
   /*printf("Total time was %d uSec.\n", total_usecs);*/          cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
   /*------ End -----------*/          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);
  end:        }
   /* chdir(pathcd);*/          
  /*system("wgnuplot graph.plt");*/        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
  strcpy(plotcmd,GNUPLOTPROGRAM);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
  system(plotcmd);        for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
  /*#ifdef windows*/        } 
   while (z[0] != 'q') {        num[i]=atol(stra);
     /* chdir(path); */          
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
     scanf("%s",z);          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;}*/
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);        i=i+1;
     else if (z[0] == 'g') system(plotcmd);      }
     else if (z[0] == 'q') exit(0);    }
   }    /* printf("ii=%d", ij);
   /*#endif */       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]));}*/
     
    
     /* 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=1; (m<= maxwav); 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){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               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=1; (m<= maxwav); 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;
         }
       }
     }
   
     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);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     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,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,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);
   
     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(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*/
   
     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,"# Age");
           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 %f %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, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     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);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     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_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_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);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     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 */
   }
   
   
Removed from v.1.41.2.2  
changed lines
  Added in v.1.65

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