Diff for /imach/src/imach.c between versions 1.49 and 1.67

version 1.49, 2002/06/20 14:03:39 version 1.67, 2003/01/28 17:41:19
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, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #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 "gnuplot"  #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  #ifdef windows
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #else  #define ODIRSEPARATOR '/'
 #define DIRSEPARATOR '/'  #else
 #endif  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";  #endif
 int erreur; /* Error number */  
 int nvar;  char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int erreur; /* Error number */
 int npar=NPARMAX;  int nvar;
 int nlstate=2; /* Number of live states */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int ndeath=1; /* Number of dead states */  int npar=NPARMAX;
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int nlstate=2; /* Number of live states */
 int popbased=0;  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int *wav; /* Number of waves for this individuual 0 is possible */  int popbased=0;
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */  int *wav; /* Number of waves for this individuual 0 is possible */
 int mle, weightopt;  int maxwav; /* Maxim number of waves */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int jmin, jmax; /* min, max spacing between 2 waves */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int mle, weightopt;
 double jmean; /* Mean space between 2 waves */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  double jmean; /* Mean space between 2 waves */
 FILE *fichtm; /* Html File */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 FILE *ficreseij;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 char filerese[FILENAMELENGTH];  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE  *ficresvij;  FILE *ficlog;
 char fileresv[FILENAMELENGTH];  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE  *ficresvpl;  FILE *ficresprobmorprev;
 char fileresvpl[FILENAMELENGTH];  FILE *fichtm; /* Html File */
 char title[MAXLINE];  FILE *ficreseij;
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 char filerest[FILENAMELENGTH];  char title[MAXLINE];
 char fileregp[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char popfile[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 #define NR_END 1  char filerest[FILENAMELENGTH];
 #define FREE_ARG char*  char fileregp[FILENAMELENGTH];
 #define FTOL 1.0e-10  char popfile[FILENAMELENGTH];
   
 #define NRANSI  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define ITMAX 200  
   #define NR_END 1
 #define TOL 2.0e-4  #define FREE_ARG char*
   #define FTOL 1.0e-10
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10  #define NRANSI 
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define ITMAX 200 
   
 #define GOLD 1.618034  #define TOL 2.0e-4 
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 static double maxarg1,maxarg2;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define GOLD 1.618034 
    #define GLIMIT 100.0 
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define TINY 1.0e-20 
 #define rint(a) floor(a+0.5)  
   static double maxarg1,maxarg2;
 static double sqrarg;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 int imx;  #define rint(a) floor(a+0.5)
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 int estepm;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
   int imx; 
 int m,nb;  int stepm;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  /* Stepm, step in month: minimum step interpolation*/
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  int estepm;
 double dateintmean=0;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 double *weight;  int m,nb;
 int **s; /* Status */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double *agedc, **covar, idx;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  double **pmmij, ***probs;
   double dateintmean=0;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  double *weight;
   int **s; /* Status */
 /**************** split *************************/  double *agedc, **covar, idx;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
    char *s;                             /* pointer */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    int  l1, l2;                         /* length counters */  double ftolhess; /* Tolerance for computing hessian */
   
    l1 = strlen( path );                 /* length of path */  /**************** split *************************/
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  {
    if ( s == NULL ) {                   /* no directory, so use current */    char  *ss;                            /* pointer */
 #if     defined(__bsd__)                /* get current working directory */    int   l1, l2;                         /* length counters */
       extern char       *getwd( );  
     l1 = strlen(path );                   /* length of path */
       if ( getwd( dirc ) == NULL ) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 #else    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       extern char       *getcwd( );    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #endif  #if     defined(__bsd__)                /* get current working directory */
          return( GLOCK_ERROR_GETCWD );      extern char *getwd( );
       }  
       strcpy( name, path );             /* we've got it */      if ( getwd( dirc ) == NULL ) {
    } else {                             /* strip direcotry from path */  #else
       s++;                              /* after this, the filename */      extern char *getcwd( );
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       strcpy( name, s );                /* save file name */  #endif
       strncpy( dirc, path, l1 - l2 );   /* now the directory */        return( GLOCK_ERROR_GETCWD );
       dirc[l1-l2] = 0;                  /* add zero */      }
    }      strcpy( name, path );               /* we've got it */
    l1 = strlen( dirc );                 /* length of directory */    } else {                              /* strip direcotry from path */
 #ifdef windows      ss++;                               /* after this, the filename */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      l2 = strlen( ss );                  /* length of filename */
 #else      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      strcpy( name, ss );         /* save file name */
 #endif      strncpy( dirc, path, l1 - l2 );     /* now the directory */
    s = strrchr( name, '.' );            /* find last / */      dirc[l1-l2] = 0;                    /* add zero */
    s++;    }
    strcpy(ext,s);                       /* save extension */    l1 = strlen( dirc );                  /* length of directory */
    l1= strlen( name);  #ifdef windows
    l2= strlen( s)+1;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    strncpy( finame, name, l1-l2);  #else
    finame[l1-l2]= 0;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    return( 0 );                         /* we're done */  #endif
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
     strcpy(ext,ss);                       /* save extension */
 /******************************************/    l1= strlen( name);
     l2= strlen(ss)+1;
 void replace(char *s, char*t)    strncpy( finame, name, l1-l2);
 {    finame[l1-l2]= 0;
   int i;    return( 0 );                          /* we're done */
   int lg=20;  }
   i=0;  
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  /******************************************/
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  void replace(char *s, char*t)
   }  {
 }    int i;
     int lg=20;
 int nbocc(char *s, char occ)    i=0;
 {    lg=strlen(t);
   int i,j=0;    for(i=0; i<= lg; i++) {
   int lg=20;      (s[i] = t[i]);
   i=0;      if (t[i]== '\\') s[i]='/';
   lg=strlen(s);    }
   for(i=0; i<= lg; i++) {  }
   if  (s[i] == occ ) j++;  
   }  int nbocc(char *s, char occ)
   return j;  {
 }    int i,j=0;
     int lg=20;
 void cutv(char *u,char *v, char*t, char occ)    i=0;
 {    lg=strlen(s);
   int i,lg,j,p=0;    for(i=0; i<= lg; i++) {
   i=0;    if  (s[i] == occ ) j++;
   for(j=0; j<=strlen(t)-1; j++) {    }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    return j;
   }  }
   
   lg=strlen(t);  void cutv(char *u,char *v, char*t, char occ)
   for(j=0; j<p; j++) {  {
     (u[j] = t[j]);    /* cuts string t into u and v where u is ended by char occ excluding it
   }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
      u[p]='\0';       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
    for(j=0; j<= lg; j++) {    i=0;
     if (j>=(p+1))(v[j-p-1] = t[j]);    for(j=0; j<=strlen(t)-1; j++) {
   }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /********************** nrerror ********************/    lg=strlen(t);
     for(j=0; j<p; j++) {
 void nrerror(char error_text[])      (u[j] = t[j]);
 {    }
   fprintf(stderr,"ERREUR ...\n");       u[p]='\0';
   fprintf(stderr,"%s\n",error_text);  
   exit(1);     for(j=0; j<= lg; j++) {
 }      if (j>=(p+1))(v[j-p-1] = t[j]);
 /*********************** vector *******************/    }
 double *vector(int nl, int nh)  }
 {  
   double *v;  /********************** nrerror ********************/
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  void nrerror(char error_text[])
   return v-nl+NR_END;  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /************************ free vector ******************/    exit(EXIT_FAILURE);
 void free_vector(double*v, int nl, int nh)  }
 {  /*********************** vector *******************/
   free((FREE_ARG)(v+nl-NR_END));  double *vector(int nl, int nh)
 }  {
     double *v;
 /************************ivector *******************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 int *ivector(long nl,long nh)    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   int *v;  }
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  /************************ free vector ******************/
   return v-nl+NR_END;  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************free ivector **************************/  }
 void free_ivector(int *v, long nl, long nh)  
 {  /************************ivector *******************************/
   free((FREE_ARG)(v+nl-NR_END));  int *ivector(long nl,long nh)
 }  {
     int *v;
 /******************* imatrix *******************************/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 int **imatrix(long nrl, long nrh, long ncl, long nch)    if (!v) nrerror("allocation failure in ivector");
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    return v-nl+NR_END;
 {  }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
   /* allocate pointers to rows */  {
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /******************* imatrix *******************************/
    int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..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()");    int **m; 
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    /* allocate pointers to rows */ 
      m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
   /* return pointer to array of pointers to rows */    m -= nrl; 
   return m;    
 }    
     /* allocate rows and set pointers to them */ 
 /****************** free_imatrix *************************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 void free_imatrix(m,nrl,nrh,ncl,nch)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       int **m;    m[nrl] += NR_END; 
       long nch,ncl,nrh,nrl;    m[nrl] -= ncl; 
      /* free an int matrix allocated by imatrix() */    
 {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    
   free((FREE_ARG) (m+nrl-NR_END));    /* return pointer to array of pointers to rows */ 
 }    return m; 
   } 
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;        int **m;
   double **m;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  { 
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   m += NR_END;    free((FREE_ARG) (m+nrl-NR_END)); 
   m -= nrl;  } 
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************* matrix *******************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double **matrix(long nrl, long nrh, long ncl, long nch)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free matrix ************************/    m -= nrl;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /******************* ma3x *******************************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    return m;
 {  }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m += NR_END;    free((FREE_ARG)(m+nrl-NR_END));
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /******************* ma3x *******************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    if (!m) nrerror("allocation failure 1 in matrix()");
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    m += NR_END;
   m[nrl][ncl] += NR_END;    m -= nrl;
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     m[nrl][j]=m[nrl][j-1]+nlay;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
   for (i=nrl+1; i<=nrh; i++) {    m[nrl] -= ncl;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       m[i][j]=m[i][j-1]+nlay;  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   return m;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 }    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
 /*************************free ma3x ************************/    for (j=ncl+1; j<=nch; j++) 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      m[nrl][j]=m[nrl][j-1]+nlay;
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    for (i=nrl+1; i<=nrh; i++) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   free((FREE_ARG)(m+nrl-NR_END));      for (j=ncl+1; j<=nch; j++) 
 }        m[i][j]=m[i][j-1]+nlay;
     }
 /***************** f1dim *************************/    return m;
 extern int ncom;  }
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  /*************************free ma3x ************************/
    void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 double f1dim(double x)  {
 {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int j;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double f;    free((FREE_ARG)(m+nrl-NR_END));
   double *xt;  }
    
   xt=vector(1,ncom);  /***************** f1dim *************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  extern int ncom; 
   f=(*nrfunc)(xt);  extern double *pcom,*xicom;
   free_vector(xt,1,ncom);  extern double (*nrfunc)(double []); 
   return f;   
 }  double f1dim(double x) 
   { 
 /*****************brent *************************/    int j; 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    double f;
 {    double *xt; 
   int iter;   
   double a,b,d,etemp;    xt=vector(1,ncom); 
   double fu,fv,fw,fx;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double ftemp;    f=(*nrfunc)(xt); 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    free_vector(xt,1,ncom); 
   double e=0.0;    return f; 
    } 
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  /*****************brent *************************/
   x=w=v=bx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   fw=fv=fx=(*f)(x);  { 
   for (iter=1;iter<=ITMAX;iter++) {    int iter; 
     xm=0.5*(a+b);    double a,b,d,etemp;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double fu,fv,fw,fx;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double ftemp;
     printf(".");fflush(stdout);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 #ifdef DEBUG    double e=0.0; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);   
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    a=(ax < cx ? ax : cx); 
 #endif    b=(ax > cx ? ax : cx); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    x=w=v=bx; 
       *xmin=x;    fw=fv=fx=(*f)(x); 
       return fx;    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
     ftemp=fu;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     if (fabs(e) > tol1) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       r=(x-w)*(fx-fv);      printf(".");fflush(stdout);
       q=(x-v)*(fx-fw);      fprintf(ficlog,".");fflush(ficlog);
       p=(x-v)*q-(x-w)*r;  #ifdef DEBUG
       q=2.0*(q-r);      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);
       if (q > 0.0) p = -p;      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);
       q=fabs(q);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       etemp=e;  #endif
       e=d;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))        *xmin=x; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));        return fx; 
       else {      } 
         d=p/q;      ftemp=fu;
         u=x+d;      if (fabs(e) > tol1) { 
         if (u-a < tol2 || b-u < tol2)        r=(x-w)*(fx-fv); 
           d=SIGN(tol1,xm-x);        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
     } else {        q=2.0*(q-r); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        etemp=e; 
     fu=(*f)(u);        e=d; 
     if (fu <= fx) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       if (u >= x) a=x; else b=x;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       SHFT(v,w,x,u)        else { 
         SHFT(fv,fw,fx,fu)          d=p/q; 
         } else {          u=x+d; 
           if (u < x) a=u; else b=u;          if (u-a < tol2 || b-u < tol2) 
           if (fu <= fw || w == x) {            d=SIGN(tol1,xm-x); 
             v=w;        } 
             w=u;      } else { 
             fv=fw;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             fw=fu;      } 
           } else if (fu <= fv || v == x || v == w) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             v=u;      fu=(*f)(u); 
             fv=fu;      if (fu <= fx) { 
           }        if (u >= x) a=x; else b=x; 
         }        SHFT(v,w,x,u) 
   }          SHFT(fv,fw,fx,fu) 
   nrerror("Too many iterations in brent");          } else { 
   *xmin=x;            if (u < x) a=u; else b=u; 
   return fx;            if (fu <= fw || w == x) { 
 }              v=w; 
               w=u; 
 /****************** mnbrak ***********************/              fv=fw; 
               fw=fu; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,            } else if (fu <= fv || v == x || v == w) { 
             double (*func)(double))              v=u; 
 {              fv=fu; 
   double ulim,u,r,q, dum;            } 
   double fu;          } 
      } 
   *fa=(*func)(*ax);    nrerror("Too many iterations in brent"); 
   *fb=(*func)(*bx);    *xmin=x; 
   if (*fb > *fa) {    return fx; 
     SHFT(dum,*ax,*bx,dum)  } 
       SHFT(dum,*fb,*fa,dum)  
       }  /****************** mnbrak ***********************/
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   while (*fb > *fc) {              double (*func)(double)) 
     r=(*bx-*ax)*(*fb-*fc);  { 
     q=(*bx-*cx)*(*fb-*fa);    double ulim,u,r,q, dum;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    double fu; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));   
     ulim=(*bx)+GLIMIT*(*cx-*bx);    *fa=(*func)(*ax); 
     if ((*bx-u)*(u-*cx) > 0.0) {    *fb=(*func)(*bx); 
       fu=(*func)(u);    if (*fb > *fa) { 
     } else if ((*cx-u)*(u-ulim) > 0.0) {      SHFT(dum,*ax,*bx,dum) 
       fu=(*func)(u);        SHFT(dum,*fb,*fa,dum) 
       if (fu < *fc) {        } 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    *cx=(*bx)+GOLD*(*bx-*ax); 
           SHFT(*fb,*fc,fu,(*func)(u))    *fc=(*func)(*cx); 
           }    while (*fb > *fc) { 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      r=(*bx-*ax)*(*fb-*fc); 
       u=ulim;      q=(*bx-*cx)*(*fb-*fa); 
       fu=(*func)(u);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     } else {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       u=(*cx)+GOLD*(*cx-*bx);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       fu=(*func)(u);      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
     SHFT(*ax,*bx,*cx,u)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       SHFT(*fa,*fb,*fc,fu)        fu=(*func)(u); 
       }        if (fu < *fc) { 
 }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 /*************** linmin ************************/            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 int ncom;        u=ulim; 
 double *pcom,*xicom;        fu=(*func)(u); 
 double (*nrfunc)(double []);      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        fu=(*func)(u); 
 {      } 
   double brent(double ax, double bx, double cx,      SHFT(*ax,*bx,*cx,u) 
                double (*f)(double), double tol, double *xmin);        SHFT(*fa,*fb,*fc,fu) 
   double f1dim(double x);        } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  } 
               double *fc, double (*func)(double));  
   int j;  /*************** linmin ************************/
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  int ncom; 
    double *pcom,*xicom;
   ncom=n;  double (*nrfunc)(double []); 
   pcom=vector(1,n);   
   xicom=vector(1,n);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   nrfunc=func;  { 
   for (j=1;j<=n;j++) {    double brent(double ax, double bx, double cx, 
     pcom[j]=p[j];                 double (*f)(double), double tol, double *xmin); 
     xicom[j]=xi[j];    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   ax=0.0;                double *fc, double (*func)(double)); 
   xx=1.0;    int j; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double xx,xmin,bx,ax; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double fx,fb,fa;
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    ncom=n; 
 #endif    pcom=vector(1,n); 
   for (j=1;j<=n;j++) {    xicom=vector(1,n); 
     xi[j] *= xmin;    nrfunc=func; 
     p[j] += xi[j];    for (j=1;j<=n;j++) { 
   }      pcom[j]=p[j]; 
   free_vector(xicom,1,n);      xicom[j]=xi[j]; 
   free_vector(pcom,1,n);    } 
 }    ax=0.0; 
     xx=1.0; 
 /*************** powell ************************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
             double (*func)(double []))  #ifdef DEBUG
 {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   void linmin(double p[], double xi[], int n, double *fret,    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               double (*func)(double []));  #endif
   int i,ibig,j;    for (j=1;j<=n;j++) { 
   double del,t,*pt,*ptt,*xit;      xi[j] *= xmin; 
   double fp,fptt;      p[j] += xi[j]; 
   double *xits;    } 
   pt=vector(1,n);    free_vector(xicom,1,n); 
   ptt=vector(1,n);    free_vector(pcom,1,n); 
   xit=vector(1,n);  } 
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************** powell ************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (*iter=1;;++(*iter)) {              double (*func)(double [])) 
     fp=(*fret);  { 
     ibig=0;    void linmin(double p[], double xi[], int n, double *fret, 
     del=0.0;                double (*func)(double [])); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    int i,ibig,j; 
     for (i=1;i<=n;i++)    double del,t,*pt,*ptt,*xit;
       printf(" %d %.12f",i, p[i]);    double fp,fptt;
     printf("\n");    double *xits;
     for (i=1;i<=n;i++) {    pt=vector(1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    ptt=vector(1,n); 
       fptt=(*fret);    xit=vector(1,n); 
 #ifdef DEBUG    xits=vector(1,n); 
       printf("fret=%lf \n",*fret);    *fret=(*func)(p); 
 #endif    for (j=1;j<=n;j++) pt[j]=p[j]; 
       printf("%d",i);fflush(stdout);    for (*iter=1;;++(*iter)) { 
       linmin(p,xit,n,fret,func);      fp=(*fret); 
       if (fabs(fptt-(*fret)) > del) {      ibig=0; 
         del=fabs(fptt-(*fret));      del=0.0; 
         ibig=i;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      for (i=1;i<=n;i++) 
       printf("%d %.12e",i,(*fret));        printf(" %d %.12f",i, p[i]);
       for (j=1;j<=n;j++) {      fprintf(ficlog," %d %.12f",i, p[i]);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      printf("\n");
         printf(" x(%d)=%.12e",j,xit[j]);      fprintf(ficlog,"\n");
       }      for (i=1;i<=n;i++) { 
       for(j=1;j<=n;j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         printf(" p=%.12e",p[j]);        fptt=(*fret); 
       printf("\n");  #ifdef DEBUG
 #endif        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #endif
 #ifdef DEBUG        printf("%d",i);fflush(stdout);
       int k[2],l;        fprintf(ficlog,"%d",i);fflush(ficlog);
       k[0]=1;        linmin(p,xit,n,fret,func); 
       k[1]=-1;        if (fabs(fptt-(*fret)) > del) { 
       printf("Max: %.12e",(*func)(p));          del=fabs(fptt-(*fret)); 
       for (j=1;j<=n;j++)          ibig=i; 
         printf(" %.12e",p[j]);        } 
       printf("\n");  #ifdef DEBUG
       for(l=0;l<=1;l++) {        printf("%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        for (j=1;j<=n;j++) {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         }          printf(" x(%d)=%.12e",j,xit[j]);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
 #endif        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
       free_vector(xit,1,n);        }
       free_vector(xits,1,n);        printf("\n");
       free_vector(ptt,1,n);        fprintf(ficlog,"\n");
       free_vector(pt,1,n);  #endif
       return;      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #ifdef DEBUG
     for (j=1;j<=n;j++) {        int k[2],l;
       ptt[j]=2.0*p[j]-pt[j];        k[0]=1;
       xit[j]=p[j]-pt[j];        k[1]=-1;
       pt[j]=p[j];        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     fptt=(*func)(ptt);        for (j=1;j<=n;j++) {
     if (fptt < fp) {          printf(" %.12e",p[j]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);          fprintf(ficlog," %.12e",p[j]);
       if (t < 0.0) {        }
         linmin(p,xit,n,fret,func);        printf("\n");
         for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
           xi[j][ibig]=xi[j][n];        for(l=0;l<=1;l++) {
           xi[j][n]=xit[j];          for (j=1;j<=n;j++) {
         }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 #ifdef DEBUG            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         for(j=1;j<=n;j++)          }
           printf(" %.12e",xit[j]);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         printf("\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 #endif        }
       }  #endif
     }  
   }  
 }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 /**** Prevalence limit ****************/        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        return; 
 {      } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
      matrix by transitions matrix until convergence is reached */      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   int i, ii,j,k;        xit[j]=p[j]-pt[j]; 
   double min, max, maxmin, maxmax,sumnew=0.;        pt[j]=p[j]; 
   double **matprod2();      } 
   double **out, cov[NCOVMAX], **pmij();      fptt=(*func)(ptt); 
   double **newm;      if (fptt < fp) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)          linmin(p,xit,n,fret,func); 
     for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=n;j++) { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);            xi[j][ibig]=xi[j][n]; 
     }            xi[j][n]=xit[j]; 
           }
    cov[1]=1.;  #ifdef DEBUG
            printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){          for(j=1;j<=n;j++){
     newm=savm;            printf(" %.12e",xit[j]);
     /* Covariates have to be included here again */            fprintf(ficlog," %.12e",xit[j]);
      cov[2]=agefin;          }
            printf("\n");
       for (k=1; k<=cptcovn;k++) {          fprintf(ficlog,"\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #endif
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        }
       }      } 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    } 
       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]]];  
   /**** Prevalence limit (stable prevalence)  ****************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       /*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);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
     savm=oldm;  
     oldm=newm;    int i, ii,j,k;
     maxmax=0.;    double min, max, maxmin, maxmax,sumnew=0.;
     for(j=1;j<=nlstate;j++){    double **matprod2();
       min=1.;    double **out, cov[NCOVMAX], **pmij();
       max=0.;    double **newm;
       for(i=1; i<=nlstate; i++) {    double agefin, delaymax=50 ; /* Max number of years to converge */
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    for (ii=1;ii<=nlstate+ndeath;ii++)
         prlim[i][j]= newm[i][j]/(1-sumnew);      for (j=1;j<=nlstate+ndeath;j++){
         max=FMAX(max,prlim[i][j]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         min=FMIN(min,prlim[i][j]);      }
       }  
       maxmin=max-min;     cov[1]=1.;
       maxmax=FMAX(maxmax,maxmin);   
     }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     if(maxmax < ftolpl){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       return prlim;      newm=savm;
     }      /* Covariates have to be included here again */
   }       cov[2]=agefin;
 }    
         for (k=1; k<=cptcovn;k++) {
 /*************** transition probabilities ***************/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        }
 {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double s1, s2;        for (k=1; k<=cptcovprod;k++)
   /*double t34;*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int i,j,j1, nc, ii, jj;  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for(i=1; i<= nlstate; i++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(j=1; j<i;j++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      savm=oldm;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      oldm=newm;
       }      maxmax=0.;
       ps[i][j]=s2;      for(j=1;j<=nlstate;j++){
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        min=1.;
     }        max=0.;
     for(j=i+1; j<=nlstate+ndeath;j++){        for(i=1; i<=nlstate; i++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          sumnew=0;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          max=FMAX(max,prlim[i][j]);
       ps[i][j]=s2;          min=FMIN(min,prlim[i][j]);
     }        }
   }        maxmin=max-min;
     /*ps[3][2]=1;*/        maxmax=FMAX(maxmax,maxmin);
       }
   for(i=1; i<= nlstate; i++){      if(maxmax < ftolpl){
      s1=0;        return prlim;
     for(j=1; j<i; j++)      }
       s1+=exp(ps[i][j]);    }
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  /*************** transition probabilities ***************/ 
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double s1, s2;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    /*double t34;*/
   } /* end i */    int i,j,j1, nc, ii, jj;
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      for(i=1; i<= nlstate; i++){
     for(jj=1; jj<= nlstate+ndeath; jj++){      for(j=1; j<i;j++){
       ps[ii][jj]=0;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       ps[ii][ii]=1;          /*s2 += param[i][j][nc]*cov[nc];*/
     }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   }          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
         ps[i][j]=s2;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
      printf("%lf ",ps[ii][jj]);      for(j=i+1; j<=nlstate+ndeath;j++){
    }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     printf("\n ");          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     printf("\n ");printf("%lf ",cov[2]);*/        }
 /*        ps[i][j]=s2;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      }
   goto end;*/    }
     return ps;      /*ps[3][2]=1;*/
 }  
     for(i=1; i<= nlstate; i++){
 /**************** Product of 2 matrices ******************/       s1=0;
       for(j=1; j<i; j++)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        s1+=exp(ps[i][j]);
 {      for(j=i+1; j<=nlstate+ndeath; j++)
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        s1+=exp(ps[i][j]);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      ps[i][i]=1./(s1+1.);
   /* in, b, out are matrice of pointers which should have been initialized      for(j=1; j<i; j++)
      before: only the contents of out is modified. The function returns        ps[i][j]= exp(ps[i][j])*ps[i][i];
      a pointer to pointers identical to out */      for(j=i+1; j<=nlstate+ndeath; j++)
   long i, j, k;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(i=nrl; i<= nrh; i++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for(k=ncolol; k<=ncoloh; k++)    } /* end i */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   return out;        ps[ii][jj]=0;
 }        ps[ii][ii]=1;
       }
     }
 /************* Higher Matrix Product ***************/  
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 {      for(jj=1; jj<= nlstate+ndeath; jj++){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month       printf("%lf ",ps[ii][jj]);
      duration (i.e. until     }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      printf("\n ");
      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).      printf("\n ");printf("%lf ",cov[2]);*/
      Model is determined by parameters x and covariates have to be  /*
      included manually here.    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
      */      return ps;
   }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /**************** Product of 2 matrices ******************/
   double **newm;  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   /* Hstepm could be zero and should return the unit matrix */  {
   for (i=1;i<=nlstate+ndeath;i++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for (j=1;j<=nlstate+ndeath;j++){       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* in, b, out are matrice of pointers which should have been initialized 
       po[i][j][0]=(i==j ? 1.0 : 0.0);       before: only the contents of out is modified. The function returns
     }       a pointer to pointers identical to out */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    long i, j, k;
   for(h=1; h <=nhstepm; h++){    for(i=nrl; i<= nrh; i++)
     for(d=1; d <=hstepm; d++){      for(k=ncolol; k<=ncoloh; k++)
       newm=savm;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /* Covariates have to be included here again */          out[i][k] +=in[i][j]*b[j][k];
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return out;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /************* Higher Matrix Product ***************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    /* Computes the transition matrix starting at age 'age' over 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/       'nhstepm*hstepm*stepm' months (i.e. until
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       nhstepm*hstepm matrices. 
       savm=oldm;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       oldm=newm;       (typically every 2 years instead of every month which is too big 
     }       for the memory).
     for(i=1; i<=nlstate+ndeath; i++)       Model is determined by parameters x and covariates have to be 
       for(j=1;j<=nlstate+ndeath;j++) {       included manually here. 
         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]);       */
          */  
       }    int i, j, d, h, k;
   } /* end h */    double **out, cov[NCOVMAX];
   return po;    double **newm;
 }  
     /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 /*************** log-likelihood *************/      for (j=1;j<=nlstate+ndeath;j++){
 double func( double *x)        oldm[i][j]=(i==j ? 1.0 : 0.0);
 {        po[i][j][0]=(i==j ? 1.0 : 0.0);
   int i, ii, j, k, mi, d, kk;      }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double **out;    for(h=1; h <=nhstepm; h++){
   double sw; /* Sum of weights */      for(d=1; d <=hstepm; d++){
   double lli; /* Individual log likelihood */        newm=savm;
   long ipmx;        /* Covariates have to be included here again */
   /*extern weight */        cov[1]=1.;
   /* We are differentiating ll according to initial status */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /*for(i=1;i<imx;i++)        for (k=1; k<=cptcovage;k++)
     printf(" %d\n",s[4][i]);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   */        for (k=1; k<=cptcovprod;k++)
   cov[1]=1.;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for(mi=1; mi<= wav[i]-1; mi++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for (ii=1;ii<=nlstate+ndeath;ii++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        savm=oldm;
       for(d=0; d<dh[mi][i]; d++){        oldm=newm;
         newm=savm;      }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      for(i=1; i<=nlstate+ndeath; i++)
         for (kk=1; kk<=cptcovage;kk++) {        for(j=1;j<=nlstate+ndeath;j++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          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]);
                   */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    } /* end h */
         savm=oldm;    return po;
         oldm=newm;  }
          
          
       } /* end mult */  /*************** log-likelihood *************/
        double func( double *x)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    int i, ii, j, k, mi, d, kk;
       ipmx +=1;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       sw += weight[i];    double **out;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double sw; /* Sum of weights */
     } /* end of wave */    double lli; /* Individual log likelihood */
   } /* end of individual */    int s1, s2;
     double bbh;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    long ipmx;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /*extern weight */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    /* We are differentiating ll according to initial status */
   return -l;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
 /*********** Maximum Likelihood Estimation ***************/    cov[1]=1.;
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for(k=1; k<=nlstate; k++) ll[k]=0.;
 {  
   int i,j, iter;    if(mle==1){
   double **xi,*delti;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double fret;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   xi=matrix(1,npar,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=npar;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=npar;j++)            for (j=1;j<=nlstate+ndeath;j++){
       xi[i][j]=(i==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Powell\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   powell(p,xi,npar,ftol,&iter,&fret,func);            }
           for(d=0; d<dh[mi][i]; d++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));            newm=savm;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /**** Computes Hessian and covariance matrix ***/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   double  **a,**y,*x,pd;            oldm=newm;
   double **hess;          } /* end mult */
   int i, j,jk;        
   int *indx;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias and large stepm.
   double hessii(double p[], double delta, int theta, double delti[]);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double hessij(double p[], double delti[], int i, int j);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   void lubksb(double **a, int npar, int *indx, double b[]) ;           * the nearest (and in case of equal distance, to the lowest) interval but now
   void ludcmp(double **a, int npar, int *indx, double *d) ;           * 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
   hess=matrix(1,npar,1,npar);           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   printf("\nCalculation of the hessian matrix. Wait...\n");           * -stepm/2 to stepm/2 .
   for (i=1;i<=npar;i++){           * For stepm=1 the results are the same as for previous versions of Imach.
     printf("%d",i);fflush(stdout);           * For stepm > 1 the results are less biased than in previous versions. 
     hess[i][i]=hessii(p,ftolhess,i,delti);           */
     /*printf(" %f ",p[i]);*/          s1=s[mw[mi][i]][i];
     /*printf(" %lf ",hess[i][i]);*/          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
   for (i=1;i<=npar;i++) {           * is higher than the multiple of stepm and negative otherwise.
     for (j=1;j<=npar;j++)  {           */
       if (j>i) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         printf(".%d%d",i,j);fflush(stdout);          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 */
         hess[i][j]=hessij(p,delti,i,j);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         hess[j][i]=hess[i][j];              /*if(lli ==000.0)*/
         /*printf(" %lf ",hess[i][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); */
       }          ipmx +=1;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   printf("\n");        } /* end of wave */
       } /* end of individual */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    }  else if(mle==2){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   a=matrix(1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   y=matrix(1,npar,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   x=vector(1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   indx=ivector(1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   for (i=1;i<=npar;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   ludcmp(a,npar,indx,&pd);            }
           for(d=0; d<=dh[mi][i]; d++){
   for (j=1;j<=npar;j++) {            newm=savm;
     for (i=1;i<=npar;i++) x[i]=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     x[j]=1;            for (kk=1; kk<=cptcovage;kk++) {
     lubksb(a,npar,indx,x);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=1;i<=npar;i++){            }
       matcov[i][j]=x[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
             oldm=newm;
   printf("\n#Hessian matrix#\n");          } /* end mult */
   for (i=1;i<=npar;i++) {        
     for (j=1;j<=npar;j++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       printf("%.3e ",hess[i][j]);          /* 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("\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
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   /* Recompute Inverse */           * (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++) a[i][j]=matcov[i][j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   ludcmp(a,npar,indx,&pd);           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   /*  printf("\n#Hessian matrix recomputed#\n");           * 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.
       y[i][j]=x[i];           */
       printf("%.3e ",y[i][j]);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     printf("\n");          /*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 */
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   */          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   free_matrix(a,1,npar,1,npar);          ipmx +=1;
   free_matrix(y,1,npar,1,npar);          sw += weight[i];
   free_vector(x,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_ivector(indx,1,npar);        } /* end of wave */
   free_matrix(hess,1,npar,1,npar);      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /*************** hessian matrix ****************/          for (ii=1;ii<=nlstate+ndeath;ii++)
 double hessii( double x[], double delta, int theta, double delti[])            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int l=1, lmax=20;            }
   double k1,k2;          for(d=0; d<dh[mi][i]; d++){
   double p2[NPARMAX+1];            newm=savm;
   double res;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            for (kk=1; kk<=cptcovage;kk++) {
   double fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int k=0,kmax=10;            }
   double l1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fx=func(x);            savm=oldm;
   for (i=1;i<=npar;i++) p2[i]=x[i];            oldm=newm;
   for(l=0 ; l <=lmax; l++){          } /* end mult */
     l1=pow(10,l);        
     delts=delt;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for(k=1 ; k <kmax; k=k+1){          /* But now since version 0.9 we anticipate for bias and large stepm.
       delt = delta*(l1*k);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       p2[theta]=x[theta] +delt;           * (in months) between two waves is not a multiple of stepm, we rounded to 
       k1=func(p2)-fx;           * the nearest (and in case of equal distance, to the lowest) interval but now
       p2[theta]=x[theta]-delt;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       k2=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       /*res= (k1-2.0*fx+k2)/delt/delt; */           * probability in order to take into account the bias as a fraction of the way
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                 * -stepm/2 to stepm/2 .
 #ifdef DEBUG           * For stepm=1 the results are the same as for previous versions of Imach.
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);           * For stepm > 1 the results are less biased than in previous versions. 
 #endif           */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          s1=s[mw[mi][i]][i];
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          s2=s[mw[mi+1][i]][i];
         k=kmax;          bbh=(double)bh[mi][i]/(double)stepm; 
       }          /* bias is positive if real duration
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */           * is higher than the multiple of stepm and negative otherwise.
         k=kmax; l=lmax*10.;           */
       }          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          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 */
         delts=delt;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       }          /*if(lli ==000.0)*/
     }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   }          ipmx +=1;
   delti[theta]=delts;          sw += weight[i];
   return res;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
 }      } /* end of individual */
     }else{  /* ml=4 no inter-extrapolation */
 double hessij( double x[], double delti[], int thetai,int thetaj)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i;        for(mi=1; mi<= wav[i]-1; mi++){
   int l=1, l1, lmax=20;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double k1,k2,k3,k4,res,fx;            for (j=1;j<=nlstate+ndeath;j++){
   double p2[NPARMAX+1];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   fx=func(x);          for(d=0; d<dh[mi][i]; d++){
   for (k=1; k<=2; k++) {            newm=savm;
     for (i=1;i<=npar;i++) p2[i]=x[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetai]=x[thetai]+delti[thetai]/k;            for (kk=1; kk<=cptcovage;kk++) {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     k1=func(p2)-fx;            }
            
     p2[thetai]=x[thetai]+delti[thetai]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     k2=func(p2)-fx;            savm=oldm;
              oldm=newm;
     p2[thetai]=x[thetai]-delti[thetai]/k;          } /* end mult */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        
     k3=func(p2)-fx;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            ipmx +=1;
     p2[thetai]=x[thetai]-delti[thetai]/k;          sw += weight[i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     k4=func(p2)-fx;        } /* end of wave */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      } /* end of individual */
 #ifdef DEBUG    } /* End of if */
     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(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 #endif    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   return res;    return -l;
 }  }
   
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  /*********** Maximum Likelihood Estimation ***************/
 {  
   int i,imax,j,k;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double big,dum,sum,temp;  {
   double *vv;    int i,j, iter;
      double **xi,*delti;
   vv=vector(1,n);    double fret;
   *d=1.0;    xi=matrix(1,npar,1,npar);
   for (i=1;i<=n;i++) {    for (i=1;i<=npar;i++)
     big=0.0;      for (j=1;j<=npar;j++)
     for (j=1;j<=n;j++)        xi[i][j]=(i==j ? 1.0 : 0.0);
       if ((temp=fabs(a[i][j])) > big) big=temp;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    powell(p,xi,npar,ftol,&iter,&fret,func);
     vv[i]=1.0/big;  
   }     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (j=1;j<=n;j++) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1;i<j;i++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
     }  /**** Computes Hessian and covariance matrix ***/
     big=0.0;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for (i=j;i<=n;i++) {  {
       sum=a[i][j];    double  **a,**y,*x,pd;
       for (k=1;k<j;k++)    double **hess;
         sum -= a[i][k]*a[k][j];    int i, j,jk;
       a[i][j]=sum;    int *indx;
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;    double hessii(double p[], double delta, int theta, double delti[]);
         imax=i;    double hessij(double p[], double delti[], int i, int j);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     }    void ludcmp(double **a, int npar, int *indx, double *d) ;
     if (j != imax) {  
       for (k=1;k<=n;k++) {    hess=matrix(1,npar,1,npar);
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    printf("\nCalculation of the hessian matrix. Wait...\n");
         a[j][k]=dum;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }    for (i=1;i<=npar;i++){
       *d = -(*d);      printf("%d",i);fflush(stdout);
       vv[imax]=vv[j];      fprintf(ficlog,"%d",i);fflush(ficlog);
     }      hess[i][i]=hessii(p,ftolhess,i,delti);
     indx[j]=imax;      /*printf(" %f ",p[i]);*/
     if (a[j][j] == 0.0) a[j][j]=TINY;      /*printf(" %lf ",hess[i][i]);*/
     if (j != n) {    }
       dum=1.0/(a[j][j]);    
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    for (i=1;i<=npar;i++) {
     }      for (j=1;j<=npar;j++)  {
   }        if (j>i) { 
   free_vector(vv,1,n);  /* Doesn't work */          printf(".%d%d",i,j);fflush(stdout);
 ;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 }          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
 void lubksb(double **a, int n, int *indx, double b[])          /*printf(" %lf ",hess[i][j]);*/
 {        }
   int i,ii=0,ip,j;      }
   double sum;    }
      printf("\n");
   for (i=1;i<=n;i++) {    fprintf(ficlog,"\n");
     ip=indx[i];  
     sum=b[ip];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     b[ip]=b[i];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     if (ii)    
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    a=matrix(1,npar,1,npar);
     else if (sum) ii=i;    y=matrix(1,npar,1,npar);
     b[i]=sum;    x=vector(1,npar);
   }    indx=ivector(1,npar);
   for (i=n;i>=1;i--) {    for (i=1;i<=npar;i++)
     sum=b[i];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    ludcmp(a,npar,indx,&pd);
     b[i]=sum/a[i][i];  
   }    for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 /************ Frequencies ********************/      lubksb(a,npar,indx,x);
 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++){ 
 {  /* Some frequencies */        matcov[i][j]=x[i];
        }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    }
   double ***freq; /* Frequencies */  
   double *pp;    printf("\n#Hessian matrix#\n");
   double pos, k2, dateintsum=0,k2cpt=0;    fprintf(ficlog,"\n#Hessian matrix#\n");
   FILE *ficresp;    for (i=1;i<=npar;i++) { 
   char fileresp[FILENAMELENGTH];      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   pp=vector(1,nlstate);        fprintf(ficlog,"%.3e ",hess[i][j]);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
   strcpy(fileresp,"p");      printf("\n");
   strcat(fileresp,fileres);      fprintf(ficlog,"\n");
   if((ficresp=fopen(fileresp,"w"))==NULL) {    }
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);    /* Recompute Inverse */
   }    for (i=1;i<=npar;i++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   j1=0;    ludcmp(a,npar,indx,&pd);
    
   j=cptcoveff;    /*  printf("\n#Hessian matrix recomputed#\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
      for (j=1;j<=npar;j++) {
   for(k1=1; k1<=j;k1++){      for (i=1;i<=npar;i++) x[i]=0;
     for(i1=1; i1<=ncodemax[k1];i1++){      x[j]=1;
       j1++;      lubksb(a,npar,indx,x);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      for (i=1;i<=npar;i++){ 
         scanf("%d", i);*/        y[i][j]=x[i];
       for (i=-1; i<=nlstate+ndeath; i++)          printf("%.3e ",y[i][j]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fprintf(ficlog,"%.3e ",y[i][j]);
           for(m=agemin; m <= agemax+3; m++)      }
             freq[i][jk][m]=0;      printf("\n");
            fprintf(ficlog,"\n");
       dateintsum=0;    }
       k2cpt=0;    */
       for (i=1; i<=imx; i++) {  
         bool=1;    free_matrix(a,1,npar,1,npar);
         if  (cptcovn>0) {    free_matrix(y,1,npar,1,npar);
           for (z1=1; z1<=cptcoveff; z1++)    free_vector(x,1,npar);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    free_ivector(indx,1,npar);
               bool=0;    free_matrix(hess,1,npar,1,npar);
         }  
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  }
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  /*************** hessian matrix ****************/
               if(agev[m][i]==0) agev[m][i]=agemax+1;  double hessii( double x[], double delta, int theta, double delti[])
               if(agev[m][i]==1) agev[m][i]=agemax+2;  {
               if (m<lastpass) {    int i;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    int l=1, lmax=20;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double k1,k2;
               }    double p2[NPARMAX+1];
                  double res;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                 dateintsum=dateintsum+k2;    double fx;
                 k2cpt++;    int k=0,kmax=10;
               }    double l1;
             }  
           }    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
              l1=pow(10,l);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
       if  (cptcovn>0) {        delt = delta*(l1*k);
         fprintf(ficresp, "\n#********** Variable ");        p2[theta]=x[theta] +delt;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        k1=func(p2)-fx;
         fprintf(ficresp, "**********\n#");        p2[theta]=x[theta]-delt;
       }        k2=func(p2)-fx;
       for(i=1; i<=nlstate;i++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       fprintf(ficresp, "\n");        
        #ifdef DEBUG
       for(i=(int)agemin; i <= (int)agemax+3; 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);
         if(i==(int)agemax+3)        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);
           printf("Total");  #endif
         else        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           printf("Age %d", i);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(jk=1; jk <=nlstate ; jk++){          k=kmax;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
             pp[jk] += freq[jk][m][i];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=-1, pos=0; m <=0 ; m++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             pos += freq[jk][m][i];          delts=delt;
           if(pp[jk]>=1.e-10)        }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      }
           else    }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    delti[theta]=delts;
         }    return res; 
     
         for(jk=1; jk <=nlstate ; jk++){  }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  double hessij( double x[], double delti[], int thetai,int thetaj)
         }  {
     int i;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    int l=1, l1, lmax=20;
           pos += pp[jk];    double k1,k2,k3,k4,res,fx;
         for(jk=1; jk <=nlstate ; jk++){    double p2[NPARMAX+1];
           if(pos>=1.e-5)    int k;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           else    fx=func(x);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (k=1; k<=2; k++) {
           if( i <= (int) agemax){      for (i=1;i<=npar;i++) p2[i]=x[i];
             if(pos>=1.e-5){      p2[thetai]=x[thetai]+delti[thetai]/k;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
               probs[i][jk][j1]= pp[jk]/pos;      k1=func(p2)-fx;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    
             }      p2[thetai]=x[thetai]+delti[thetai]/k;
             else      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      k2=func(p2)-fx;
           }    
         }      p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(jk=-1; jk <=nlstate+ndeath; jk++)      k3=func(p2)-fx;
           for(m=-1; m <=nlstate+ndeath; m++)    
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      p2[thetai]=x[thetai]-delti[thetai]/k;
         if(i <= (int) agemax)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           fprintf(ficresp,"\n");      k4=func(p2)-fx;
         printf("\n");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       }  #ifdef DEBUG
     }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   dateintmean=dateintsum/k2cpt;  #endif
      }
   fclose(ficresp);    return res;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  }
   free_vector(pp,1,nlstate);  
    /************** Inverse of matrix **************/
   /* End of Freq */  void ludcmp(double **a, int n, int *indx, double *d) 
 }  { 
     int i,imax,j,k; 
 /************ Prevalence ********************/    double big,dum,sum,temp; 
 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)    double *vv; 
 {  /* Some frequencies */   
      vv=vector(1,n); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    *d=1.0; 
   double ***freq; /* Frequencies */    for (i=1;i<=n;i++) { 
   double *pp;      big=0.0; 
   double pos, k2;      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
   pp=vector(1,nlstate);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      vv[i]=1.0/big; 
      } 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for (j=1;j<=n;j++) { 
   j1=0;      for (i=1;i<j;i++) { 
          sum=a[i][j]; 
   j=cptcoveff;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        a[i][j]=sum; 
        } 
   for(k1=1; k1<=j;k1++){      big=0.0; 
     for(i1=1; i1<=ncodemax[k1];i1++){      for (i=j;i<=n;i++) { 
       j1++;        sum=a[i][j]; 
              for (k=1;k<j;k++) 
       for (i=-1; i<=nlstate+ndeath; i++)            sum -= a[i][k]*a[k][j]; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          a[i][j]=sum; 
           for(m=agemin; m <= agemax+3; m++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
             freq[i][jk][m]=0;          big=dum; 
                imax=i; 
       for (i=1; i<=imx; i++) {        } 
         bool=1;      } 
         if  (cptcovn>0) {      if (j != imax) { 
           for (z1=1; z1<=cptcoveff; z1++)        for (k=1;k<=n;k++) { 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          dum=a[imax][k]; 
               bool=0;          a[imax][k]=a[j][k]; 
         }          a[j][k]=dum; 
         if (bool==1) {        } 
           for(m=firstpass; m<=lastpass; m++){        *d = -(*d); 
             k2=anint[m][i]+(mint[m][i]/12.);        vv[imax]=vv[j]; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      } 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      indx[j]=imax; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      if (a[j][j] == 0.0) a[j][j]=TINY; 
               if (m<lastpass) {      if (j != n) { 
                 if (calagedate>0)        dum=1.0/(a[j][j]); 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                 else      } 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    } 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    free_vector(vv,1,n);  /* Doesn't work */
               }  ;
             }  } 
           }  
         }  void lubksb(double **a, int n, int *indx, double b[]) 
       }  { 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int i,ii=0,ip,j; 
         for(jk=1; jk <=nlstate ; jk++){    double sum; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)   
             pp[jk] += freq[jk][m][i];    for (i=1;i<=n;i++) { 
         }      ip=indx[i]; 
         for(jk=1; jk <=nlstate ; jk++){      sum=b[ip]; 
           for(m=-1, pos=0; m <=0 ; m++)      b[ip]=b[i]; 
             pos += freq[jk][m][i];      if (ii) 
         }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
              else if (sum) ii=i; 
         for(jk=1; jk <=nlstate ; jk++){      b[i]=sum; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
             pp[jk] += freq[jk][m][i];    for (i=n;i>=1;i--) { 
         }      sum=b[i]; 
              for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      b[i]=sum/a[i][i]; 
            } 
         for(jk=1; jk <=nlstate ; jk++){      } 
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  /************ Frequencies ********************/
               probs[i][jk][j1]= pp[jk]/pos;  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 */
           }    
         }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
            int first;
       }    double ***freq; /* Frequencies */
     }    double *pp;
   }    double pos, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
      char fileresp[FILENAMELENGTH];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    
   free_vector(pp,1,nlstate);    pp=vector(1,nlstate);
      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 }  /* End of Freq */    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
 /************* Waves Concatenation ***************/    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 {      exit(0);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    }
      Death is a valid wave (if date is known).    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    j1=0;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    
      and mw[mi+1][i]. dh depends on stepm.    j=cptcoveff;
      */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   int i, mi, m;    first=1;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   int j, k=0,jk, ju, jl;        j1++;
   double sum=0.;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   jmin=1e+5;          scanf("%d", i);*/
   jmax=-1;        for (i=-1; i<=nlstate+ndeath; i++)  
   jmean=0.;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   for(i=1; i<=imx; i++){            for(m=agemin; m <= agemax+3; m++)
     mi=0;              freq[i][jk][m]=0;
     m=firstpass;        
     while(s[m][i] <= nlstate){        dateintsum=0;
       if(s[m][i]>=1)        k2cpt=0;
         mw[++mi][i]=m;        for (i=1; i<=imx; i++) {
       if(m >=lastpass)          bool=1;
         break;          if  (cptcovn>0) {
       else            for (z1=1; z1<=cptcoveff; z1++) 
         m++;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }/* end while */                bool=0;
     if (s[m][i] > nlstate){          }
       mi++;     /* Death is another wave */          if (bool==1){
       /* if(mi==0)  never been interviewed correctly before death */            for(m=firstpass; m<=lastpass; m++){
          /* Only death is a correct wave */              k2=anint[m][i]+(mint[m][i]/12.);
       mw[mi][i]=m;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     }                if(agev[m][i]==0) agev[m][i]=agemax+1;
                 if(agev[m][i]==1) agev[m][i]=agemax+2;
     wav[i]=mi;                if (m<lastpass) {
     if(mi==0)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
   }                }
                 
   for(i=1; i<=imx; i++){                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
     for(mi=1; mi<wav[i];mi++){                  dateintsum=dateintsum+k2;
       if (stepm <=0)                  k2cpt++;
         dh[mi][i]=1;                }
       else{              }
         if (s[mw[mi+1][i]][i] > nlstate) {            }
           if (agedc[i] < 2*AGESUP) {          }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        }
           if(j==0) j=1;  /* Survives at least one month after exam */         
           k=k+1;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;        if  (cptcovn>0) {
           sum=sum+j;          fprintf(ficresp, "\n#********** Variable "); 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresp, "**********\n#");
         }        }
         else{        for(i=1; i<=nlstate;i++) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           k=k+1;        fprintf(ficresp, "\n");
           if (j >= jmax) jmax=j;        
           else if (j <= jmin)jmin=j;        for(i=(int)agemin; i <= (int)agemax+3; i++){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          if(i==(int)agemax+3){
           sum=sum+j;            fprintf(ficlog,"Total");
         }          }else{
         jk= j/stepm;            if(first==1){
         jl= j -jk*stepm;              first=0;
         ju= j -(jk+1)*stepm;              printf("See log file for details...\n");
         if(jl <= -ju)            }
           dh[mi][i]=jk;            fprintf(ficlog,"Age %d", i);
         else          }
           dh[mi][i]=jk+1;          for(jk=1; jk <=nlstate ; jk++){
         if(dh[mi][i]==0)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           dh[mi][i]=1; /* At least one step */              pp[jk] += freq[jk][m][i]; 
       }          }
     }          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pos=0; m <=0 ; m++)
   jmean=sum/k;              pos += freq[jk][m][i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            if(pp[jk]>=1.e-10){
  }              if(first==1){
 /*********** Tricode ****************************/              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 void tricode(int *Tvar, int **nbcode, int imx)              }
 {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int Ndum[20],ij=1, k, j, i;            }else{
   int cptcode=0;              if(first==1)
   cptcoveff=0;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   for (k=0; k<19; k++) Ndum[k]=0;            }
   for (k=1; k<=7; k++) ncodemax[k]=0;          }
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=imx; i++) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       ij=(int)(covar[Tvar[j]][i]);              pp[jk] += freq[jk][m][i];
       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,pos=0; jk <=nlstate ; jk++)
     }            pos += pp[jk];
           for(jk=1; jk <=nlstate ; jk++){
     for (i=0; i<=cptcode; i++) {            if(pos>=1.e-5){
       if(Ndum[i]!=0) ncodemax[j]++;              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     ij=1;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
               if(first==1)
     for (i=1; i<=ncodemax[j]; i++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for (k=0; k<=19; k++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         if (Ndum[k] != 0) {            }
           nbcode[Tvar[j]][ij]=k;            if( i <= (int) agemax){
                        if(pos>=1.e-5){
           ij++;                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
         }                probs[i][jk][j1]= pp[jk]/pos;
         if (ij > ncodemax[j]) break;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       }                }
     }              else
   }                  fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
             }
  for (k=0; k<19; k++) Ndum[k]=0;          }
           
  for (i=1; i<=ncovmodel-2; i++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
       ij=Tvar[i];            for(m=-1; m <=nlstate+ndeath; m++)
       Ndum[ij]++;              if(freq[jk][m][i] !=0 ) {
     }              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]);
  for (i=1; i<=10; i++) {              }
    if((Ndum[i]!=0) && (i<=ncovcol)){          if(i <= (int) agemax)
      Tvaraff[ij]=i;            fprintf(ficresp,"\n");
      ij++;          if(first==1)
    }            printf("Others in log...\n");
  }          fprintf(ficlog,"\n");
          }
     cptcoveff=ij-1;      }
 }    }
     dateintmean=dateintsum/k2cpt; 
 /*********** Health Expectancies ****************/   
     fclose(ficresp);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
 {    
   /* Health expectancies */    /* End of Freq */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  }
   double age, agelim, hf;  
   double ***p3mat,***varhe;  /************ Prevalence ********************/
   double **dnewm,**doldm;  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)
   double *xp;  {  /* Some frequencies */
   double **gp, **gm;   
   double ***gradg, ***trgradg;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   int theta;    double ***freq; /* Frequencies */
     double *pp;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    double pos, k2;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate*2,1,npar);    pp=vector(1,nlstate);
   doldm=matrix(1,nlstate*2,1,nlstate*2);    
      freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   fprintf(ficreseij,"# Health expectancies\n");    j1=0;
   fprintf(ficreseij,"# Age");    
   for(i=1; i<=nlstate;i++)    j=cptcoveff;
     for(j=1; j<=nlstate;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    
   fprintf(ficreseij,"\n");    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   if(estepm < stepm){        j1++;
     printf ("Problem %d lower than %d\n",estepm, stepm);        
   }        for (i=-1; i<=nlstate+ndeath; i++)  
   else  hstepm=estepm;            for (jk=-1; jk<=nlstate+ndeath; jk++)  
   /* We compute the life expectancy from trapezoids spaced every estepm months            for(m=agemin; m <= agemax+3; m++)
    * This is mainly to measure the difference between two models: for example              freq[i][jk][m]=0;
    * if stepm=24 months pijx are given only every 2 years and by summing them       
    * we are calculating an estimate of the Life Expectancy assuming a linear        for (i=1; i<=imx; i++) {
    * progression inbetween and thus overestimating or underestimating according          bool=1;
    * to the curvature of the survival function. If, for the same date, we          if  (cptcovn>0) {
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            for (z1=1; z1<=cptcoveff; z1++) 
    * to compare the new estimate of Life expectancy with the same linear              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    * hypothesis. A more precise result, taking into account a more precise                bool=0;
    * curvature will be obtained if estepm is as small as stepm. */          } 
           if (bool==1) { 
   /* For example we decided to compute the life expectancy with the smallest unit */            for(m=firstpass; m<=lastpass; m++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              k2=anint[m][i]+(mint[m][i]/12.);
      nhstepm is the number of hstepm from age to agelim              if ((k2>=dateprev1) && (k2<=dateprev2)) {
      nstepm is the number of stepm from age to agelin.                if(agev[m][i]==0) agev[m][i]=agemax+1;
      Look at hpijx to understand the reason of that which relies in memory size                if(agev[m][i]==1) agev[m][i]=agemax+2;
      and note for a fixed period like estepm months */                if (m<lastpass) {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                  if (calagedate>0) 
      survival function given by stepm (the optimization length). Unfortunately it                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
      means that if the survival funtion is printed only each two years of age and if                  else
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      results. So we changed our mind and took the option of the best precision.                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
   */                }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              }
             }
   agelim=AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     /* nhstepm age range expressed in number of stepm */        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          for(jk=1; jk <=nlstate ; jk++){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     /* if (stepm >= YEARM) hstepm=1;*/              pp[jk] += freq[jk][m][i]; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);            for(m=-1, pos=0; m <=0 ; m++)
     gp=matrix(0,nhstepm,1,nlstate*2);              pos += freq[jk][m][i];
     gm=matrix(0,nhstepm,1,nlstate*2);          }
           
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          for(jk=1; jk <=nlstate ; jk++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                pp[jk] += freq[jk][m][i];
            }
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
           
     /* Computing Variances of health expectancies */          for(jk=1; jk <=nlstate ; jk++){    
             if( i <= (int) agemax){
      for(theta=1; theta <=npar; theta++){              if(pos>=1.e-5){
       for(i=1; i<=npar; i++){                probs[i][jk][j1]= pp[jk]/pos;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              }
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }/* end jk */
          }/* end i */
       cptj=0;      } /* end i1 */
       for(j=1; j<= nlstate; j++){    } /* end k1 */
         for(i=1; i<=nlstate; i++){  
           cptj=cptj+1;    
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    free_vector(pp,1,nlstate);
           }    
         }  }  /* End of Freq */
       }  
        /************* Waves Concatenation ***************/
        
       for(i=1; i<=npar; i++)  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)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             Death is a valid wave (if date is known).
       cptj=0;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for(j=1; j<= nlstate; j++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(i=1;i<=nlstate;i++){       and mw[mi+1][i]. dh depends on stepm.
           cptj=cptj+1;       */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int i, mi, m;
           }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         }       double sum=0., jmean=0.;*/
       }    int first;
       for(j=1; j<= nlstate*2; j++)    int j, k=0,jk, ju, jl;
         for(h=0; h<=nhstepm-1; h++){    double sum=0.;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    first=0;
         }    jmin=1e+5;
      }    jmax=-1;
        jmean=0.;
 /* End theta */    for(i=1; i<=imx; i++){
       mi=0;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      m=firstpass;
       while(s[m][i] <= nlstate){
      for(h=0; h<=nhstepm-1; h++)        if(s[m][i]>=1)
       for(j=1; j<=nlstate*2;j++)          mw[++mi][i]=m;
         for(theta=1; theta <=npar; theta++)        if(m >=lastpass)
           trgradg[h][j][theta]=gradg[h][theta][j];          break;
              else
           m++;
      for(i=1;i<=nlstate*2;i++)      }/* end while */
       for(j=1;j<=nlstate*2;j++)      if (s[m][i] > nlstate){
         varhe[i][j][(int)age] =0.;        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
      printf("%d|",(int)age);fflush(stdout);           /* Only death is a correct wave */
      for(h=0;h<=nhstepm-1;h++){        mw[mi][i]=m;
       for(k=0;k<=nhstepm-1;k++){      }
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      wav[i]=mi;
         for(i=1;i<=nlstate*2;i++)      if(mi==0){
           for(j=1;j<=nlstate*2;j++)        if(first==0){
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
       }          first=1;
     }        }
     /* Computing expectancies */        if(first==1){
     for(i=1; i<=nlstate;i++)          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
       for(j=1; j<=nlstate;j++)        }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      } /* end mi==0 */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    }
            
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         }        if (stepm <=0)
           dh[mi][i]=1;
     fprintf(ficreseij,"%3.0f",age );        else{
     cptj=0;          if (s[mw[mi+1][i]][i] > nlstate) {
     for(i=1; i<=nlstate;i++)            if (agedc[i] < 2*AGESUP) {
       for(j=1; j<=nlstate;j++){            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         cptj++;            if(j==0) j=1;  /* Survives at least one month after exam */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );            k=k+1;
       }            if (j >= jmax) jmax=j;
     fprintf(ficreseij,"\n");            if (j <= jmin) jmin=j;
                sum=sum+j;
     free_matrix(gm,0,nhstepm,1,nlstate*2);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
     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);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   }            k=k+1;
   printf("\n");            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
   free_vector(xp,1,npar);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   free_matrix(dnewm,1,nlstate*2,1,npar);            sum=sum+j;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          }
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          jk= j/stepm;
 }          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
 /************ Variance ******************/          if(mle <=1){ 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)            if(jl==0){
 {              dh[mi][i]=jk;
   /* Variance of health expectancies */              bh[mi][i]=0;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            }else{ /* We want a negative bias in order to only have interpolation ie
   double **newm;                    * at the price of an extra matrix product in likelihood */
   double **dnewm,**doldm;              dh[mi][i]=jk+1;
   int i, j, nhstepm, hstepm, h, nstepm ;              bh[mi][i]=ju;
   int k, cptcode;            }
   double *xp;          }else{
   double **gp, **gm;            if(jl <= -ju){
   double ***gradg, ***trgradg;              dh[mi][i]=jk;
   double ***p3mat;              bh[mi][i]=jl;       /* bias is positive if real duration
   double age,agelim, hf;                                   * is higher than the multiple of stepm and negative otherwise.
   int theta;                                   */
             }
   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");            else{
   fprintf(ficresvij,"# Age");              dh[mi][i]=jk+1;
   for(i=1; i<=nlstate;i++)              bh[mi][i]=ju;
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            if(dh[mi][i]==0){
   fprintf(ficresvij,"\n");              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   xp=vector(1,npar);              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);
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);            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);
            }
   if(estepm < stepm){        } /* end if mle */
     printf ("Problem %d lower than %d\n",estepm, stepm);      } /* end wave */
   }    }
   else  hstepm=estepm;      jmean=sum/k;
   /* For example we decided to compute the life expectancy with the smallest unit */    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      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  /*********** Tricode ****************************/
      and note for a fixed period like k years */  void tricode(int *Tvar, int **nbcode, int imx)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  {
      survival function given by stepm (the optimization length). Unfortunately it    
      means that if the survival funtion is printed only each two years of age and if    int Ndum[20],ij=1, k, j, i, maxncov=19;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    int cptcode=0;
      results. So we changed our mind and took the option of the best precision.    cptcoveff=0; 
   */   
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (k=0; k<maxncov; k++) Ndum[k]=0;
   agelim = AGESUP;    for (k=1; k<=7; k++) ncodemax[k]=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                 modality*/ 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     gp=matrix(0,nhstepm,1,nlstate);        Ndum[ij]++; /*store the modality */
     gm=matrix(0,nhstepm,1,nlstate);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     for(theta=1; theta <=npar; theta++){                                         Tvar[j]. If V=sex and male is 0 and 
       for(i=1; i<=npar; i++){ /* Computes gradient */                                         female is 1, then  cptcode=1.*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (i=0; i<=cptcode; i++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        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 */
       }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)      ij=1; 
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1; i<=ncodemax[j]; i++) {
       }        for (k=0; k<= maxncov; k++) {
            if (Ndum[k] != 0) {
       for(j=1; j<= nlstate; j++){            nbcode[Tvar[j]][ij]=k; 
         for(h=0; h<=nhstepm; h++){            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            ij++;
         }          }
       }          if (ij > ncodemax[j]) break; 
            }  
       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);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   for (k=0; k< maxncov; k++) Ndum[k]=0;
    
       if (popbased==1) {   for (i=1; i<=ncovmodel-2; i++) { 
         for(i=1; i<=nlstate;i++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           prlim[i][i]=probs[(int)age][i][ij];     ij=Tvar[i];
       }     Ndum[ij]++;
    }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){   ij=1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)   for (i=1; i<= maxncov; i++) {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];     if((Ndum[i]!=0) && (i<=ncovcol)){
         }       Tvaraff[ij]=i; /*For printing */
       }       ij++;
      }
       for(j=1; j<= nlstate; j++)   }
         for(h=0; h<=nhstepm; h++){   
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
     } /* End theta */  
   /*********** Health Expectancies ****************/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
   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(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  {
         for(theta=1; theta <=npar; theta++)    /* Health expectancies */
           trgradg[h][j][theta]=gradg[h][theta][j];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double ***p3mat,***varhe;
     for(i=1;i<=nlstate;i++)    double **dnewm,**doldm;
       for(j=1;j<=nlstate;j++)    double *xp;
         vareij[i][j][(int)age] =0.;    double **gp, **gm;
     double ***gradg, ***trgradg;
     for(h=0;h<=nhstepm;h++){    int theta;
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    xp=vector(1,npar);
         for(i=1;i<=nlstate;i++)    dnewm=matrix(1,nlstate*2,1,npar);
           for(j=1;j<=nlstate;j++)    doldm=matrix(1,nlstate*2,1,nlstate*2);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    
       }    fprintf(ficreseij,"# Health expectancies\n");
     }    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
     fprintf(ficresvij,"%.0f ",age );      for(j=1; j<=nlstate;j++)
     for(i=1; i<=nlstate;i++)        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(j=1; j<=nlstate;j++){    fprintf(ficreseij,"\n");
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }    if(estepm < stepm){
     fprintf(ficresvij,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_matrix(gp,0,nhstepm,1,nlstate);    }
     free_matrix(gm,0,nhstepm,1,nlstate);    else  hstepm=estepm;   
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* We compute the life expectancy from trapezoids spaced every estepm months
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);     * This is mainly to measure the difference between two models: for example
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * if stepm=24 months pijx are given only every 2 years and by summing them
   } /* End age */     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression in between and thus overestimating or underestimating according
   free_vector(xp,1,npar);     * to the curvature of the survival function. If, for the same date, we 
   free_matrix(doldm,1,nlstate,1,npar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   free_matrix(dnewm,1,nlstate,1,nlstate);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 }     * curvature will be obtained if estepm is as small as stepm. */
   
 /************ Variance of prevlim ******************/    /* For example we decided to compute the life expectancy with the smallest unit */
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 {       nhstepm is the number of hstepm from age to agelim 
   /* Variance of prevalence limit */       nstepm is the number of stepm from age to agelin. 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       Look at hpijx to understand the reason of that which relies in memory size
   double **newm;       and note for a fixed period like estepm months */
   double **dnewm,**doldm;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int i, j, nhstepm, hstepm;       survival function given by stepm (the optimization length). Unfortunately it
   int k, cptcode;       means that if the survival funtion is printed only each two years of age and if
   double *xp;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double *gp, *gm;       results. So we changed our mind and took the option of the best precision.
   double **gradg, **trgradg;    */
   double age,agelim;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int theta;  
        agelim=AGESUP;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresvpl,"# Age");      /* nhstepm age range expressed in number of stepm */
   for(i=1; i<=nlstate;i++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       fprintf(ficresvpl," %1d-%1d",i,i);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficresvpl,"\n");      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   xp=vector(1,npar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   dnewm=matrix(1,nlstate,1,npar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   doldm=matrix(1,nlstate,1,nlstate);      gp=matrix(0,nhstepm,1,nlstate*2);
        gm=matrix(0,nhstepm,1,nlstate*2);
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   agelim = AGESUP;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);      /* Computing Variances of health expectancies */
     gm=vector(1,nlstate);  
        for(theta=1; theta <=npar; theta++){
     for(theta=1; theta <=npar; theta++){        for(i=1; i<=npar; i++){ 
       for(i=1; i<=npar; i++){ /* Computes gradient */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
       for(i=1;i<=nlstate;i++)        cptj=0;
         gp[i] = prlim[i][i];        for(j=1; j<= nlstate; j++){
              for(i=1; i<=nlstate; i++){
       for(i=1; i<=npar; i++) /* Computes gradient */            cptj=cptj+1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for(i=1;i<=nlstate;i++)            }
         gm[i] = prlim[i][i];          }
         }
       for(i=1;i<=nlstate;i++)       
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       
     } /* End theta */        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
     trgradg =matrix(1,nlstate,1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
     for(j=1; j<=nlstate;j++)        cptj=0;
       for(theta=1; theta <=npar; theta++)        for(j=1; j<= nlstate; j++){
         trgradg[j][theta]=gradg[theta][j];          for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
     for(i=1;i<=nlstate;i++)            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       varpl[i][(int)age] =0.;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          }
     for(i=1;i<=nlstate;i++)        }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for(j=1; j<= nlstate*2; j++)
           for(h=0; h<=nhstepm-1; h++){
     fprintf(ficresvpl,"%.0f ",age );            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       } 
     fprintf(ficresvpl,"\n");     
     free_vector(gp,1,nlstate);  /* End theta */
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*2;j++)
   free_vector(xp,1,npar);          for(theta=1; theta <=npar; theta++)
   free_matrix(doldm,1,nlstate,1,npar);            trgradg[h][j][theta]=gradg[h][theta][j];
   free_matrix(dnewm,1,nlstate,1,nlstate);       
   
 }       for(i=1;i<=nlstate*2;i++)
         for(j=1;j<=nlstate*2;j++)
 /************ Variance of one-step probabilities  ******************/          varhe[i][j][(int)age] =0.;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  
 {       printf("%d|",(int)age);fflush(stdout);
   int i, j=0,  i1, k1, l1, t, tj;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   int k2, l2, j1,  z1;       for(h=0;h<=nhstepm-1;h++){
   int k=0,l, cptcode;        for(k=0;k<=nhstepm-1;k++){
   int first=1;          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   double **dnewm,**doldm;          for(i=1;i<=nlstate*2;i++)
   double *xp;            for(j=1;j<=nlstate*2;j++)
   double *gp, *gm;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   double **gradg, **trgradg;        }
   double **mu;      }
   double age,agelim, cov[NCOVMAX];      /* Computing expectancies */
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      for(i=1; i<=nlstate;i++)
   int theta;        for(j=1; j<=nlstate;j++)
   char fileresprob[FILENAMELENGTH];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   char fileresprobcov[FILENAMELENGTH];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   char fileresprobcor[FILENAMELENGTH];            
   /* 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]);*/
   double ***varpij;  
           }
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);      fprintf(ficreseij,"%3.0f",age );
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      cptj=0;
     printf("Problem with resultfile: %s\n", fileresprob);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   strcpy(fileresprobcov,"probcov");          cptj++;
   strcat(fileresprobcov,fileres);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        }
     printf("Problem with resultfile: %s\n", fileresprobcov);      fprintf(ficreseij,"\n");
   }     
   strcpy(fileresprobcor,"probcor");      free_matrix(gm,0,nhstepm,1,nlstate*2);
   strcat(fileresprobcor,fileres);      free_matrix(gp,0,nhstepm,1,nlstate*2);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
     printf("Problem with resultfile: %s\n", fileresprobcor);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    }
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    printf("\n");
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    fprintf(ficlog,"\n");
    
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    free_vector(xp,1,npar);
   fprintf(ficresprob,"# Age");    free_matrix(dnewm,1,nlstate*2,1,npar);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
   fprintf(ficresprobcov,"# Age");    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  }
   fprintf(ficresprobcov,"# Age");  
   /************ Variance ******************/
   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)
   for(i=1; i<=nlstate;i++)  {
     for(j=1; j<=(nlstate+ndeath);j++){    /* Variance of health expectancies */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    /* double **newm;*/
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    double **dnewm,**doldm;
     }      double **dnewmp,**doldmp;
   fprintf(ficresprob,"\n");    int i, j, nhstepm, hstepm, h, nstepm ;
   fprintf(ficresprobcov,"\n");    int k, cptcode;
   fprintf(ficresprobcor,"\n");    double *xp;
   xp=vector(1,npar);    double **gp, **gm;  /* for var eij */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    double ***gradg, ***trgradg; /*for var eij */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    double **gradgp, **trgradgp; /* for var p point j */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    double *gpp, *gmp; /* for var p point j */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   first=1;    double ***p3mat;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    double age,agelim, hf;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    double ***mobaverage;
     exit(0);    int theta;
   }    char digit[4];
   else{    char digitp[25];
     fprintf(ficgp,"\n# Routine varprob");  
   }    char fileresprobmorprev[FILENAMELENGTH];
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);    if(popbased==1){
     exit(0);      if(mobilav!=0)
   }        strcpy(digitp,"-populbased-mobilav-");
   else{      else strcpy(digitp,"-populbased-nomobil-");
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");    }
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    else 
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");      strcpy(digitp,"-stablbased-");
   
   }    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   cov[1]=1;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   tj=cptcoveff;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      }
   j1=0;    }
   for(t=1; t<=tj;t++){  
     for(i1=1; i1<=ncodemax[t];i1++){    strcpy(fileresprobmorprev,"prmorprev"); 
       j1++;    sprintf(digit,"%-d",ij);
          /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       if  (cptcovn>0) {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         fprintf(ficresprob, "\n#********** Variable ");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    strcat(fileresprobmorprev,fileres);
         fprintf(ficresprob, "**********\n#");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         fprintf(ficresprobcov, "\n#********** Variable ");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficresprobcov, "**********\n#");    }
            printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficgp, "\n#********** Variable ");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
         fprintf(ficgp, "**********\n#");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
            for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              fprintf(ficresprobmorprev," p.%-d SE",j);
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");      for(i=1; i<=nlstate;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    }  
            fprintf(ficresprobmorprev,"\n");
         fprintf(ficresprobcor, "\n#********** Variable ");        if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         fprintf(ficgp, "**********\n#");          fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      exit(0);
          }
       for (age=bage; age<=fage; age ++){    else{
         cov[2]=age;      fprintf(ficgp,"\n# Routine varevsij");
         for (k=1; k<=cptcovn;k++) {    }
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
         }      printf("Problem with html file: %s\n", optionfilehtm);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         for (k=1; k<=cptcovprod;k++)      exit(0);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    }
            else{
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         gp=vector(1,(nlstate)*(nlstate+ndeath));    }
         gm=vector(1,(nlstate)*(nlstate+ndeath));    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
         for(theta=1; theta <=npar; theta++){    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<=npar; i++)    fprintf(ficresvij,"# Age");
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
              fprintf(ficresvij,"\n");
           k=0;  
           for(i=1; i<= (nlstate); i++){    xp=vector(1,npar);
             for(j=1; j<=(nlstate+ndeath);j++){    dnewm=matrix(1,nlstate,1,npar);
               k=k+1;    doldm=matrix(1,nlstate,1,nlstate);
               gp[k]=pmmij[i][j];    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
             }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }  
              gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           for(i=1; i<=npar; i++)    gpp=vector(nlstate+1,nlstate+ndeath);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    gmp=vector(nlstate+1,nlstate+ndeath);
        trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    
           k=0;    if(estepm < stepm){
           for(i=1; i<=(nlstate); i++){      printf ("Problem %d lower than %d\n",estepm, stepm);
             for(j=1; j<=(nlstate+ndeath);j++){    }
               k=k+1;    else  hstepm=estepm;   
               gm[k]=pmmij[i][j];    /* For example we decided to compute the life expectancy with the smallest unit */
             }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           }       nhstepm is the number of hstepm from age to agelim 
             nstepm is the number of stepm from age to agelin. 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)       Look at hpijx to understand the reason of that which relies in memory size
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];         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
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)       means that if the survival funtion is printed every two years of age and if
           for(theta=1; theta <=npar; theta++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             trgradg[j][theta]=gradg[theta][j];       results. So we changed our mind and took the option of the best precision.
            */
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    agelim = AGESUP;
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         pmij(pmmij,cov,ncovmodel,x,nlstate);      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 */
         k=0;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(i=1; i<=(nlstate); i++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           for(j=1; j<=(nlstate+ndeath);j++){      gp=matrix(0,nhstepm,1,nlstate);
             k=k+1;      gm=matrix(0,nhstepm,1,nlstate);
             mu[k][(int) age]=pmmij[i][j];  
           }  
         }      for(theta=1; theta <=npar; theta++){
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             varpij[i][j][(int)age] = doldm[i][j];        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         /*printf("\n%d ",(int)age);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        if (popbased==1) {
      }*/          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
         fprintf(ficresprob,"\n%d ",(int)age);              prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficresprobcov,"\n%d ",(int)age);          }else{ /* mobilav */ 
         fprintf(ficresprobcor,"\n%d ",(int)age);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);        for(j=1; j<= nlstate; j++){
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);          for(h=0; h<=nhstepm; h++){
         }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         i=0;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         for (k=1; k<=(nlstate);k++){          }
           for (l=1; l<=(nlstate+ndeath);l++){        }
             i=i++;        /* This for computing probability of death (h=1 means
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);           computed over hstepm matrices product = hstepm*stepm months) 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);           as a weighted average of prlim.
             for (j=1; j<=i;j++){        */
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));          for(i=1; i<= nlstate; i++)
             }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           }        }    
         }/* end of loop for state */        /* end probability of death */
       } /* end of loop for age */  
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       for (k1=1; k1<=(nlstate);k1++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (l1=1; l1<=(nlstate+ndeath);l1++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           if(l1==k1) continue;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           i=(k1-1)*(nlstate+ndeath)+l1;   
           for (k2=1; k2<=(nlstate);k2++){        if (popbased==1) {
             for (l2=1; l2<=(nlstate+ndeath);l2++){          if(mobilav ==0){
               if(l2==k2) continue;            for(i=1; i<=nlstate;i++)
               j=(k2-1)*(nlstate+ndeath)+l2;              prlim[i][i]=probs[(int)age][i][ij];
               if(j<=i) continue;          }else{ /* mobilav */ 
               for (age=bage; age<=fage; age ++){            for(i=1; i<=nlstate;i++)
                 if ((int)age %5==0){              prlim[i][i]=mobaverage[(int)age][i][ij];
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;          }
                   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 ;        for(j=1; j<= nlstate; j++){
                   mu2=mu[j][(int) age]/stepm*YEARM;          for(h=0; h<=nhstepm; h++){
                   /* Computing eigen value of matrix of covariance */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));          }
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);        }
                   /* Eigen vectors */        /* This for computing probability of death (h=1 means
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));           computed over hstepm matrices product = hstepm*stepm months) 
                   v21=sqrt(1.-v11*v11);           as a weighted average of prlim.
                   v12=-v21;        */
                   v22=v11;        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
                   /*printf(fignu*/          for(i=1; i<= nlstate; i++)
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */            gmp[j] += prlim[i][i]*p3mat[i][j][1];
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */        }    
                   if(first==1){        /* end probability of death */
                     first=0;  
                     fprintf(ficgp,"\nset parametric;set nolabel");        for(j=1; j<= nlstate; j++) /* vareij */
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);          for(h=0; h<=nhstepm; h++){
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);          }
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);        }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\      } /* End theta */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   }else{  
                     first=0;      for(h=0; h<=nhstepm; h++) /* veij */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);        for(j=1; j<=nlstate;j++)
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);          for(theta=1; theta <=npar; theta++)
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\            trgradg[h][j][theta]=gradg[h][theta][j];
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
                   }/* if first */        for(theta=1; theta <=npar; theta++)
                 } /* age mod 5 */          trgradgp[j][theta]=gradgp[theta][j];
               } /* end loop age */  
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               first=1;      for(i=1;i<=nlstate;i++)
             } /*l12 */        for(j=1;j<=nlstate;j++)
           } /* k12 */          vareij[i][j][(int)age] =0.;
         } /*l1 */  
       }/* k1 */      for(h=0;h<=nhstepm;h++){
     } /* loop covariates */        for(k=0;k<=nhstepm;k++){
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for(i=1;i<=nlstate;i++)
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);            for(j=1;j<=nlstate;j++)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
   }      }
   free_vector(xp,1,npar);  
   fclose(ficresprob);      /* pptj */
   fclose(ficresprobcov);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fclose(ficresprobcor);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   fclose(ficgp);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   fclose(fichtm);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
 }          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
 /******************* Printing html file ***********/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                   int lastpass, int stepm, int weightopt, char model[],\   
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      if (popbased==1) {
                   int popforecast, int estepm ,\        if(mobilav ==0){
                   double jprev1, double mprev1,double anprev1, \          for(i=1; i<=nlstate;i++)
                   double jprev2, double mprev2,double anprev2){            prlim[i][i]=probs[(int)age][i][ij];
   int jj1, k1, i1, cpt;        }else{ /* mobilav */ 
   /*char optionfilehtm[FILENAMELENGTH];*/          for(i=1; i<=nlstate;i++)
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {            prlim[i][i]=mobaverage[(int)age][i][ij];
     printf("Problem with %s \n",optionfilehtm), exit(0);        }
   }      }
       
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      /* This for computing probability of death (h=1 means
  - 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         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n         as a weighted average of prlim.
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      */
  - Life expectancies by age and initial health status (estepm=%2d months):      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
    <a href=\"e%s\">e%s</a> <br>\n</li>", \        for(i=1; i<= nlstate; i++)
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n      /* end probability of death */
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        for(i=1; i<=nlstate;i++){
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        }
       } 
  if(popforecast==1) fprintf(fichtm,"\n      fprintf(ficresprobmorprev,"\n");
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      fprintf(ficresvij,"%.0f ",age );
         <br>",fileres,fileres,fileres,fileres);      for(i=1; i<=nlstate;i++)
  else        for(j=1; j<=nlstate;j++){
    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(ficresvij," %.4f", vareij[i][j][(int)age]);
 fprintf(fichtm," <li><b>Graphs</b></li><p>");        }
       fprintf(ficresvij,"\n");
  m=cptcoveff;      free_matrix(gp,0,nhstepm,1,nlstate);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
  jj1=0;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
  for(k1=1; k1<=m;k1++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(i1=1; i1<=ncodemax[k1];i1++){    } /* End age */
      jj1++;    free_vector(gpp,nlstate+1,nlstate+ndeath);
      if (cptcovn > 0) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        for (cpt=1; cpt<=cptcoveff;cpt++)    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      /* Pij */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      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>  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      /* Quasi-incidences */    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
      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>    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
        /* Stable prevalence in each health state */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
        for(cpt=1; cpt<nlstate;cpt++){    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    /*  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);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  */
        }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    free_vector(xp,1,npar);
 interval) in state (%d): v%s%d%d.png <br>    free_matrix(doldm,1,nlstate,1,nlstate);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      free_matrix(dnewm,1,nlstate,1,npar);
      }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      for(cpt=1; cpt<=nlstate;cpt++) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      }    fclose(ficresprobmorprev);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    fclose(ficgp);
 health expectancies in states (1) and (2): e%s%d.png<br>    fclose(fichtm);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  }
    }  
  }  /************ Variance of prevlim ******************/
 fclose(fichtm);  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)
 }  {
     /* Variance of prevalence limit */
 /******************* Gnuplot file **************/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    double **newm;
     double **dnewm,**doldm;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int i, j, nhstepm, hstepm;
   int ng;    int k, cptcode;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    double *xp;
     printf("Problem with file %s",optionfilegnuplot);    double *gp, *gm;
   }    double **gradg, **trgradg;
     double age,agelim;
 #ifdef windows    int theta;
     fprintf(ficgp,"cd \"%s\" \n",pathc);     
 #endif    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
 m=pow(2,cptcoveff);    fprintf(ficresvpl,"# Age");
      for(i=1; i<=nlstate;i++)
  /* 1eme*/        fprintf(ficresvpl," %1d-%1d",i,i);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficresvpl,"\n");
    for (k1=1; k1<= m ; k1 ++) {  
     xp=vector(1,npar);
 #ifdef windows    dnewm=matrix(1,nlstate,1,npar);
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    doldm=matrix(1,nlstate,1,nlstate);
      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);    
 #endif    hstepm=1*YEARM; /* Every year of age */
 #ifdef unix    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    agelim = AGESUP;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #endif      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
 for (i=1; i<= nlstate ; i ++) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      gradg=matrix(1,npar,1,nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gp=vector(1,nlstate);
 }      gm=vector(1,nlstate);
     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 ++) {      for(theta=1; theta <=npar; theta++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1; i<=npar; i++){ /* Computes gradient */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 }        }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      for (i=1; i<= nlstate ; i ++) {        for(i=1;i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          gp[i] = prlim[i][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");      
 }          for(i=1; i<=npar; i++) /* Computes gradient */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 #ifdef unix        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for(i=1;i<=nlstate;i++)
 #endif          gm[i] = prlim[i][i];
    }  
   }        for(i=1;i<=nlstate;i++)
   /*2 eme*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      trgradg =matrix(1,nlstate,1,npar);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);  
          for(j=1; j<=nlstate;j++)
     for (i=1; i<= nlstate+1 ; i ++) {        for(theta=1; theta <=npar; theta++)
       k=2*i;          trgradg[j][theta]=gradg[theta][j];
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {      for(i=1;i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        varpl[i][(int)age] =0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 }        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      for(i=1;i<=nlstate;i++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficresvpl,"%.0f ",age );
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
         else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 }        fprintf(ficresvpl,"\n");
       fprintf(ficgp,"\" t\"\" w l 0,");      free_vector(gp,1,nlstate);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      free_vector(gm,1,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {      free_matrix(gradg,1,npar,1,nlstate);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      free_matrix(trgradg,1,nlstate,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } /* End age */
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    free_vector(xp,1,npar);
       else fprintf(ficgp,"\" t\"\" w l 0,");    free_matrix(doldm,1,nlstate,1,npar);
     }    free_matrix(dnewm,1,nlstate,1,nlstate);
   }  
    }
   /*3eme*/  
   /************ Variance of one-step probabilities  ******************/
   for (k1=1; k1<= m ; k1 ++) {  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     for (cpt=1; cpt<= nlstate ; cpt ++) {  {
       k=2+nlstate*(2*cpt-2);    int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int k2, l2, j1,  z1;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    int k=0,l, cptcode;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    int first=1, first1;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double **dnewm,**doldm;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    double *xp;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    double *gp, *gm;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double **gradg, **trgradg;
     double **mu;
 */    double age,agelim, cov[NCOVMAX];
       for (i=1; i< nlstate ; i ++) {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         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);    int theta;
     char fileresprob[FILENAMELENGTH];
       }    char fileresprobcov[FILENAMELENGTH];
     }    char fileresprobcor[FILENAMELENGTH];
   }  
      double ***varpij;
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {    strcpy(fileresprob,"prob"); 
     for (cpt=1; cpt<nlstate ; cpt ++) {    strcat(fileresprob,fileres);
       k=3;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      printf("Problem with resultfile: %s\n", fileresprob);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
       for (i=1; i< nlstate ; i ++)    strcpy(fileresprobcov,"probcov"); 
         fprintf(ficgp,"+$%d",k+i+1);    strcat(fileresprobcov,fileres);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
            printf("Problem with resultfile: %s\n", fileresprobcov);
       l=3+(nlstate+ndeath)*cpt;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    }
       for (i=1; i< nlstate ; i ++) {    strcpy(fileresprobcor,"probcor"); 
         l=3+(nlstate+ndeath)*cpt;    strcat(fileresprobcor,fileres);
         fprintf(ficgp,"+$%d",l+i+1);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }    }
   }      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   /* proba elementaires */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for(k=1; k <=(nlstate+ndeath); k++){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       if (k != i) {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for(j=1; j <=ncovmodel; j++){    
            fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficresprob,"# Age");
           jk++;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           fprintf(ficgp,"\n");    fprintf(ficresprobcov,"# Age");
         }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       }    fprintf(ficresprobcov,"# Age");
     }  
    }  
     for(i=1; i<=nlstate;i++)
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/      for(j=1; j<=(nlstate+ndeath);j++){
      for(jk=1; jk <=m; jk++) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
        if (ng==2)        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");      }  
        else    fprintf(ficresprob,"\n");
          fprintf(ficgp,"\nset title \"Probability\"\n");    fprintf(ficresprobcov,"\n");
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    fprintf(ficresprobcor,"\n");
        i=1;    xp=vector(1,npar);
        for(k2=1; k2<=nlstate; k2++) {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
          k3=i;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
          for(k=1; k<=(nlstate+ndeath); k++) {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
            if (k != k2){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
              if(ng==2)    first=1;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
              else      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
              ij=1;      exit(0);
              for(j=3; j <=ncovmodel; j++) {    }
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    else{
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(ficgp,"\n# Routine varprob");
                  ij++;    }
                }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
                else      printf("Problem with html file: %s\n", optionfilehtm);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
              }      exit(0);
              fprintf(ficgp,")/(1");    }
                  else{
              for(k1=1; k1 <=nlstate; k1++){        fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      fprintf(fichtm,"\n");
                ij=1;  
                for(j=3; j <=ncovmodel; j++){      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      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");
                    ij++;  
                  }    }
                  else  
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    cov[1]=1;
                }    tj=cptcoveff;
                fprintf(ficgp,")");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
              }    j1=0;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    for(t=1; t<=tj;t++){
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      for(i1=1; i1<=ncodemax[t];i1++){ 
              i=i+ncovmodel;        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]]);
      }          fprintf(ficresprob, "**********\n#");
    }          fprintf(ficresprobcov, "\n#********** Variable "); 
    fclose(ficgp);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }  /* end gnuplot */          fprintf(ficresprobcov, "**********\n#");
           
           fprintf(ficgp, "\n#********** Variable "); 
 /*************** Moving average **************/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          fprintf(ficgp, "**********\n#");
           
   int i, cpt, cptcod;          
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       for (i=1; i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           mobaverage[(int)agedeb][i][cptcod]=0.;          
              fprintf(ficresprobcor, "\n#********** Variable ");    
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for (i=1; i<=nlstate;i++){          fprintf(ficgp, "**********\n#");    
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
           for (cpt=0;cpt<=4;cpt++){        
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for (age=bage; age<=fage; age ++){ 
           }          cov[2]=age;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for (k=1; k<=cptcovn;k++) {
         }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       }          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
 }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 /************** Forecasting ******************/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          gp=vector(1,(nlstate)*(nlstate+ndeath));
            gm=vector(1,(nlstate)*(nlstate+ndeath));
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      
   int *popage;          for(theta=1; theta <=npar; theta++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for(i=1; i<=npar; i++)
   double *popeffectif,*popcount;              xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double ***p3mat;            
   char fileresf[FILENAMELENGTH];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
  agelim=AGESUP;            k=0;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                k=k+1;
                  gp[k]=pmmij[i][j];
                }
   strcpy(fileresf,"f");            }
   strcat(fileresf,fileres);            
   if((ficresf=fopen(fileresf,"w"))==NULL) {            for(i=1; i<=npar; i++)
     printf("Problem with forecast resultfile: %s\n", fileresf);              xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }      
   printf("Computing forecasting: result on file '%s' \n", fileresf);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   if (mobilav==1) {                k=k+1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                gm[k]=pmmij[i][j];
     movingaverage(agedeb, fage, ageminpar, mobaverage);              }
   }            }
        
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   if (stepm<=12) stepsize=1;              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
            }
   agelim=AGESUP;  
            for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   hstepm=1;            for(theta=1; theta <=npar; theta++)
   hstepm=hstepm/stepm;              trgradg[j][theta]=gradg[theta][j];
   yp1=modf(dateintmean,&yp);          
   anprojmean=yp;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   yp2=modf((yp1*12),&yp);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   mprojmean=yp;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   yp1=modf((yp2*30.5),&yp);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   jprojmean=yp;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if(jprojmean==0) jprojmean=1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if(mprojmean==0) jprojmean=1;  
            pmij(pmmij,cov,ncovmodel,x,nlstate);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          
            k=0;
   for(cptcov=1;cptcov<=i2;cptcov++){          for(i=1; i<=(nlstate); i++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(j=1; j<=(nlstate+ndeath);j++){
       k=k+1;              k=k+1;
       fprintf(ficresf,"\n#******");              mu[k][(int) age]=pmmij[i][j];
       for(j=1;j<=cptcoveff;j++) {            }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficresf,"******\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficresf,"# StartingAge FinalAge");              varpij[i][j][(int)age] = doldm[i][j];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
                /*printf("\n%d ",(int)age);
                  for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         fprintf(ficresf,"\n");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         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--){          fprintf(ficresprob,"\n%d ",(int)age);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          fprintf(ficresprobcov,"\n%d ",(int)age);
           nhstepm = nhstepm/hstepm;          fprintf(ficresprobcor,"\n%d ",(int)age);
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           oldm=oldms;savm=savms;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                    fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           for (h=0; h<=nhstepm; h++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
             if (h==(int) (calagedate+YEARM*cpt)) {          }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          i=0;
             }          for (k=1; k<=(nlstate);k++){
             for(j=1; j<=nlstate+ndeath;j++) {            for (l=1; l<=(nlstate+ndeath);l++){ 
               kk1=0.;kk2=0;              i=i++;
               for(i=1; i<=nlstate;i++) {                            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                 if (mobilav==1)              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              for (j=1; j<=i;j++){
                 else {                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                 }              }
                            }
               }          }/* end of loop for state */
               if (h==(int)(calagedate+12*cpt)){        } /* end of loop for age */
                 fprintf(ficresf," %.3f", kk1);  
                                /* Confidence intervalle of pij  */
               }        /*
             }          fprintf(ficgp,"\nset noparametric;unset label");
           }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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);
     }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   fclose(ficresf);        first1=1;
 }        for (k2=1; k2<=(nlstate);k2++){
 /************** Forecasting ******************/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){            if(l2==k2) continue;
              j=(k2-1)*(nlstate+ndeath)+l2;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            for (k1=1; k1<=(nlstate);k1++){
   int *popage;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                if(l1==k1) continue;
   double *popeffectif,*popcount;                i=(k1-1)*(nlstate+ndeath)+l1;
   double ***p3mat,***tabpop,***tabpopprev;                if(i<=j) continue;
   char filerespop[FILENAMELENGTH];                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   agelim=AGESUP;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;                    mu1=mu[i][(int) age]/stepm*YEARM ;
                      mu2=mu[j][(int) age]/stepm*YEARM;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                    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.;
   strcpy(filerespop,"pop");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   strcat(filerespop,fileres);                    /* Eigen vectors */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     printf("Problem with forecast resultfile: %s\n", filerespop);                    /*v21=sqrt(1.-v11*v11); *//* error */
   }                    v21=(lc1-v1)/cv12*v11;
   printf("Computing forecasting: result on file '%s' \n", filerespop);                    v12=-v21;
                     v22=v11;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                    tnalp=v21/v11;
                     if(first1==1){
   if (mobilav==1) {                      first1=0;
     mobaverage= ma3x(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);
     movingaverage(agedeb, fage, ageminpar, mobaverage);                    }
   }                    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*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   if (stepm<=12) stepsize=1;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                      if(first==1){
   agelim=AGESUP;                      first=0;
                        fprintf(ficgp,"\nset parametric;unset label");
   hstepm=1;                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   hstepm=hstepm/stepm;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                        fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   if (popforecast==1) {                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     if((ficpop=fopen(popfile,"r"))==NULL) {                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       printf("Problem with population file : %s\n",popfile);exit(0);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     popage=ivector(0,AGESUP);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     popeffectif=vector(0,AGESUP);                      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",\
     popcount=vector(0,AGESUP);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                  mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     i=1;                      }else{
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                      first=0;
                          fprintf(fichtm," %d (%.3f),",(int) age, c12);
     imx=i;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                      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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   for(cptcov=1;cptcov<=i2;cptcov++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                    }/* if first */
       k=k+1;                  } /* age mod 5 */
       fprintf(ficrespop,"\n#******");                } /* end loop age */
       for(j=1;j<=cptcoveff;j++) {                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                first=1;
       }              } /*l12 */
       fprintf(ficrespop,"******\n");            } /* k12 */
       fprintf(ficrespop,"# Age");          } /*l1 */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        }/* k1 */
       if (popforecast==1)  fprintf(ficrespop," [Population]");      } /* loop covariates */
          }
       for (cpt=0; cpt<=0;cpt++) {    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
            free_vector(xp,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fclose(ficresprob);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fclose(ficresprobcov);
           nhstepm = nhstepm/hstepm;    fclose(ficresprobcor);
              fclose(ficgp);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(fichtm);
           oldm=oldms;savm=savms;  }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
          
           for (h=0; h<=nhstepm; h++){  /******************* Printing html file ***********/
             if (h==(int) (calagedate+YEARM*cpt)) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                    int lastpass, int stepm, int weightopt, char model[],\
             }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
             for(j=1; j<=nlstate+ndeath;j++) {                    int popforecast, int estepm ,\
               kk1=0.;kk2=0;                    double jprev1, double mprev1,double anprev1, \
               for(i=1; i<=nlstate;i++) {                                  double jprev2, double mprev2,double anprev2){
                 if (mobilav==1)    int jj1, k1, i1, cpt;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /*char optionfilehtm[FILENAMELENGTH];*/
                 else {    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      printf("Problem with %s \n",optionfilehtm), exit(0);
                 }      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
               }    }
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
                   /*fprintf(ficrespop," %.3f", kk1);   - 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
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
               }   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
             }   - Life expectancies by age and initial health status (estepm=%2d months): 
             for(i=1; i<=nlstate;i++){     <a href=\"e%s\">e%s</a> <br>\n</li>", \
               kk1=0.;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];   m=cptcoveff;
             }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)   jj1=0;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);   for(k1=1; k1<=m;k1++){
           }     for(i1=1; i1<=ncodemax[k1];i1++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       jj1++;
         }       if (cptcovn > 0) {
       }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for (cpt=1; cpt<=cptcoveff;cpt++) 
   /******/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {       }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);         /* Pij */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       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>
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           nhstepm = nhstepm/hstepm;       /* Quasi-incidences */
                 fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           oldm=oldms;savm=savms;         /* Stable prevalence in each health state */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           for(cpt=1; cpt<nlstate;cpt++){
           for (h=0; h<=nhstepm; h++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
             if (h==(int) (calagedate+YEARM*cpt)) {  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);         }
             }       for(cpt=1; cpt<=nlstate;cpt++) {
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
               kk1=0.;kk2=0;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
               for(i=1; i<=nlstate;i++) {                     }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];           fprintf(fichtm,"\n<br>- Total life expectancy by age and
               }  health expectancies in states (1) and (2): e%s%d.png<br>
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
             }     } /* end i1 */
           }   }/* End k1 */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   fprintf(fichtm,"</ul>");
         }  
       }  
    }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   if (popforecast==1) {   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     free_ivector(popage,0,AGESUP);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     free_vector(popeffectif,0,AGESUP);   - 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);
     free_vector(popcount,0,AGESUP);  
   }   if(popforecast==1) fprintf(fichtm,"\n
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   fclose(ficrespop);          <br>",fileres,fileres,fileres,fileres);
 }   else 
      fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
 /***********************************************/  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 /**************** Main Program *****************/  
 /***********************************************/   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 int main(int argc, char *argv[])  
 {   jj1=0;
    for(k1=1; k1<=m;k1++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;     for(i1=1; i1<=ncodemax[k1];i1++){
   double agedeb, agefin,hf;       jj1++;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   double fret;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   double **xi,tmp,delta;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   double dum; /* Dummy variable */       }
   double ***p3mat;       for(cpt=1; cpt<=nlstate;cpt++) {
   int *indx;         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   char line[MAXLINE], linepar[MAXLINE];  interval) in state (%d): v%s%d%d.png <br>
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   int firstobs=1, lastobs=10;       }
   int sdeb, sfin; /* Status at beginning and end */     } /* end i1 */
   int c,  h , cpt,l;   }/* End k1 */
   int ju,jl, mi;   fprintf(fichtm,"</ul>");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  fclose(fichtm);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  }
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  /******************* Gnuplot file **************/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   double bage, fage, age, agelim, agebase;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   double ftolpl=FTOL;    int ng;
   double **prlim;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double *severity;      printf("Problem with file %s",optionfilegnuplot);
   double ***param; /* Matrix of parameters */      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   double  *p;    }
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */    /*#ifdef windows */
   double *delti; /* Scale */      fprintf(ficgp,"cd \"%s\" \n",pathc);
   double ***eij, ***vareij;      /*#endif */
   double **varpl; /* Variances of prevalence limits by age */  m=pow(2,cptcoveff);
   double *epj, vepp;    
   double kk1, kk2;   /* 1eme*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   char *alph[]={"a","a","b","c","d","e"}, str[4];       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
   char z[1]="c", occ;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 #include <sys/time.h>         else fprintf(ficgp," \%%*lf (\%%*lf)");
 #include <time.h>       }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       fprintf(ficgp,"\" t\"Stable 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 ++) {
   /* long total_usecs;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   struct timeval start_time, end_time;         else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
   getcwd(pathcd, size);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   printf("\n%s",version);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   if(argc <=1){       }  
     printf("\nEnter the parameter file name: ");       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     scanf("%s",pathtot);     }
   }    }
   else{    /*2 eme*/
     strcpy(pathtot,argv[1]);    
   }    for (k1=1; k1<= m ; k1 ++) { 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   /*cygwin_split_path(pathtot,path,optionfile);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      
   /* cutv(path,optionfile,pathtot,'\\');*/      for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for (j=1; j<= nlstate+1 ; j ++) {
   chdir(path);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   replace(pathc,path);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
 /*-------- arguments in the command line --------*/        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   strcpy(fileres,"r");        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
   strcat(fileres, optionfilefiname);        for (j=1; j<= nlstate+1 ; j ++) {
   strcat(fileres,".txt");    /* Other files have txt extension */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*---------arguments file --------*/        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     printf("Problem with optionfile %s\n",optionfile);        for (j=1; j<= nlstate+1 ; j ++) {
     goto end;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   strcpy(filereso,"o");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   strcat(filereso,fileres);        else fprintf(ficgp,"\" t\"\" w l 0,");
   if((ficparo=fopen(filereso,"w"))==NULL) {      }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    }
   }    
     /*3eme*/
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    for (k1=1; k1<= m ; k1 ++) { 
     ungetc(c,ficpar);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     fgets(line, MAXLINE, ficpar);        k=2+nlstate*(2*cpt-2);
     puts(line);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     fputs(line,ficparo);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   ungetc(c,ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   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);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);        */
     fgets(line, MAXLINE, ficpar);        for (i=1; i< nlstate ; i ++) {
     puts(line);          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);
     fputs(line,ficparo);          
   }        } 
   ungetc(c,ficpar);      }
      }
        
   covar=matrix(0,NCOVMAX,1,n);    /* CV preval stat */
   cptcovn=0;    for (k1=1; k1<= m ; k1 ++) { 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
   ncovmodel=2+cptcovn;        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        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);
          
   /* Read guess parameters */        for (i=1; i< nlstate ; i ++)
   /* Reads comments: lines beginning with '#' */          fprintf(ficgp,"+$%d",k+i+1);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     ungetc(c,ficpar);        
     fgets(line, MAXLINE, ficpar);        l=3+(nlstate+ndeath)*cpt;
     puts(line);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     fputs(line,ficparo);        for (i=1; i< nlstate ; i ++) {
   }          l=3+(nlstate+ndeath)*cpt;
   ungetc(c,ficpar);          fprintf(ficgp,"+$%d",l+i+1);
          }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     for(i=1; i <=nlstate; i++)      } 
     for(j=1; j <=nlstate+ndeath-1; j++){    }  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       fprintf(ficparo,"%1d%1d",i1,j1);    /* proba elementaires */
       printf("%1d%1d",i,j);    for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k<=ncovmodel;k++){      for(k=1; k <=(nlstate+ndeath); k++){
         fscanf(ficpar," %lf",&param[i][j][k]);        if (k != i) {
         printf(" %lf",param[i][j][k]);          for(j=1; j <=ncovmodel; j++){
         fprintf(ficparo," %lf",param[i][j][k]);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       }            jk++; 
       fscanf(ficpar,"\n");            fprintf(ficgp,"\n");
       printf("\n");          }
       fprintf(ficparo,"\n");        }
     }      }
       }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   p=param[1][1];       for(jk=1; jk <=m; jk++) {
           fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   /* Reads comments: lines beginning with '#' */         if (ng==2)
   while((c=getc(ficpar))=='#' && c!= EOF){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     ungetc(c,ficpar);         else
     fgets(line, MAXLINE, ficpar);           fprintf(ficgp,"\nset title \"Probability\"\n");
     puts(line);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     fputs(line,ficparo);         i=1;
   }         for(k2=1; k2<=nlstate; k2++) {
   ungetc(c,ficpar);           k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);             if (k != k2){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */               if(ng==2)
   for(i=1; i <=nlstate; i++){                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     for(j=1; j <=nlstate+ndeath-1; j++){               else
       fscanf(ficpar,"%1d%1d",&i1,&j1);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
       printf("%1d%1d",i,j);               ij=1;
       fprintf(ficparo,"%1d%1d",i1,j1);               for(j=3; j <=ncovmodel; j++) {
       for(k=1; k<=ncovmodel;k++){                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         fscanf(ficpar,"%le",&delti3[i][j][k]);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         printf(" %le",delti3[i][j][k]);                   ij++;
         fprintf(ficparo," %le",delti3[i][j][k]);                 }
       }                 else
       fscanf(ficpar,"\n");                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       printf("\n");               }
       fprintf(ficparo,"\n");               fprintf(ficgp,")/(1");
     }               
   }               for(k1=1; k1 <=nlstate; k1++){   
   delti=delti3[1][1];                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   ij=1;
   /* Reads comments: lines beginning with '#' */                 for(j=3; j <=ncovmodel; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     ungetc(c,ficpar);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     fgets(line, MAXLINE, ficpar);                     ij++;
     puts(line);                   }
     fputs(line,ficparo);                   else
   }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   ungetc(c,ficpar);                 }
                   fprintf(ficgp,")");
   matcov=matrix(1,npar,1,npar);               }
   for(i=1; i <=npar; i++){               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     fscanf(ficpar,"%s",&str);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     printf("%s",str);               i=i+ncovmodel;
     fprintf(ficparo,"%s",str);             }
     for(j=1; j <=i; j++){           } /* end k */
       fscanf(ficpar," %le",&matcov[i][j]);         } /* end k2 */
       printf(" %.5le",matcov[i][j]);       } /* end jk */
       fprintf(ficparo," %.5le",matcov[i][j]);     } /* end ng */
     }     fclose(ficgp); 
     fscanf(ficpar,"\n");  }  /* end gnuplot */
     printf("\n");  
     fprintf(ficparo,"\n");  
   }  /*************** Moving average **************/
   for(i=1; i <=npar; i++)  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    int i, cpt, cptcod;
        int modcovmax =1;
   printf("\n");    int mobilavrange, mob;
     double age;
   
     /*-------- Rewriting paramater file ----------*/    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
      strcpy(rfileres,"r");    /* "Rparameterfile */                             a covariate has 2 modalities */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     if((ficres =fopen(rfileres,"w"))==NULL) {      if(mobilav==1) mobilavrange=5; /* default */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      else mobilavrange=mobilav;
     }      for (age=bage; age<=fage; age++)
     fprintf(ficres,"#%s\n",version);        for (i=1; i<=nlstate;i++)
              for (cptcod=1;cptcod<=modcovmax;cptcod++)
     /*-------- data file ----------*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     if((fic=fopen(datafile,"r"))==NULL)    {      /* We keep the original values on the extreme ages bage, fage and for 
       printf("Problem with datafile: %s\n", datafile);goto end;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     }         we use a 5 terms etc. until the borders are no more concerned. 
       */ 
     n= lastobs;      for (mob=3;mob <=mobilavrange;mob=mob+2){
     severity = vector(1,maxwav);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     outcome=imatrix(1,maxwav+1,1,n);          for (i=1; i<=nlstate;i++){
     num=ivector(1,n);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     moisnais=vector(1,n);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
     annais=vector(1,n);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     moisdc=vector(1,n);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     andc=vector(1,n);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     agedc=vector(1,n);                }
     cod=ivector(1,n);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     weight=vector(1,n);            }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          }
     mint=matrix(1,maxwav,1,n);        }/* end age */
     anint=matrix(1,maxwav,1,n);      }/* end mob */
     s=imatrix(1,maxwav+1,1,n);    }else return -1;
     adl=imatrix(1,maxwav+1,1,n);        return 0;
     tab=ivector(1,NCOVMAX);  }/* End movingaverage */
     ncodemax=ivector(1,8);  
   
     i=1;  /************** Forecasting ******************/
     while (fgets(line, MAXLINE, fic) != NULL)    {  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){
       if ((i >= firstobs) && (i <=lastobs)) {    
            int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
         for (j=maxwav;j>=1;j--){    int *popage;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
           strcpy(line,stra);    double *popeffectif,*popcount;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double ***p3mat;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double ***mobaverage;
         }    char fileresf[FILENAMELENGTH];
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);   agelim=AGESUP;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);   
    
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    strcpy(fileresf,"f"); 
         for (j=ncovcol;j>=1;j--){    strcat(fileresf,fileres);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if((ficresf=fopen(fileresf,"w"))==NULL) {
         }      printf("Problem with forecast resultfile: %s\n", fileresf);
         num[i]=atol(stra);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
            }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    printf("Computing forecasting: result on file '%s' \n", fileresf);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
         i=i+1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       }  
     }    if (mobilav!=0) {
     /* printf("ii=%d", ij);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        scanf("%d",i);*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   imx=i-1; /* Number of individuals */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   /* 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;    stepsize=(int) (stepm+YEARM-1)/YEARM;
     }*/    if (stepm<=12) stepsize=1;
    /*  for (i=1; i<=imx; i++){    
      if (s[4][i]==9)  s[4][i]=-1;    agelim=AGESUP;
      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]));}*/    
      hstepm=1;
      hstepm=hstepm/stepm; 
   /* Calculation of the number of parameter from char model*/    yp1=modf(dateintmean,&yp);
   Tvar=ivector(1,15);    anprojmean=yp;
   Tprod=ivector(1,15);    yp2=modf((yp1*12),&yp);
   Tvaraff=ivector(1,15);    mprojmean=yp;
   Tvard=imatrix(1,15,1,2);    yp1=modf((yp2*30.5),&yp);
   Tage=ivector(1,15);          jprojmean=yp;
        if(jprojmean==0) jprojmean=1;
   if (strlen(model) >1){    if(mprojmean==0) jprojmean=1;
     j=0, j1=0, k1=1, k2=1;    
     j=nbocc(model,'+');    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     j1=nbocc(model,'*');    
     cptcovn=j+1;    for(cptcov=1;cptcov<=i2;cptcov++){
     cptcovprod=j1;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
            k=k+1;
     strcpy(modelsav,model);        fprintf(ficresf,"\n#******");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for(j=1;j<=cptcoveff;j++) {
       printf("Error. Non available option model=%s ",model);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       goto end;        }
     }        fprintf(ficresf,"******\n");
            fprintf(ficresf,"# StartingAge FinalAge");
     for(i=(j+1); i>=1;i--){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
       cutv(stra,strb,modelsav,'+');        
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
       /*scanf("%d",i);*/          fprintf(ficresf,"\n");
       if (strchr(strb,'*')) {          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
           cptcovprod--;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           cutv(strb,stre,strd,'V');            nhstepm = nhstepm/hstepm; 
           Tvar[i]=atoi(stre);            
           cptcovage++;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             Tage[cptcovage]=i;            oldm=oldms;savm=savms;
             /*printf("stre=%s ", stre);*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         }          
         else if (strcmp(strd,"age")==0) {            for (h=0; h<=nhstepm; h++){
           cptcovprod--;              if (h==(int) (calagedate+YEARM*cpt)) {
           cutv(strb,stre,strc,'V');                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
           Tvar[i]=atoi(stre);              } 
           cptcovage++;              for(j=1; j<=nlstate+ndeath;j++) {
           Tage[cptcovage]=i;                kk1=0.;kk2=0;
         }                for(i=1; i<=nlstate;i++) {              
         else {                  if (mobilav==1) 
           cutv(strb,stre,strc,'V');                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
           Tvar[i]=ncovcol+k1;                  else {
           cutv(strb,strc,strd,'V');                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
           Tprod[k1]=i;                  }
           Tvard[k1][1]=atoi(strc);                  
           Tvard[k1][2]=atoi(stre);                }
           Tvar[cptcovn+k2]=Tvard[k1][1];                if (h==(int)(calagedate+12*cpt)){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                  fprintf(ficresf," %.3f", kk1);
           for (k=1; k<=lastobs;k++)                          
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                }
           k1++;              }
           k2=k2+2;            }
         }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }          }
       else {        }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      }
        /*  scanf("%d",i);*/    }
       cutv(strd,strc,strb,'V');         
       Tvar[i]=atoi(strc);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }  
       strcpy(modelsav,stra);      fclose(ficresf);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  }
         scanf("%d",i);*/  /************** 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;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int *popage;
   printf("cptcovprod=%d ", cptcovprod);    double calagedate, agelim, kk1, kk2;
   scanf("%d ",i);*/    double *popeffectif,*popcount;
     fclose(fic);    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     /*  if(mle==1){*/    char filerespop[FILENAMELENGTH];
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     /*-calculation of age at interview from date of interview and age at death -*/    agelim=AGESUP;
     agev=matrix(1,maxwav,1,imx);    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     for (i=1; i<=imx; i++) {    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
       for(m=2; (m<= maxwav); m++) {    
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    
          anint[m][i]=9999;    strcpy(filerespop,"pop"); 
          s[m][i]=-1;    strcat(filerespop,fileres);
        }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      printf("Problem with forecast resultfile: %s\n", filerespop);
       }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }    }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {    if (mobilav!=0) {
             if(agedc[i]>0)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               if(moisdc[i]!=99 && andc[i]!=9999)      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                 agev[m][i]=agedc[i];        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            else {      }
               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;
             }    
           }    agelim=AGESUP;
           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]);    hstepm=1;
             if(mint[m][i]==99 || anint[m][i]==9999)    hstepm=hstepm/stepm; 
               agev[m][i]=1;    
             else if(agev[m][i] <agemin){    if (popforecast==1) {
               agemin=agev[m][i];      if((ficpop=fopen(popfile,"r"))==NULL) {
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        printf("Problem with population file : %s\n",popfile);exit(0);
             }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
             else if(agev[m][i] >agemax){      } 
               agemax=agev[m][i];      popage=ivector(0,AGESUP);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      popeffectif=vector(0,AGESUP);
             }      popcount=vector(0,AGESUP);
             /*agev[m][i]=anint[m][i]-annais[i];*/      
             /*   agev[m][i] = age[i]+2*m;*/      i=1;   
           }      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
           else { /* =9 */     
             agev[m][i]=1;      imx=i;
             s[m][i]=-1;      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
           }    }
         }  
         else /*= 0 Unknown */    for(cptcov=1;cptcov<=i2;cptcov++){
           agev[m][i]=1;     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       }        k=k+1;
            fprintf(ficrespop,"\n#******");
     }        for(j=1;j<=cptcoveff;j++) {
     for (i=1; i<=imx; i++)  {          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       for(m=1; (m<= maxwav); m++){        }
         if (s[m][i] > (nlstate+ndeath)) {        fprintf(ficrespop,"******\n");
           printf("Error: Wrong value in nlstate or ndeath\n");          fprintf(ficrespop,"# Age");
           goto end;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         }        if (popforecast==1)  fprintf(ficrespop," [Population]");
       }        
     }        for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
     free_vector(severity,1,maxwav);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     free_imatrix(outcome,1,maxwav+1,1,n);            nhstepm = nhstepm/hstepm; 
     free_vector(moisnais,1,n);            
     free_vector(annais,1,n);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* free_matrix(mint,1,maxwav,1,n);            oldm=oldms;savm=savms;
        free_matrix(anint,1,maxwav,1,n);*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     free_vector(moisdc,1,n);          
     free_vector(andc,1,n);            for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                    fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     wav=ivector(1,imx);              } 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              for(j=1; j<=nlstate+ndeath;j++) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                kk1=0.;kk2=0;
                    for(i=1; i<=nlstate;i++) {              
     /* Concatenates waves */                  if (mobilav==1) 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                    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];
       Tcode=ivector(1,100);                  }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                }
       ncodemax[1]=1;                if (h==(int)(calagedate+12*cpt)){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                          /*fprintf(ficrespop," %.3f", kk1);
    codtab=imatrix(1,100,1,10);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
    h=0;                }
    m=pow(2,cptcoveff);              }
                for(i=1; i<=nlstate;i++){
    for(k=1;k<=cptcoveff; k++){                kk1=0.;
      for(i=1; i <=(m/pow(2,k));i++){                  for(j=1; j<=nlstate;j++){
        for(j=1; j <= ncodemax[k]; j++){                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                  }
            h++;                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
            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]);*/  
          }              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
        }                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
      }            }
    }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    /* 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);  
       }        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
       printf("\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--){ 
       scanf("%d",i);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                nhstepm = nhstepm/hstepm; 
    /* Calculates basic frequencies. Computes observed prevalence at single age            
        and prints on file fileres'p'. */            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);  
                for (h=0; h<=nhstepm; h++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if (h==(int) (calagedate+YEARM*cpt)) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              } 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for(j=1; j<=nlstate+ndeath;j++) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                kk1=0.;kk2=0;
                      for(i=1; i<=nlstate;i++) {              
     /* For Powell, parameters are in a vector p[] starting at p[1]                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
        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 (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
               }
     if(mle==1){            }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }          }
            }
     /*--------- 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);    }
     
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if (popforecast==1) {
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      free_ivector(popage,0,AGESUP);
    for(i=1,jk=1; i <=nlstate; i++){      free_vector(popeffectif,0,AGESUP);
      for(k=1; k <=(nlstate+ndeath); k++){      free_vector(popcount,0,AGESUP);
        if (k != i)    }
          {    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            printf("%d%d ",i,k);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            fprintf(ficres,"%1d%1d ",i,k);    fclose(ficrespop);
            for(j=1; j <=ncovmodel; j++){  }
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);  /***********************************************/
              jk++;  /**************** Main Program *****************/
            }  /***********************************************/
            printf("\n");  
            fprintf(ficres,"\n");  int main(int argc, char *argv[])
          }  {
      }    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    }    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
  if(mle==1){    double agedeb, agefin,hf;
     /* Computing hessian and covariance matrix */    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);    double fret;
  }    double **xi,tmp,delta;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");    double dum; /* Dummy variable */
      for(i=1,jk=1; i <=nlstate; i++){    double ***p3mat;
       for(j=1; j <=nlstate+ndeath; j++){    double ***mobaverage;
         if (j!=i) {    int *indx;
           fprintf(ficres,"%1d%1d",i,j);    char line[MAXLINE], linepar[MAXLINE];
           printf("%1d%1d",i,j);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
           for(k=1; k<=ncovmodel;k++){    int firstobs=1, lastobs=10;
             printf(" %.5e",delti[jk]);    int sdeb, sfin; /* Status at beginning and end */
             fprintf(ficres," %.5e",delti[jk]);    int c,  h , cpt,l;
             jk++;    int ju,jl, mi;
           }    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
           printf("\n");    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
           fprintf(ficres,"\n");    int mobilav=0,popforecast=0;
         }    int hstepm, nhstepm;
       }    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
      }  
        double bage, fage, age, agelim, agebase;
     k=1;    double ftolpl=FTOL;
     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");    double **prlim;
     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");    double *severity;
     for(i=1;i<=npar;i++){    double ***param; /* Matrix of parameters */
       /*  if (k>nlstate) k=1;    double  *p;
       i1=(i-1)/(ncovmodel*nlstate)+1;    double **matcov; /* Matrix of covariance */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double ***delti3; /* Scale */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double *delti; /* Scale */
       fprintf(ficres,"%3d",i);    double ***eij, ***vareij;
       printf("%3d",i);    double **varpl; /* Variances of prevalence limits by age */
       for(j=1; j<=i;j++){    double *epj, vepp;
         fprintf(ficres," %.5e",matcov[i][j]);    double kk1, kk2;
         printf(" %.5e",matcov[i][j]);    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
       }  
       fprintf(ficres,"\n");    char *alph[]={"a","a","b","c","d","e"}, str[4];
       printf("\n");  
       k++;  
     }    char z[1]="c", occ;
      #include <sys/time.h>
     while((c=getc(ficpar))=='#' && c!= EOF){  #include <time.h>
       ungetc(c,ficpar);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
       fgets(line, MAXLINE, ficpar);   
       puts(line);    /* long total_usecs;
       fputs(line,ficparo);       struct timeval start_time, end_time;
     }    
     ungetc(c,ficpar);       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     estepm=0;    getcwd(pathcd, size);
     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;    printf("\n%s",version);
     if (fage <= 2) {    if(argc <=1){
       bage = ageminpar;      printf("\nEnter the parameter file name: ");
       fage = agemaxpar;      scanf("%s",pathtot);
     }    }
        else{
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      strcpy(pathtot,argv[1]);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
      /*cygwin_split_path(pathtot,path,optionfile);
     while((c=getc(ficpar))=='#' && c!= EOF){      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     ungetc(c,ficpar);    /* cutv(path,optionfile,pathtot,'\\');*/
     fgets(line, MAXLINE, ficpar);  
     puts(line);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     fputs(line,ficparo);    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   }    chdir(path);
   ungetc(c,ficpar);    replace(pathc,path);
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    /*-------- arguments in the command line --------*/
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    /* Log file */
          strcat(filelog, optionfilefiname);
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(filelog,".log");    /* */
     ungetc(c,ficpar);    if((ficlog=fopen(filelog,"w"))==NULL)    {
     fgets(line, MAXLINE, ficpar);      printf("Problem with logfile %s\n",filelog);
     puts(line);      goto end;
     fputs(line,ficparo);    }
   }    fprintf(ficlog,"Log filename:%s\n",filelog);
   ungetc(c,ficpar);    fprintf(ficlog,"\n%s",version);
      fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    fflush(ficlog);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  
     /* */
   fscanf(ficpar,"pop_based=%d\n",&popbased);    strcpy(fileres,"r");
   fprintf(ficparo,"pop_based=%d\n",popbased);      strcat(fileres, optionfilefiname);
   fprintf(ficres,"pop_based=%d\n",popbased);      strcat(fileres,".txt");    /* Other files have txt extension */
    
   while((c=getc(ficpar))=='#' && c!= EOF){    /*---------arguments file --------*/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     puts(line);      printf("Problem with optionfile %s\n",optionfile);
     fputs(line,ficparo);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   }      goto end;
   ungetc(c,ficpar);    }
   
   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);    strcpy(filereso,"o");
 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);    strcat(filereso,fileres);
 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);    if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
 while((c=getc(ficpar))=='#' && c!= EOF){      goto end;
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /* Reads comments: lines beginning with '#' */
     fputs(line,ficparo);    while((c=getc(ficpar))=='#' && c!= EOF){
   }      ungetc(c,ficpar);
   ungetc(c,ficpar);      fgets(line, MAXLINE, ficpar);
       puts(line);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      fputs(line,ficparo);
   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);    ungetc(c,ficpar);
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    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);
 /*------------ gnuplot -------------*/    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);
   strcpy(optionfilegnuplot,optionfilefiname);    while((c=getc(ficpar))=='#' && c!= EOF){
   strcat(optionfilegnuplot,".gp");      ungetc(c,ficpar);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      fgets(line, MAXLINE, ficpar);
     printf("Problem with file %s",optionfilegnuplot);      puts(line);
   }      fputs(line,ficparo);
   fclose(ficgp);    }
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    ungetc(c,ficpar);
 /*--------- index.htm --------*/    
      
   strcpy(optionfilehtm,optionfile);    covar=matrix(0,NCOVMAX,1,n); 
   strcat(optionfilehtm,".htm");    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   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    /* Read guess parameters */
 \n    /* Reads comments: lines beginning with '#' */
 Total number of observations=%d <br>\n    while((c=getc(ficpar))=='#' && c!= EOF){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      ungetc(c,ficpar);
 <hr  size=\"2\" color=\"#EC5E5E\">      fgets(line, MAXLINE, ficpar);
  <ul><li><h4>Parameter files</h4>\n      puts(line);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      fputs(line,ficparo);
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    }
   fclose(fichtm);    ungetc(c,ficpar);
     
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      for(i=1; i <=nlstate; i++)
 /*------------ free_vector  -------------*/      for(j=1; j <=nlstate+ndeath-1; j++){
  chdir(path);        fscanf(ficpar,"%1d%1d",&i1,&j1);
          fprintf(ficparo,"%1d%1d",i1,j1);
  free_ivector(wav,1,imx);        if(mle==1)
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          printf("%1d%1d",i,j);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          fprintf(ficlog,"%1d%1d",i,j);
  free_ivector(num,1,n);        for(k=1; k<=ncovmodel;k++){
  free_vector(agedc,1,n);          fscanf(ficpar," %lf",&param[i][j][k]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          if(mle==1){
  fclose(ficparo);            printf(" %lf",param[i][j][k]);
  fclose(ficres);            fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
   /*--------------- Prevalence limit --------------*/            fprintf(ficlog," %lf",param[i][j][k]);
            fprintf(ficparo," %lf",param[i][j][k]);
   strcpy(filerespl,"pl");        }
   strcat(filerespl,fileres);        fscanf(ficpar,"\n");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        if(mle==1)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          printf("\n");
   }        fprintf(ficlog,"\n");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        fprintf(ficparo,"\n");
   fprintf(ficrespl,"#Prevalence limit\n");      }
   fprintf(ficrespl,"#Age ");    
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   fprintf(ficrespl,"\n");  
      p=param[1][1];
   prlim=matrix(1,nlstate,1,nlstate);    
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* Reads comments: lines beginning with '#' */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    while((c=getc(ficpar))=='#' && c!= EOF){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      ungetc(c,ficpar);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fgets(line, MAXLINE, ficpar);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      puts(line);
   k=0;      fputs(line,ficparo);
   agebase=ageminpar;    }
   agelim=agemaxpar;    ungetc(c,ficpar);
   ftolpl=1.e-10;  
   i1=cptcoveff;    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   if (cptcovn < 1){i1=1;}    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
   for(cptcov=1;cptcov<=i1;cptcov++){      for(j=1; j <=nlstate+ndeath-1; j++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fscanf(ficpar,"%1d%1d",&i1,&j1);
         k=k+1;        printf("%1d%1d",i,j);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficrespl,"\n#******");        for(k=1; k<=ncovmodel;k++){
         for(j=1;j<=cptcoveff;j++)          fscanf(ficpar,"%le",&delti3[i][j][k]);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf(" %le",delti3[i][j][k]);
         fprintf(ficrespl,"******\n");          fprintf(ficparo," %le",delti3[i][j][k]);
                }
         for (age=agebase; age<=agelim; age++){        fscanf(ficpar,"\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        printf("\n");
           fprintf(ficrespl,"%.0f",age );        fprintf(ficparo,"\n");
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");    delti=delti3[1][1];
         }    
       }    /* Reads comments: lines beginning with '#' */
     }    while((c=getc(ficpar))=='#' && c!= EOF){
   fclose(ficrespl);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   /*------------- h Pij x at various ages ------------*/      puts(line);
        fputs(line,ficparo);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    ungetc(c,ficpar);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    
   }    matcov=matrix(1,npar,1,npar);
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1; i <=npar; i++){
        fscanf(ficpar,"%s",&str);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      if(mle==1)
   /*if (stepm<=24) stepsize=2;*/        printf("%s",str);
       fprintf(ficlog,"%s",str);
   agelim=AGESUP;      fprintf(ficparo,"%s",str);
   hstepm=stepsize*YEARM; /* Every year of age */      for(j=1; j <=i; j++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
   /* hstepm=1;   aff par mois*/          printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        else
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficlog," %.5le",matcov[i][j]);
       k=k+1;        fprintf(ficparo," %.5le",matcov[i][j]);
         fprintf(ficrespij,"\n#****** ");      }
         for(j=1;j<=cptcoveff;j++)      fscanf(ficpar,"\n");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if(mle==1)
         fprintf(ficrespij,"******\n");        printf("\n");
              fprintf(ficlog,"\n");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      fprintf(ficparo,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
           /*      nhstepm=nhstepm*YEARM; aff par mois*/        matcov[i][j]=matcov[j][i];
      
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if(mle==1)
           oldm=oldms;savm=savms;      printf("\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficlog,"\n");
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    /*-------- Rewriting paramater file ----------*/
               fprintf(ficrespij," %1d-%1d",i,j);    strcpy(rfileres,"r");    /* "Rparameterfile */
           fprintf(ficrespij,"\n");    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
            for (h=0; h<=nhstepm; h++){    strcat(rfileres,".");    /* */
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    strcat(rfileres,optionfilext);    /* Other files have txt extension */
             for(i=1; i<=nlstate;i++)    if((ficres =fopen(rfileres,"w"))==NULL) {
               for(j=1; j<=nlstate+ndeath;j++)      printf("Problem writing new parameter file: %s\n", fileres);goto end;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
             fprintf(ficrespij,"\n");    }
              }    fprintf(ficres,"#%s\n",version);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
           fprintf(ficrespij,"\n");    /*-------- 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;
     }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  
     n= lastobs;
   fclose(ficrespij);    severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
   /*---------- Forecasting ------------------*/    moisnais=vector(1,n);
   if((stepm == 1) && (strcmp(model,".")==0)){    annais=vector(1,n);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    moisdc=vector(1,n);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    andc=vector(1,n);
   }    agedc=vector(1,n);
   else{    cod=ivector(1,n);
     erreur=108;    weight=vector(1,n);
     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);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   }    mint=matrix(1,maxwav,1,n);
      anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
   /*---------- Health expectancies and variances ------------*/    tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    i=1;
   if((ficrest=fopen(filerest,"w"))==NULL) {    while (fgets(line, MAXLINE, fic) != NULL)    {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      if ((i >= firstobs) && (i <=lastobs)) {
   }          
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
   strcpy(filerese,"e");          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   strcat(filerese,fileres);          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   if((ficreseij=fopen(filerese,"w"))==NULL) {        }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          
   }        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
  strcpy(fileresv,"v");        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
   strcat(fileresv,fileres);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
   }        for (j=ncovcol;j>=1;j--){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   calagedate=-1;        } 
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        num[i]=atol(stra);
           
   k=0;        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
   for(cptcov=1;cptcov<=i1;cptcov++){          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;}*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;        i=i+1;
       fprintf(ficrest,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* printf("ii=%d", ij);
       fprintf(ficrest,"******\n");       scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    /* for (i=1; i<=imx; i++){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       fprintf(ficreseij,"******\n");      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;
       fprintf(ficresvij,"\n#****** ");      }*/
       for(j=1;j<=cptcoveff;j++)     /*  for (i=1; i<=imx; i++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       if (s[4][i]==9)  s[4][i]=-1; 
       fprintf(ficresvij,"******\n");       printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   
       oldm=oldms;savm=savms;    /* Calculation of the number of parameter from char model*/
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
      Tprod=ivector(1,15); 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    Tvaraff=ivector(1,15); 
       oldm=oldms;savm=savms;    Tvard=imatrix(1,15,1,2);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    Tage=ivector(1,15);      
         
     if (strlen(model) >1){ /* If there is at least 1 covariate */
        j=0, j1=0, k1=1, k2=1;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      j=nbocc(model,'+'); /* j=Number of '+' */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      j1=nbocc(model,'*'); /* j1=Number of '*' */
       fprintf(ficrest,"\n");      cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       epj=vector(1,nlstate+1);      
       for(age=bage; age <=fage ;age++){      strcpy(modelsav,model); 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         if (popbased==1) {        printf("Error. Non available option model=%s ",model);
           for(i=1; i<=nlstate;i++)        fprintf(ficlog,"Error. Non available option model=%s ",model);
             prlim[i][i]=probs[(int)age][i][k];        goto end;
         }      }
              
         fprintf(ficrest," %4.0f",age);      /* This loop fills the array Tvar from the string 'model'.*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      for(i=(j+1); i>=1;i--){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           }        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           epj[nlstate+1] +=epj[j];        /*scanf("%d",i);*/
         }        if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
         for(i=1, vepp=0.;i <=nlstate;i++)          if (strcmp(strc,"age")==0) { /* Vn*age */
           for(j=1;j <=nlstate;j++)            cptcovprod--;
             vepp += vareij[i][j][(int)age];            cutv(strb,stre,strd,'V');
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
         for(j=1;j <=nlstate;j++){            cptcovage++;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              Tage[cptcovage]=i;
         }              /*printf("stre=%s ", stre);*/
         fprintf(ficrest,"\n");          }
       }          else if (strcmp(strd,"age")==0) { /* or age*Vn */
     }            cptcovprod--;
   }            cutv(strb,stre,strc,'V');
 free_matrix(mint,1,maxwav,1,n);            Tvar[i]=atoi(stre);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);            cptcovage++;
     free_vector(weight,1,n);            Tage[cptcovage]=i;
   fclose(ficreseij);          }
   fclose(ficresvij);          else {  /* Age is not in the model */
   fclose(ficrest);            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
   fclose(ficpar);            Tvar[i]=ncovcol+k1;
   free_vector(epj,1,nlstate+1);            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
              Tprod[k1]=i;
   /*------- Variance limit prevalence------*/              Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
   strcpy(fileresvpl,"vpl");            Tvar[cptcovn+k2]=Tvard[k1][1];
   strcat(fileresvpl,fileres);            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            for (k=1; k<=lastobs;k++) 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
     exit(0);            k1++;
   }            k2=k2+2;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          }
         }
   k=0;        else { /* no more sum */
   for(cptcov=1;cptcov<=i1;cptcov++){          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         /*  scanf("%d",i);*/
       k=k+1;        cutv(strd,strc,strb,'V');
       fprintf(ficresvpl,"\n#****** ");        Tvar[i]=atoi(strc);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        strcpy(modelsav,stra);  
       fprintf(ficresvpl,"******\n");        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                scanf("%d",i);*/
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      } /* end of loop + */
       oldm=oldms;savm=savms;    } /* end model */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    
     }    /*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*/
   
   fclose(ficresvpl);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
   /*---------- End : free ----------------*/    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      scanf("%d ",i);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fclose(fic);*/
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
        /*  if(mle==1){*/
      if (weightopt != 1) { /* Maximisation without weights*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      for(i=1;i<=n;i++) weight[i]=1.0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      /*-calculation of age at interview from date of interview and age at death -*/
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    agev=matrix(1,maxwav,1,imx);
    
   free_matrix(matcov,1,npar,1,npar);    for (i=1; i<=imx; i++) {
   free_vector(delti,1,npar);      for(m=2; (m<= maxwav); m++) {
   free_matrix(agev,1,maxwav,1,imx);        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          anint[m][i]=9999;
           s[m][i]=-1;
   fprintf(fichtm,"\n</body>");        }
   fclose(fichtm);        if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
   fclose(ficgp);      }
      }
   
   if(erreur >0)    for (i=1; i<=imx; i++)  {
     printf("End of Imach with error or warning %d\n",erreur);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
   else   printf("End of Imach\n");      for(m=1; (m<= maxwav); m++){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        if(s[m][i] >0){
            if (s[m][i] >= nlstate+1) {
   /* 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);*/            if(agedc[i]>0)
   /*printf("Total time was %d uSec.\n", total_usecs);*/              if(moisdc[i]!=99 && andc[i]!=9999)
   /*------ End -----------*/                agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
  end:                if (andc[i]!=9999){
 #ifdef windows                  printf("Warning negative age at death: %d line:%d\n",num[i],i);
   /* chdir(pathcd);*/                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
 #endif                  agev[m][i]=-1;
  /*system("wgnuplot graph.plt");*/                }
  /*system("../gp37mgw/wgnuplot graph.plt");*/              }
  /*system("cd ../gp37mgw");*/          }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          else if(s[m][i] !=9){ /* Should no more exist */
  strcpy(plotcmd,GNUPLOTPROGRAM);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
  strcat(plotcmd," ");            if(mint[m][i]==99 || anint[m][i]==9999)
  strcat(plotcmd,optionfilegnuplot);              agev[m][i]=1;
  system(plotcmd);            else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
 #ifdef windows              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
   while (z[0] != 'q') {            }
     /* chdir(path); */            else if(agev[m][i] >agemax){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");              agemax=agev[m][i];
     scanf("%s",z);              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
     if (z[0] == 'c') system("./imach");            }
     else if (z[0] == 'e') system(optionfilehtm);            /*agev[m][i]=anint[m][i]-annais[i];*/
     else if (z[0] == 'g') system(plotcmd);            /*     agev[m][i] = age[i]+2*m;*/
     else if (z[0] == 'q') exit(0);          }
   }          else { /* =9 */
 #endif            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.1.49  
changed lines
  Added in v.1.67


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>