Diff for /imach/src/imach.c between versions 1.52 and 1.66

version 1.52, 2002/07/19 18:49:30 version 1.66, 2003/01/28 17:23:35
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 '\\'
 #define ODIRSEPARATOR '/'  #define ODIRSEPARATOR '/'
 #else  #else
 #define DIRSEPARATOR '/'  #define DIRSEPARATOR '/'
 #define ODIRSEPARATOR '\\'  #define ODIRSEPARATOR '\\'
 #endif  #endif
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
 int erreur; /* Error number */  int erreur; /* Error number */
 int nvar;  int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav; /* Maxim number of waves */
 int jmin, jmax; /* min, max spacing between 2 waves */  int jmin, jmax; /* min, max spacing between 2 waves */
 int mle, weightopt;  int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double jmean; /* Mean space between 2 waves */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double **oldm, **newm, **savm; /* Working pointers to matrices */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double jmean; /* Mean space between 2 waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 FILE *ficlog;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficresprobmorprev;  FILE *ficlog;
 FILE *fichtm; /* Html File */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE *ficreseij;  FILE *ficresprobmorprev;
 char filerese[FILENAMELENGTH];  FILE *fichtm; /* Html File */
 FILE  *ficresvij;  FILE *ficreseij;
 char fileresv[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvij;
 char fileresvpl[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 char title[MAXLINE];  FILE  *ficresvpl;
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char filelog[FILENAMELENGTH]; /* Log file */
 char popfile[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  char popfile[FILENAMELENGTH];
   
 #define NR_END 1  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define FREE_ARG char*  
 #define FTOL 1.0e-10  #define NR_END 1
   #define FREE_ARG char*
 #define NRANSI  #define FTOL 1.0e-10
 #define ITMAX 200  
   #define NRANSI 
 #define TOL 2.0e-4  #define ITMAX 200 
   
 #define CGOLD 0.3819660  #define TOL 2.0e-4 
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 #define GOLD 1.618034  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 static double maxarg1,maxarg2;  #define TINY 1.0e-20 
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  static double maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #define rint(a) floor(a+0.5)    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 static double sqrarg;  #define rint(a) floor(a+0.5)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 int imx;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  int imx; 
   int stepm;
 int estepm;  /* Stepm, step in month: minimum step interpolation*/
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
   int estepm;
 int m,nb;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int m,nb;
 double **pmmij, ***probs, ***mobaverage;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double dateintmean=0;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 double *weight;  double dateintmean=0;
 int **s; /* Status */  
 double *agedc, **covar, idx;  double *weight;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **s; /* Status */
   double *agedc, **covar, idx;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double ftolhess; /* Tolerance for computing hessian */  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /**************** split *************************/  double ftolhess; /* Tolerance for computing hessian */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  /**************** split *************************/
    char *s;                             /* pointer */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    int  l1, l2;                         /* length counters */  {
     char  *ss;                            /* pointer */
    l1 = strlen( path );                 /* length of path */    int   l1, l2;                         /* length counters */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    l1 = strlen(path );                   /* length of path */
    if ( s == NULL ) {                   /* no directory, so use current */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    if ( ss == NULL ) {                   /* no directory, so use current */
 #if     defined(__bsd__)                /* get current working directory */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       extern char       *getwd( );        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   #if     defined(__bsd__)                /* get current working directory */
       if ( getwd( dirc ) == NULL ) {      extern char *getwd( );
 #else  
       extern char       *getcwd( );      if ( getwd( dirc ) == NULL ) {
   #else
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {      extern char *getcwd( );
 #endif  
          return( GLOCK_ERROR_GETCWD );      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }  #endif
       strcpy( name, path );             /* we've got it */        return( GLOCK_ERROR_GETCWD );
    } else {                             /* strip direcotry from path */      }
       s++;                              /* after this, the filename */      strcpy( name, path );               /* we've got it */
       l2 = strlen( s );                 /* length of filename */    } else {                              /* strip direcotry from path */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      ss++;                               /* after this, the filename */
       strcpy( name, s );                /* save file name */      l2 = strlen( ss );                  /* length of filename */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       dirc[l1-l2] = 0;                  /* add zero */      strcpy( name, ss );         /* save file name */
    }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
    l1 = strlen( dirc );                 /* length of directory */      dirc[l1-l2] = 0;                    /* add zero */
 #ifdef windows    }
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    l1 = strlen( dirc );                  /* length of directory */
 #else  #ifdef windows
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 #endif  #else
    s = strrchr( name, '.' );            /* find last / */    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    s++;  #endif
    strcpy(ext,s);                       /* save extension */    ss = strrchr( name, '.' );            /* find last / */
    l1= strlen( name);    ss++;
    l2= strlen( s)+1;    strcpy(ext,ss);                       /* save extension */
    strncpy( finame, name, l1-l2);    l1= strlen( name);
    finame[l1-l2]= 0;    l2= strlen(ss)+1;
    return( 0 );                         /* we're done */    strncpy( finame, name, l1-l2);
 }    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   }
 /******************************************/  
   
 void replace(char *s, char*t)  /******************************************/
 {  
   int i;  void replace(char *s, char*t)
   int lg=20;  {
   i=0;    int i;
   lg=strlen(t);    int lg=20;
   for(i=0; i<= lg; i++) {    i=0;
     (s[i] = t[i]);    lg=strlen(t);
     if (t[i]== '\\') s[i]='/';    for(i=0; i<= lg; i++) {
   }      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 int nbocc(char *s, char occ)  }
 {  
   int i,j=0;  int nbocc(char *s, char occ)
   int lg=20;  {
   i=0;    int i,j=0;
   lg=strlen(s);    int lg=20;
   for(i=0; i<= lg; i++) {    i=0;
   if  (s[i] == occ ) j++;    lg=strlen(s);
   }    for(i=0; i<= lg; i++) {
   return j;    if  (s[i] == occ ) j++;
 }    }
     return j;
 void cutv(char *u,char *v, char*t, char occ)  }
 {  
   /* cuts string t into u and v where u is ended by char occ excluding it  void cutv(char *u,char *v, char*t, char occ)
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  {
      gives u="abcedf" and v="ghi2j" */    /* cuts string t into u and v where u is ended by char occ excluding it
   int i,lg,j,p=0;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   i=0;       gives u="abcedf" and v="ghi2j" */
   for(j=0; j<=strlen(t)-1; j++) {    int i,lg,j,p=0;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    i=0;
   }    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   lg=strlen(t);    }
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    lg=strlen(t);
   }    for(j=0; j<p; j++) {
      u[p]='\0';      (u[j] = t[j]);
     }
    for(j=0; j<= lg; j++) {       u[p]='\0';
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }     for(j=0; j<= lg; j++) {
 }      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
 /********************** nrerror ********************/  }
   
 void nrerror(char error_text[])  /********************** nrerror ********************/
 {  
   fprintf(stderr,"ERREUR ...\n");  void nrerror(char error_text[])
   fprintf(stderr,"%s\n",error_text);  {
   exit(1);    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
 /*********************** vector *******************/    exit(EXIT_FAILURE);
 double *vector(int nl, int nh)  }
 {  /*********************** vector *******************/
   double *v;  double *vector(int nl, int nh)
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  {
   if (!v) nrerror("allocation failure in vector");    double *v;
   return v-nl+NR_END;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /************************ free vector ******************/  }
 void free_vector(double*v, int nl, int nh)  
 {  /************************ free vector ******************/
   free((FREE_ARG)(v+nl-NR_END));  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /************************ivector *******************************/  }
 int *ivector(long nl,long nh)  
 {  /************************ivector *******************************/
   int *v;  int *ivector(long nl,long nh)
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    int *v;
   return v-nl+NR_END;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /******************free ivector **************************/  }
 void free_ivector(int *v, long nl, long nh)  
 {  /******************free ivector **************************/
   free((FREE_ARG)(v+nl-NR_END));  void free_ivector(int *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /******************* imatrix *******************************/  }
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /******************* imatrix *******************************/
 {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   int **m;  { 
      long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   /* allocate pointers to rows */    int **m; 
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    /* allocate pointers to rows */ 
   m += NR_END;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   m -= nrl;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
      m -= nrl; 
   /* allocate rows and set pointers to them */    
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* allocate rows and set pointers to them */ 
   m[nrl] += NR_END;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m[nrl] -= ncl;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
      m[nrl] += NR_END; 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    m[nrl] -= ncl; 
      
   /* return pointer to array of pointers to rows */    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   return m;    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /****************** free_imatrix *************************/  } 
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /****************** free_imatrix *************************/
       long nch,ncl,nrh,nrl;  void free_imatrix(m,nrl,nrh,ncl,nch)
      /* free an int matrix allocated by imatrix() */        int **m;
 {        long nch,ncl,nrh,nrl; 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));       /* free an int matrix allocated by imatrix() */ 
   free((FREE_ARG) (m+nrl-NR_END));  { 
 }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
 /******************* matrix *******************************/  } 
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  /******************* matrix *******************************/
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  double **matrix(long nrl, long nrh, long ncl, long nch)
   double **m;  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    double **m;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   m -= nrl;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m -= nrl;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m[nrl] -= ncl;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    m[nrl] -= ncl;
   return m;  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 /*************************free matrix ************************/  }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  /*************************free matrix ************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /******************* ma3x *******************************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double ***m;  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    double ***m;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   m -= nrl;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m -= nrl;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m[nrl] -= ncl;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    m[nrl] -= ncl;
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   m[nrl][ncl] -= nll;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for (j=ncl+1; j<=nch; j++)    m[nrl][ncl] += NR_END;
     m[nrl][j]=m[nrl][j-1]+nlay;    m[nrl][ncl] -= nll;
      for (j=ncl+1; j<=nch; j++) 
   for (i=nrl+1; i<=nrh; i++) {      m[nrl][j]=m[nrl][j-1]+nlay;
     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][j]=m[i][j-1]+nlay;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   }      for (j=ncl+1; j<=nch; j++) 
   return m;        m[i][j]=m[i][j-1]+nlay;
 }    }
     return m;
 /*************************free ma3x ************************/  }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  /*************************free ma3x ************************/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /***************** f1dim *************************/  }
 extern int ncom;  
 extern double *pcom,*xicom;  /***************** f1dim *************************/
 extern double (*nrfunc)(double []);  extern int ncom; 
    extern double *pcom,*xicom;
 double f1dim(double x)  extern double (*nrfunc)(double []); 
 {   
   int j;  double f1dim(double x) 
   double f;  { 
   double *xt;    int j; 
      double f;
   xt=vector(1,ncom);    double *xt; 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];   
   f=(*nrfunc)(xt);    xt=vector(1,ncom); 
   free_vector(xt,1,ncom);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   return f;    f=(*nrfunc)(xt); 
 }    free_vector(xt,1,ncom); 
     return f; 
 /*****************brent *************************/  } 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /*****************brent *************************/
   int iter;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double a,b,d,etemp;  { 
   double fu,fv,fw,fx;    int iter; 
   double ftemp;    double a,b,d,etemp;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    double fu,fv,fw,fx;
   double e=0.0;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
   a=(ax < cx ? ax : cx);    double e=0.0; 
   b=(ax > cx ? ax : cx);   
   x=w=v=bx;    a=(ax < cx ? ax : cx); 
   fw=fv=fx=(*f)(x);    b=(ax > cx ? ax : cx); 
   for (iter=1;iter<=ITMAX;iter++) {    x=w=v=bx; 
     xm=0.5*(a+b);    fw=fv=fx=(*f)(x); 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for (iter=1;iter<=ITMAX;iter++) { 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      xm=0.5*(a+b); 
     printf(".");fflush(stdout);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     fprintf(ficlog,".");fflush(ficlog);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 #ifdef DEBUG      printf(".");fflush(stdout);
     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);      fprintf(ficlog,".");fflush(ficlog);
     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);  #ifdef DEBUG
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      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);
 #endif      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       *xmin=x;  #endif
       return fx;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     }        *xmin=x; 
     ftemp=fu;        return fx; 
     if (fabs(e) > tol1) {      } 
       r=(x-w)*(fx-fv);      ftemp=fu;
       q=(x-v)*(fx-fw);      if (fabs(e) > tol1) { 
       p=(x-v)*q-(x-w)*r;        r=(x-w)*(fx-fv); 
       q=2.0*(q-r);        q=(x-v)*(fx-fw); 
       if (q > 0.0) p = -p;        p=(x-v)*q-(x-w)*r; 
       q=fabs(q);        q=2.0*(q-r); 
       etemp=e;        if (q > 0.0) p = -p; 
       e=d;        q=fabs(q); 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))        etemp=e; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));        e=d; 
       else {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         d=p/q;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         u=x+d;        else { 
         if (u-a < tol2 || b-u < tol2)          d=p/q; 
           d=SIGN(tol1,xm-x);          u=x+d; 
       }          if (u-a < tol2 || b-u < tol2) 
     } else {            d=SIGN(tol1,xm-x); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));        } 
     }      } else { 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     fu=(*f)(u);      } 
     if (fu <= fx) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       if (u >= x) a=x; else b=x;      fu=(*f)(u); 
       SHFT(v,w,x,u)      if (fu <= fx) { 
         SHFT(fv,fw,fx,fu)        if (u >= x) a=x; else b=x; 
         } else {        SHFT(v,w,x,u) 
           if (u < x) a=u; else b=u;          SHFT(fv,fw,fx,fu) 
           if (fu <= fw || w == x) {          } else { 
             v=w;            if (u < x) a=u; else b=u; 
             w=u;            if (fu <= fw || w == x) { 
             fv=fw;              v=w; 
             fw=fu;              w=u; 
           } else if (fu <= fv || v == x || v == w) {              fv=fw; 
             v=u;              fw=fu; 
             fv=fu;            } else if (fu <= fv || v == x || v == w) { 
           }              v=u; 
         }              fv=fu; 
   }            } 
   nrerror("Too many iterations in brent");          } 
   *xmin=x;    } 
   return fx;    nrerror("Too many iterations in brent"); 
 }    *xmin=x; 
     return fx; 
 /****************** mnbrak ***********************/  } 
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /****************** mnbrak ***********************/
             double (*func)(double))  
 {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double ulim,u,r,q, dum;              double (*func)(double)) 
   double fu;  { 
      double ulim,u,r,q, dum;
   *fa=(*func)(*ax);    double fu; 
   *fb=(*func)(*bx);   
   if (*fb > *fa) {    *fa=(*func)(*ax); 
     SHFT(dum,*ax,*bx,dum)    *fb=(*func)(*bx); 
       SHFT(dum,*fb,*fa,dum)    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
   *cx=(*bx)+GOLD*(*bx-*ax);        SHFT(dum,*fb,*fa,dum) 
   *fc=(*func)(*cx);        } 
   while (*fb > *fc) {    *cx=(*bx)+GOLD*(*bx-*ax); 
     r=(*bx-*ax)*(*fb-*fc);    *fc=(*func)(*cx); 
     q=(*bx-*cx)*(*fb-*fa);    while (*fb > *fc) { 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      r=(*bx-*ax)*(*fb-*fc); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      q=(*bx-*cx)*(*fb-*fa); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     if ((*bx-u)*(u-*cx) > 0.0) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       fu=(*func)(u);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {      if ((*bx-u)*(u-*cx) > 0.0) { 
       fu=(*func)(u);        fu=(*func)(u); 
       if (fu < *fc) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        fu=(*func)(u); 
           SHFT(*fb,*fc,fu,(*func)(u))        if (fu < *fc) { 
           }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {            SHFT(*fb,*fc,fu,(*func)(u)) 
       u=ulim;            } 
       fu=(*func)(u);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     } else {        u=ulim; 
       u=(*cx)+GOLD*(*cx-*bx);        fu=(*func)(u); 
       fu=(*func)(u);      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
     SHFT(*ax,*bx,*cx,u)        fu=(*func)(u); 
       SHFT(*fa,*fb,*fc,fu)      } 
       }      SHFT(*ax,*bx,*cx,u) 
 }        SHFT(*fa,*fb,*fc,fu) 
         } 
 /*************** linmin ************************/  } 
   
 int ncom;  /*************** linmin ************************/
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  int ncom; 
    double *pcom,*xicom;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  double (*nrfunc)(double []); 
 {   
   double brent(double ax, double bx, double cx,  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                double (*f)(double), double tol, double *xmin);  { 
   double f1dim(double x);    double brent(double ax, double bx, double cx, 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,                 double (*f)(double), double tol, double *xmin); 
               double *fc, double (*func)(double));    double f1dim(double x); 
   int j;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double xx,xmin,bx,ax;                double *fc, double (*func)(double)); 
   double fx,fb,fa;    int j; 
      double xx,xmin,bx,ax; 
   ncom=n;    double fx,fb,fa;
   pcom=vector(1,n);   
   xicom=vector(1,n);    ncom=n; 
   nrfunc=func;    pcom=vector(1,n); 
   for (j=1;j<=n;j++) {    xicom=vector(1,n); 
     pcom[j]=p[j];    nrfunc=func; 
     xicom[j]=xi[j];    for (j=1;j<=n;j++) { 
   }      pcom[j]=p[j]; 
   ax=0.0;      xicom[j]=xi[j]; 
   xx=1.0;    } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    ax=0.0; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    xx=1.0; 
 #ifdef DEBUG    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #ifdef DEBUG
 #endif    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (j=1;j<=n;j++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     xi[j] *= xmin;  #endif
     p[j] += xi[j];    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
   free_vector(xicom,1,n);      p[j] += xi[j]; 
   free_vector(pcom,1,n);    } 
 }    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 /*************** powell ************************/  } 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   void linmin(double p[], double xi[], int n, double *fret,              double (*func)(double [])) 
               double (*func)(double []));  { 
   int i,ibig,j;    void linmin(double p[], double xi[], int n, double *fret, 
   double del,t,*pt,*ptt,*xit;                double (*func)(double [])); 
   double fp,fptt;    int i,ibig,j; 
   double *xits;    double del,t,*pt,*ptt,*xit;
   pt=vector(1,n);    double fp,fptt;
   ptt=vector(1,n);    double *xits;
   xit=vector(1,n);    pt=vector(1,n); 
   xits=vector(1,n);    ptt=vector(1,n); 
   *fret=(*func)(p);    xit=vector(1,n); 
   for (j=1;j<=n;j++) pt[j]=p[j];    xits=vector(1,n); 
   for (*iter=1;;++(*iter)) {    *fret=(*func)(p); 
     fp=(*fret);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     ibig=0;    for (*iter=1;;++(*iter)) { 
     del=0.0;      fp=(*fret); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      ibig=0; 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      del=0.0; 
     for (i=1;i<=n;i++)      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       printf(" %d %.12f",i, p[i]);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     fprintf(ficlog," %d %.12f",i, p[i]);      for (i=1;i<=n;i++) 
     printf("\n");        printf(" %d %.12f",i, p[i]);
     fprintf(ficlog,"\n");      fprintf(ficlog," %d %.12f",i, p[i]);
     for (i=1;i<=n;i++) {      printf("\n");
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      fprintf(ficlog,"\n");
       fptt=(*fret);      for (i=1;i<=n;i++) { 
 #ifdef DEBUG        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       printf("fret=%lf \n",*fret);        fptt=(*fret); 
       fprintf(ficlog,"fret=%lf \n",*fret);  #ifdef DEBUG
 #endif        printf("fret=%lf \n",*fret);
       printf("%d",i);fflush(stdout);        fprintf(ficlog,"fret=%lf \n",*fret);
       fprintf(ficlog,"%d",i);fflush(ficlog);  #endif
       linmin(p,xit,n,fret,func);        printf("%d",i);fflush(stdout);
       if (fabs(fptt-(*fret)) > del) {        fprintf(ficlog,"%d",i);fflush(ficlog);
         del=fabs(fptt-(*fret));        linmin(p,xit,n,fret,func); 
         ibig=i;        if (fabs(fptt-(*fret)) > del) { 
       }          del=fabs(fptt-(*fret)); 
 #ifdef DEBUG          ibig=i; 
       printf("%d %.12e",i,(*fret));        } 
       fprintf(ficlog,"%d %.12e",i,(*fret));  #ifdef DEBUG
       for (j=1;j<=n;j++) {        printf("%d %.12e",i,(*fret));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        fprintf(ficlog,"%d %.12e",i,(*fret));
         printf(" x(%d)=%.12e",j,xit[j]);        for (j=1;j<=n;j++) {
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
       for(j=1;j<=n;j++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         printf(" p=%.12e",p[j]);        }
         fprintf(ficlog," p=%.12e",p[j]);        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       printf("\n");          fprintf(ficlog," p=%.12e",p[j]);
       fprintf(ficlog,"\n");        }
 #endif        printf("\n");
     }        fprintf(ficlog,"\n");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #endif
 #ifdef DEBUG      } 
       int k[2],l;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       k[0]=1;  #ifdef DEBUG
       k[1]=-1;        int k[2],l;
       printf("Max: %.12e",(*func)(p));        k[0]=1;
       fprintf(ficlog,"Max: %.12e",(*func)(p));        k[1]=-1;
       for (j=1;j<=n;j++) {        printf("Max: %.12e",(*func)(p));
         printf(" %.12e",p[j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         fprintf(ficlog," %.12e",p[j]);        for (j=1;j<=n;j++) {
       }          printf(" %.12e",p[j]);
       printf("\n");          fprintf(ficlog," %.12e",p[j]);
       fprintf(ficlog,"\n");        }
       for(l=0;l<=1;l++) {        printf("\n");
         for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        for(l=0;l<=1;l++) {
           printf("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++) {
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 #endif          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   #endif
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);        free_vector(xit,1,n); 
       free_vector(pt,1,n);        free_vector(xits,1,n); 
       return;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        return; 
     for (j=1;j<=n;j++) {      } 
       ptt[j]=2.0*p[j]-pt[j];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       xit[j]=p[j]-pt[j];      for (j=1;j<=n;j++) { 
       pt[j]=p[j];        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
     fptt=(*func)(ptt);        pt[j]=p[j]; 
     if (fptt < fp) {      } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      fptt=(*func)(ptt); 
       if (t < 0.0) {      if (fptt < fp) { 
         linmin(p,xit,n,fret,func);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         for (j=1;j<=n;j++) {        if (t < 0.0) { 
           xi[j][ibig]=xi[j][n];          linmin(p,xit,n,fret,func); 
           xi[j][n]=xit[j];          for (j=1;j<=n;j++) { 
         }            xi[j][ibig]=xi[j][n]; 
 #ifdef DEBUG            xi[j][n]=xit[j]; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          }
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #ifdef DEBUG
         for(j=1;j<=n;j++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           printf(" %.12e",xit[j]);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog," %.12e",xit[j]);          for(j=1;j<=n;j++){
         }            printf(" %.12e",xit[j]);
         printf("\n");            fprintf(ficlog," %.12e",xit[j]);
         fprintf(ficlog,"\n");          }
 #endif          printf("\n");
       }          fprintf(ficlog,"\n");
     }  #endif
   }        }
 }      } 
     } 
 /**** Prevalence limit ****************/  } 
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /**** Prevalence limit (stable prevalence)  ****************/
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
      matrix by transitions matrix until convergence is reached */  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   int i, ii,j,k;       matrix by transitions matrix until convergence is reached */
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();    int i, ii,j,k;
   double **out, cov[NCOVMAX], **pmij();    double min, max, maxmin, maxmax,sumnew=0.;
   double **newm;    double **matprod2();
   double agefin, delaymax=50 ; /* Max number of years to converge */    double **out, cov[NCOVMAX], **pmij();
     double **newm;
   for (ii=1;ii<=nlstate+ndeath;ii++)    double agefin, delaymax=50 ; /* Max number of years to converge */
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    cov[1]=1.;      }
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */     cov[1]=1.;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){   
     newm=savm;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Covariates have to be included here again */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      cov[2]=agefin;      newm=savm;
        /* Covariates have to be included here again */
       for (k=1; k<=cptcovn;k++) {       cov[2]=agefin;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        for (k=1; k<=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];          /*      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<=cptcovprod;k++)        }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     savm=oldm;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     oldm=newm;  
     maxmax=0.;      savm=oldm;
     for(j=1;j<=nlstate;j++){      oldm=newm;
       min=1.;      maxmax=0.;
       max=0.;      for(j=1;j<=nlstate;j++){
       for(i=1; i<=nlstate; i++) {        min=1.;
         sumnew=0;        max=0.;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        for(i=1; i<=nlstate; i++) {
         prlim[i][j]= newm[i][j]/(1-sumnew);          sumnew=0;
         max=FMAX(max,prlim[i][j]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         min=FMIN(min,prlim[i][j]);          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          max=FMAX(max,prlim[i][j]);
       maxmin=max-min;          min=FMIN(min,prlim[i][j]);
       maxmax=FMAX(maxmax,maxmin);        }
     }        maxmin=max-min;
     if(maxmax < ftolpl){        maxmax=FMAX(maxmax,maxmin);
       return prlim;      }
     }      if(maxmax < ftolpl){
   }        return prlim;
 }      }
     }
 /*************** transition probabilities ***************/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*************** transition probabilities ***************/ 
 {  
   double s1, s2;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /*double t34;*/  {
   int i,j,j1, nc, ii, jj;    double s1, s2;
     /*double t34;*/
     for(i=1; i<= nlstate; i++){    int i,j,j1, nc, ii, jj;
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      for(i=1; i<= nlstate; i++){
         /*s2 += param[i][j][nc]*cov[nc];*/      for(j=1; j<i;j++){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          /*s2 += param[i][j][nc]*cov[nc];*/
       }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       ps[i][j]=s2;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        }
     }        ps[i][j]=s2;
     for(j=i+1; j<=nlstate+ndeath;j++){        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      for(j=i+1; j<=nlstate+ndeath;j++){
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       }          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       ps[i][j]=s2;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     }        }
   }        ps[i][j]=s2;
     /*ps[3][2]=1;*/      }
     }
   for(i=1; i<= nlstate; i++){      /*ps[3][2]=1;*/
      s1=0;  
     for(j=1; j<i; j++)    for(i=1; i<= nlstate; i++){
       s1+=exp(ps[i][j]);       s1=0;
     for(j=i+1; j<=nlstate+ndeath; j++)      for(j=1; j<i; j++)
       s1+=exp(ps[i][j]);        s1+=exp(ps[i][j]);
     ps[i][i]=1./(s1+1.);      for(j=i+1; j<=nlstate+ndeath; j++)
     for(j=1; j<i; j++)        s1+=exp(ps[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      ps[i][i]=1./(s1+1.);
     for(j=i+1; j<=nlstate+ndeath; j++)      for(j=1; j<i; j++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      for(j=i+1; j<=nlstate+ndeath; j++)
   } /* end i */        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    } /* end i */
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       ps[ii][ii]=1;      for(jj=1; jj<= nlstate+ndeath; jj++){
     }        ps[ii][jj]=0;
   }        ps[ii][ii]=1;
       }
     }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
    }      for(jj=1; jj<= nlstate+ndeath; jj++){
     printf("\n ");       printf("%lf ",ps[ii][jj]);
     }     }
     printf("\n ");printf("%lf ",cov[2]);*/      printf("\n ");
 /*      }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      printf("\n ");printf("%lf ",cov[2]);*/
   goto end;*/  /*
     return ps;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 }    goto end;*/
       return ps;
 /**************** Product of 2 matrices ******************/  }
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /**************** Product of 2 matrices ******************/
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  {
   /* in, b, out are matrice of pointers which should have been initialized    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      before: only the contents of out is modified. The function returns       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      a pointer to pointers identical to out */    /* in, b, out are matrice of pointers which should have been initialized 
   long i, j, k;       before: only the contents of out is modified. The function returns
   for(i=nrl; i<= nrh; i++)       a pointer to pointers identical to out */
     for(k=ncolol; k<=ncoloh; k++)    long i, j, k;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(i=nrl; i<= nrh; i++)
         out[i][k] +=in[i][j]*b[j][k];      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
   return out;          out[i][k] +=in[i][j]*b[j][k];
 }  
     return out;
   }
 /************* 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 )  /************* Higher Matrix Product ***************/
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* Computes the transition matrix starting at age 'age' over 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step       'nhstepm*hstepm*stepm' months (i.e. until
      (typically every 2 years instead of every month which is too big).       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      Model is determined by parameters x and covariates have to be       nhstepm*hstepm matrices. 
      included manually here.       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
      */       for the memory).
        Model is determined by parameters x and covariates have to be 
   int i, j, d, h, k;       included manually here. 
   double **out, cov[NCOVMAX];  
   double **newm;       */
   
   /* Hstepm could be zero and should return the unit matrix */    int i, j, d, h, k;
   for (i=1;i<=nlstate+ndeath;i++)    double **out, cov[NCOVMAX];
     for (j=1;j<=nlstate+ndeath;j++){    double **newm;
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);    /* Hstepm could be zero and should return the unit matrix */
     }    for (i=1;i<=nlstate+ndeath;i++)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for (j=1;j<=nlstate+ndeath;j++){
   for(h=1; h <=nhstepm; h++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for(d=1; d <=hstepm; d++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       newm=savm;      }
       /* Covariates have to be included here again */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       cov[1]=1.;    for(h=1; h <=nhstepm; h++){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for(d=1; d <=hstepm; d++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        newm=savm;
       for (k=1; k<=cptcovage;k++)        /* Covariates have to be included here again */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        cov[1]=1.;
       for (k=1; k<=cptcovprod;k++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         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<=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];
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        for (k=1; k<=cptcovprod;k++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       oldm=newm;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     for(i=1; i<=nlstate+ndeath; i++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1;j<=nlstate+ndeath;j++) {        savm=oldm;
         po[i][j][h]=newm[i][j];        oldm=newm;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      }
          */      for(i=1; i<=nlstate+ndeath; i++)
       }        for(j=1;j<=nlstate+ndeath;j++) {
   } /* end h */          po[i][j][h]=newm[i][j];
   return po;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
 }           */
         }
     } /* end h */
 /*************** log-likelihood *************/    return po;
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*************** log-likelihood *************/
   double **out;  double func( double *x)
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    int i, ii, j, k, mi, d, kk;
   long ipmx;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   /*extern weight */    double **out;
   /* We are differentiating ll according to initial status */    double sw; /* Sum of weights */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double lli; /* Individual log likelihood */
   /*for(i=1;i<imx;i++)    int s1, s2;
     printf(" %d\n",s[4][i]);    double bbh;
   */    long ipmx;
   cov[1]=1.;    /*extern weight */
     /* We are differentiating ll according to initial status */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    /*for(i=1;i<imx;i++) 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      printf(" %d\n",s[4][i]);
     for(mi=1; mi<= wav[i]-1; mi++){    */
       for (ii=1;ii<=nlstate+ndeath;ii++)    cov[1]=1.;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    if(mle==1){
         for (kk=1; kk<=cptcovage;kk++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            for (j=1;j<=nlstate+ndeath;j++){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         savm=oldm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         oldm=newm;            }
                  for(d=0; d<dh[mi][i]; d++){
                    newm=savm;
       } /* end mult */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                  for (kk=1; kk<=cptcovage;kk++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/            }
       ipmx +=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       sw += weight[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;            savm=oldm;
     } /* end of wave */            oldm=newm;
   } /* end of individual */          } /* end mult */
         
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          /* But now since version 0.9 we anticipate for bias and large stepm.
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   return -l;           * (in months) between two waves is not a multiple of stepm, we rounded to 
 }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 /*********** Maximum Likelihood Estimation ***************/           * 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
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))           * -stepm/2 to stepm/2 .
 {           * For stepm=1 the results are the same as for previous versions of Imach.
   int i,j, iter;           * For stepm > 1 the results are less biased than in previous versions. 
   double **xi,*delti;           */
   double fret;          s1=s[mw[mi][i]][i];
   xi=matrix(1,npar,1,npar);          s2=s[mw[mi+1][i]][i];
   for (i=1;i<=npar;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
     for (j=1;j<=npar;j++)          /* bias is positive if real duration
       xi[i][j]=(i==j ? 1.0 : 0.0);           * is higher than the multiple of stepm and negative otherwise.
   printf("Powell\n");  fprintf(ficlog,"Powell\n");           */
   powell(p,xi,npar,ftol,&iter,&fret,func);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          /*if(lli ==000.0)*/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          /*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;
 /**** Computes Hessian and covariance matrix ***/        } /* end of wave */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      } /* end of individual */
 {    }  else if(mle==2){
   double  **a,**y,*x,pd;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **hess;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, j,jk;        for(mi=1; mi<= wav[i]-1; mi++){
   int *indx;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   double hessii(double p[], double delta, int theta, double delti[]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double hessij(double p[], double delti[], int i, int j);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   void lubksb(double **a, int npar, int *indx, double b[]) ;            }
   void ludcmp(double **a, int npar, int *indx, double *d) ;          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   hess=matrix(1,npar,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   printf("\nCalculation of the hessian matrix. Wait...\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");            }
   for (i=1;i<=npar;i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("%d",i);fflush(stdout);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficlog,"%d",i);fflush(ficlog);            savm=oldm;
     hess[i][i]=hessii(p,ftolhess,i,delti);            oldm=newm;
     /*printf(" %f ",p[i]);*/          } /* end mult */
     /*printf(" %lf ",hess[i][i]);*/        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias and large stepm.
   for (i=1;i<=npar;i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (j=1;j<=npar;j++)  {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       if (j>i) {           * the nearest (and in case of equal distance, to the lowest) interval but now
         printf(".%d%d",i,j);fflush(stdout);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         hess[i][j]=hessij(p,delti,i,j);           * probability in order to take into account the bias as a fraction of the way
         hess[j][i]=hess[i][j];               * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         /*printf(" %lf ",hess[i][j]);*/           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   printf("\n");          s1=s[mw[mi][i]][i];
   fprintf(ficlog,"\n");          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          /* bias is positive if real duration
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");           * is higher than the multiple of stepm and negative otherwise.
             */
   a=matrix(1,npar,1,npar);          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 */
   y=matrix(1,npar,1,npar);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   x=vector(1,npar);          /*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 */
   indx=ivector(1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (i=1;i<=npar;i++)          /*if(lli ==000.0)*/
     for (j=1;j<=npar;j++) a[i][j]=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); */
   ludcmp(a,npar,indx,&pd);          ipmx +=1;
           sw += weight[i];
   for (j=1;j<=npar;j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++) x[i]=0;        } /* end of wave */
     x[j]=1;      } /* end of individual */
     lubksb(a,npar,indx,x);    }  else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1;i<=npar;i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       matcov[i][j]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   printf("\n#Hessian matrix#\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficlog,"\n#Hessian matrix#\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++) {            }
     for (j=1;j<=npar;j++) {          for(d=0; d<dh[mi][i]; d++){
       printf("%.3e ",hess[i][j]);            newm=savm;
       fprintf(ficlog,"%.3e ",hess[i][j]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     printf("\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficlog,"\n");            }
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Recompute Inverse */            savm=oldm;
   for (i=1;i<=npar;i++)            oldm=newm;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          } /* end mult */
   ludcmp(a,npar,indx,&pd);        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   /*  printf("\n#Hessian matrix recomputed#\n");          /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (j=1;j<=npar;j++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (i=1;i<=npar;i++) x[i]=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
     x[j]=1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     lubksb(a,npar,indx,x);           * (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
       y[i][j]=x[i];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       printf("%.3e ",y[i][j]);           * -stepm/2 to stepm/2 .
       fprintf(ficlog,"%.3e ",y[i][j]);           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
     printf("\n");           */
     fprintf(ficlog,"\n");          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   */          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
   free_matrix(a,1,npar,1,npar);           * is higher than the multiple of stepm and negative otherwise.
   free_matrix(y,1,npar,1,npar);           */
   free_vector(x,1,npar);          /* 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 */
   free_ivector(indx,1,npar);          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 */
   free_matrix(hess,1,npar,1,npar);          /*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;
           sw += weight[i];
 /*************** hessian matrix ****************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 double hessii( double x[], double delta, int theta, double delti[])        } /* end of wave */
 {      } /* end of individual */
   int i;    }else{  /* ml=4 no inter-extrapolation */
   int l=1, lmax=20;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double k1,k2;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double p2[NPARMAX+1];        for(mi=1; mi<= wav[i]-1; mi++){
   double res;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            for (j=1;j<=nlstate+ndeath;j++){
   double fx;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k=0,kmax=10;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double l1;            }
           for(d=0; d<dh[mi][i]; d++){
   fx=func(x);            newm=savm;
   for (i=1;i<=npar;i++) p2[i]=x[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(l=0 ; l <=lmax; l++){            for (kk=1; kk<=cptcovage;kk++) {
     l1=pow(10,l);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     delts=delt;            }
     for(k=1 ; k <kmax; k=k+1){          
       delt = delta*(l1*k);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       p2[theta]=x[theta] +delt;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       k1=func(p2)-fx;            savm=oldm;
       p2[theta]=x[theta]-delt;            oldm=newm;
       k2=func(p2)-fx;          } /* end mult */
       /*res= (k1-2.0*fx+k2)/delt/delt; */        
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                ipmx +=1;
 #ifdef DEBUG          sw += weight[i];
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       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);        } /* end of wave */
 #endif      } /* end of individual */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    } /* End of if */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         k=kmax;    /* 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 */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    return -l;
         k=kmax; l=lmax*10.;  }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /*********** Maximum Likelihood Estimation ***************/
       }  
     }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
   delti[theta]=delts;    int i,j, iter;
   return res;    double **xi,*delti;
      double fret;
 }    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
 double hessij( double x[], double delti[], int thetai,int thetaj)      for (j=1;j<=npar;j++)
 {        xi[i][j]=(i==j ? 1.0 : 0.0);
   int i;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int l=1, l1, lmax=20;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   int k;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fx=func(x);  
   for (k=1; k<=2; k++) {  }
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  /**** Computes Hessian and covariance matrix ***/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     k1=func(p2)-fx;  {
      double  **a,**y,*x,pd;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double **hess;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    int i, j,jk;
     k2=func(p2)-fx;    int *indx;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    double hessii(double p[], double delta, int theta, double delti[]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double hessij(double p[], double delti[], int i, int j);
     k3=func(p2)-fx;    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    hess=matrix(1,npar,1,npar);
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    printf("\nCalculation of the hessian matrix. Wait...\n");
 #ifdef DEBUG    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    for (i=1;i<=npar;i++){
     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);      printf("%d",i);fflush(stdout);
 #endif      fprintf(ficlog,"%d",i);fflush(ficlog);
   }      hess[i][i]=hessii(p,ftolhess,i,delti);
   return res;      /*printf(" %f ",p[i]);*/
 }      /*printf(" %lf ",hess[i][i]);*/
     }
 /************** Inverse of matrix **************/    
 void ludcmp(double **a, int n, int *indx, double *d)    for (i=1;i<=npar;i++) {
 {      for (j=1;j<=npar;j++)  {
   int i,imax,j,k;        if (j>i) { 
   double big,dum,sum,temp;          printf(".%d%d",i,j);fflush(stdout);
   double *vv;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
            hess[i][j]=hessij(p,delti,i,j);
   vv=vector(1,n);          hess[j][i]=hess[i][j];    
   *d=1.0;          /*printf(" %lf ",hess[i][j]);*/
   for (i=1;i<=n;i++) {        }
     big=0.0;      }
     for (j=1;j<=n;j++)    }
       if ((temp=fabs(a[i][j])) > big) big=temp;    printf("\n");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    fprintf(ficlog,"\n");
     vv[i]=1.0/big;  
   }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   for (j=1;j<=n;j++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=1;i<j;i++) {    
       sum=a[i][j];    a=matrix(1,npar,1,npar);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    y=matrix(1,npar,1,npar);
       a[i][j]=sum;    x=vector(1,npar);
     }    indx=ivector(1,npar);
     big=0.0;    for (i=1;i<=npar;i++)
     for (i=j;i<=n;i++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       sum=a[i][j];    ludcmp(a,npar,indx,&pd);
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];    for (j=1;j<=npar;j++) {
       a[i][j]=sum;      for (i=1;i<=npar;i++) x[i]=0;
       if ( (dum=vv[i]*fabs(sum)) >= big) {      x[j]=1;
         big=dum;      lubksb(a,npar,indx,x);
         imax=i;      for (i=1;i<=npar;i++){ 
       }        matcov[i][j]=x[i];
     }      }
     if (j != imax) {    }
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];    printf("\n#Hessian matrix#\n");
         a[imax][k]=a[j][k];    fprintf(ficlog,"\n#Hessian matrix#\n");
         a[j][k]=dum;    for (i=1;i<=npar;i++) { 
       }      for (j=1;j<=npar;j++) { 
       *d = -(*d);        printf("%.3e ",hess[i][j]);
       vv[imax]=vv[j];        fprintf(ficlog,"%.3e ",hess[i][j]);
     }      }
     indx[j]=imax;      printf("\n");
     if (a[j][j] == 0.0) a[j][j]=TINY;      fprintf(ficlog,"\n");
     if (j != n) {    }
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /* Recompute Inverse */
     }    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   free_vector(vv,1,n);  /* Doesn't work */    ludcmp(a,npar,indx,&pd);
 ;  
 }    /*  printf("\n#Hessian matrix recomputed#\n");
   
 void lubksb(double **a, int n, int *indx, double b[])    for (j=1;j<=npar;j++) {
 {      for (i=1;i<=npar;i++) x[i]=0;
   int i,ii=0,ip,j;      x[j]=1;
   double sum;      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   for (i=1;i<=n;i++) {        y[i][j]=x[i];
     ip=indx[i];        printf("%.3e ",y[i][j]);
     sum=b[ip];        fprintf(ficlog,"%.3e ",y[i][j]);
     b[ip]=b[i];      }
     if (ii)      printf("\n");
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      fprintf(ficlog,"\n");
     else if (sum) ii=i;    }
     b[i]=sum;    */
   }  
   for (i=n;i>=1;i--) {    free_matrix(a,1,npar,1,npar);
     sum=b[i];    free_matrix(y,1,npar,1,npar);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    free_vector(x,1,npar);
     b[i]=sum/a[i][i];    free_ivector(indx,1,npar);
   }    free_matrix(hess,1,npar,1,npar);
 }  
   
 /************ Frequencies ********************/  }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  
 {  /* Some frequencies */  /*************** hessian matrix ****************/
    double hessii( double x[], double delta, int theta, double delti[])
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  {
   int first;    int i;
   double ***freq; /* Frequencies */    int l=1, lmax=20;
   double *pp;    double k1,k2;
   double pos, k2, dateintsum=0,k2cpt=0;    double p2[NPARMAX+1];
   FILE *ficresp;    double res;
   char fileresp[FILENAMELENGTH];    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      double fx;
   pp=vector(1,nlstate);    int k=0,kmax=10;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double l1;
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);    fx=func(x);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    for (i=1;i<=npar;i++) p2[i]=x[i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);    for(l=0 ; l <=lmax; l++){
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      l1=pow(10,l);
     exit(0);      delts=delt;
   }      for(k=1 ; k <kmax; k=k+1){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        delt = delta*(l1*k);
   j1=0;        p2[theta]=x[theta] +delt;
          k1=func(p2)-fx;
   j=cptcoveff;        p2[theta]=x[theta]-delt;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
   first=1;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   for(k1=1; k1<=j;k1++){  #ifdef DEBUG
     for(i1=1; i1<=ncodemax[k1];i1++){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       j1++;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  #endif
         scanf("%d", i);*/        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for (i=-1; i<=nlstate+ndeath; i++)          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for (jk=-1; jk<=nlstate+ndeath; jk++)            k=kmax;
           for(m=agemin; m <= agemax+3; m++)        }
             freq[i][jk][m]=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                k=kmax; l=lmax*10.;
       dateintsum=0;        }
       k2cpt=0;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for (i=1; i<=imx; i++) {          delts=delt;
         bool=1;        }
         if  (cptcovn>0) {      }
           for (z1=1; z1<=cptcoveff; z1++)    }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    delti[theta]=delts;
               bool=0;    return res; 
         }    
         if (bool==1) {  }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  double hessij( double x[], double delti[], int thetai,int thetaj)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  {
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int i;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int l=1, l1, lmax=20;
               if (m<lastpass) {    double k1,k2,k3,k4,res,fx;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double p2[NPARMAX+1];
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    int k;
               }  
                  fx=func(x);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    for (k=1; k<=2; k++) {
                 dateintsum=dateintsum+k2;      for (i=1;i<=npar;i++) p2[i]=x[i];
                 k2cpt++;      p2[thetai]=x[thetai]+delti[thetai]/k;
               }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             }      k1=func(p2)-fx;
           }    
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
              k2=func(p2)-fx;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
       if  (cptcovn>0) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         fprintf(ficresp, "\n#********** Variable ");      k3=func(p2)-fx;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(ficresp, "**********\n#");      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       fprintf(ficresp, "\n");  #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);
       for(i=(int)agemin; i <= (int)agemax+3; i++){      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         if(i==(int)agemax+3){  #endif
           fprintf(ficlog,"Total");    }
         }else{    return res;
           if(first==1){  }
             first=0;  
             printf("See log file for details...\n");  /************** Inverse of matrix **************/
           }  void ludcmp(double **a, int n, int *indx, double *d) 
           fprintf(ficlog,"Age %d", i);  { 
         }    int i,imax,j,k; 
         for(jk=1; jk <=nlstate ; jk++){    double big,dum,sum,temp; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double *vv; 
             pp[jk] += freq[jk][m][i];   
         }    vv=vector(1,n); 
         for(jk=1; jk <=nlstate ; jk++){    *d=1.0; 
           for(m=-1, pos=0; m <=0 ; m++)    for (i=1;i<=n;i++) { 
             pos += freq[jk][m][i];      big=0.0; 
           if(pp[jk]>=1.e-10){      for (j=1;j<=n;j++) 
             if(first==1){        if ((temp=fabs(a[i][j])) > big) big=temp; 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             }      vv[i]=1.0/big; 
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    } 
           }else{    for (j=1;j<=n;j++) { 
             if(first==1)      for (i=1;i<j;i++) { 
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        sum=a[i][j]; 
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           }        a[i][j]=sum; 
         }      } 
       big=0.0; 
         for(jk=1; jk <=nlstate ; jk++){      for (i=j;i<=n;i++) { 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        sum=a[i][j]; 
             pp[jk] += freq[jk][m][i];        for (k=1;k<j;k++) 
         }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         for(jk=1,pos=0; jk <=nlstate ; jk++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           pos += pp[jk];          big=dum; 
         for(jk=1; jk <=nlstate ; jk++){          imax=i; 
           if(pos>=1.e-5){        } 
             if(first==1)      } 
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      if (j != imax) { 
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for (k=1;k<=n;k++) { 
           }else{          dum=a[imax][k]; 
             if(first==1)          a[imax][k]=a[j][k]; 
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          a[j][k]=dum; 
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        } 
           }        *d = -(*d); 
           if( i <= (int) agemax){        vv[imax]=vv[j]; 
             if(pos>=1.e-5){      } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      indx[j]=imax; 
               probs[i][jk][j1]= pp[jk]/pos;      if (a[j][j] == 0.0) a[j][j]=TINY; 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      if (j != n) { 
             }        dum=1.0/(a[j][j]); 
             else        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      } 
           }    } 
         }    free_vector(vv,1,n);  /* Doesn't work */
          ;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  } 
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) {  void lubksb(double **a, int n, int *indx, double b[]) 
             if(first==1)  { 
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    int i,ii=0,ip,j; 
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);    double sum; 
             }   
         if(i <= (int) agemax)    for (i=1;i<=n;i++) { 
           fprintf(ficresp,"\n");      ip=indx[i]; 
         if(first==1)      sum=b[ip]; 
           printf("Others in log...\n");      b[ip]=b[i]; 
         fprintf(ficlog,"\n");      if (ii) 
       }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     }      else if (sum) ii=i; 
   }      b[i]=sum; 
   dateintmean=dateintsum/k2cpt;    } 
      for (i=n;i>=1;i--) { 
   fclose(ficresp);      sum=b[i]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   free_vector(pp,1,nlstate);      b[i]=sum/a[i][i]; 
      } 
   /* End of Freq */  } 
 }  
   /************ Frequencies ********************/
 /************ Prevalence ********************/  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)
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  {  /* Some frequencies */
 {  /* Some frequencies */    
      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp;
   double pos, k2;    double pos, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
   pp=vector(1,nlstate);    char fileresp[FILENAMELENGTH];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    
      pp=vector(1,nlstate);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   j1=0;    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   j=cptcoveff;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   for(k1=1; k1<=j;k1++){      exit(0);
     for(i1=1; i1<=ncodemax[k1];i1++){    }
       j1++;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
          j1=0;
       for (i=-1; i<=nlstate+ndeath; i++)      
         for (jk=-1; jk<=nlstate+ndeath; jk++)      j=cptcoveff;
           for(m=agemin; m <= agemax+3; m++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             freq[i][jk][m]=0;  
          first=1;
       for (i=1; i<=imx; i++) {  
         bool=1;    for(k1=1; k1<=j;k1++){
         if  (cptcovn>0) {      for(i1=1; i1<=ncodemax[k1];i1++){
           for (z1=1; z1<=cptcoveff; z1++)        j1++;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
               bool=0;          scanf("%d", i);*/
         }        for (i=-1; i<=nlstate+ndeath; i++)  
         if (bool==1) {          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           for(m=firstpass; m<=lastpass; m++){            for(m=agemin; m <= agemax+3; m++)
             k2=anint[m][i]+(mint[m][i]/12.);              freq[i][jk][m]=0;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        
               if(agev[m][i]==0) agev[m][i]=agemax+1;        dateintsum=0;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        k2cpt=0;
               if (m<lastpass) {        for (i=1; i<=imx; i++) {
                 if (calagedate>0)          bool=1;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          if  (cptcovn>0) {
                 else            for (z1=1; z1<=cptcoveff; z1++) 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];                bool=0;
               }          }
             }          if (bool==1){
           }            for(m=firstpass; m<=lastpass; m++){
         }              k2=anint[m][i]+(mint[m][i]/12.);
       }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){                if(agev[m][i]==0) agev[m][i]=agemax+1;
         for(jk=1; jk <=nlstate ; jk++){                if(agev[m][i]==1) agev[m][i]=agemax+2;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                if (m<lastpass) {
             pp[jk] += freq[jk][m][i];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         }                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
         for(jk=1; jk <=nlstate ; jk++){                }
           for(m=-1, pos=0; m <=0 ; m++)                
             pos += freq[jk][m][i];                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
         }                  dateintsum=dateintsum+k2;
                          k2cpt++;
         for(jk=1; jk <=nlstate ; jk++){                }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              }
             pp[jk] += freq[jk][m][i];            }
         }          }
                }
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];         
                fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         for(jk=1; jk <=nlstate ; jk++){      
           if( i <= (int) agemax){        if  (cptcovn>0) {
             if(pos>=1.e-5){          fprintf(ficresp, "\n#********** Variable "); 
               probs[i][jk][j1]= pp[jk]/pos;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             }          fprintf(ficresp, "**********\n#");
           }        }
         }/* end jk */        for(i=1; i<=nlstate;i++) 
       }/* end i */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     } /* end i1 */        fprintf(ficresp, "\n");
   } /* end k1 */        
         for(i=(int)agemin; i <= (int)agemax+3; i++){
            if(i==(int)agemax+3){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            fprintf(ficlog,"Total");
   free_vector(pp,1,nlstate);          }else{
              if(first==1){
 }  /* End of Freq */              first=0;
               printf("See log file for details...\n");
 /************* Waves Concatenation ***************/            }
             fprintf(ficlog,"Age %d", i);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          }
 {          for(jk=1; jk <=nlstate ; jk++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      Death is a valid wave (if date is known).              pp[jk] += freq[jk][m][i]; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for(jk=1; jk <=nlstate ; jk++){
      and mw[mi+1][i]. dh depends on stepm.            for(m=-1, pos=0; m <=0 ; m++)
      */              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
   int i, mi, m;              if(first==1){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      double sum=0., jmean=0.;*/              }
   int first;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int j, k=0,jk, ju, jl;            }else{
   double sum=0.;              if(first==1)
   first=0;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   jmin=1e+5;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   jmax=-1;            }
   jmean=0.;          }
   for(i=1; i<=imx; i++){  
     mi=0;          for(jk=1; jk <=nlstate ; jk++){
     m=firstpass;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     while(s[m][i] <= nlstate){              pp[jk] += freq[jk][m][i];
       if(s[m][i]>=1)          }
         mw[++mi][i]=m;  
       if(m >=lastpass)          for(jk=1,pos=0; jk <=nlstate ; jk++)
         break;            pos += pp[jk];
       else          for(jk=1; jk <=nlstate ; jk++){
         m++;            if(pos>=1.e-5){
     }/* end while */              if(first==1)
     if (s[m][i] > nlstate){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       mi++;     /* Death is another wave */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       /* if(mi==0)  never been interviewed correctly before death */            }else{
          /* Only death is a correct wave */              if(first==1)
       mw[mi][i]=m;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     wav[i]=mi;            if( i <= (int) agemax){
     if(mi==0){              if(pos>=1.e-5){
       if(first==0){                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);                probs[i][jk][j1]= pp[jk]/pos;
         first=1;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       }              }
       if(first==1){              else
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
       }            }
     } /* end mi==0 */          }
   }          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
   for(i=1; i<=imx; i++){            for(m=-1; m <=nlstate+ndeath; m++)
     for(mi=1; mi<wav[i];mi++){              if(freq[jk][m][i] !=0 ) {
       if (stepm <=0)              if(first==1)
         dh[mi][i]=1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       else{                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         if (s[mw[mi+1][i]][i] > nlstate) {              }
           if (agedc[i] < 2*AGESUP) {          if(i <= (int) agemax)
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            fprintf(ficresp,"\n");
           if(j==0) j=1;  /* Survives at least one month after exam */          if(first==1)
           k=k+1;            printf("Others in log...\n");
           if (j >= jmax) jmax=j;          fprintf(ficlog,"\n");
           if (j <= jmin) jmin=j;        }
           sum=sum+j;      }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    }
           }    dateintmean=dateintsum/k2cpt; 
         }   
         else{    fclose(ficresp);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
           k=k+1;    free_vector(pp,1,nlstate);
           if (j >= jmax) jmax=j;    
           else if (j <= jmin)jmin=j;    /* End of Freq */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  }
           sum=sum+j;  
         }  /************ Prevalence ********************/
         jk= j/stepm;  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)
         jl= j -jk*stepm;  {  /* Some frequencies */
         ju= j -(jk+1)*stepm;   
         if(jl <= -ju)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           dh[mi][i]=jk;    double ***freq; /* Frequencies */
         else    double *pp;
           dh[mi][i]=jk+1;    double pos, k2;
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */    pp=vector(1,nlstate);
       }    
     }    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   }    j1=0;
   jmean=sum/k;    
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    j=cptcoveff;
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  }    
     for(k1=1; k1<=j;k1++){
 /*********** Tricode ****************************/      for(i1=1; i1<=ncodemax[k1];i1++){
 void tricode(int *Tvar, int **nbcode, int imx)        j1++;
 {        
   int Ndum[20],ij=1, k, j, i;        for (i=-1; i<=nlstate+ndeath; i++)  
   int cptcode=0;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   cptcoveff=0;            for(m=agemin; m <= agemax+3; m++)
                freq[i][jk][m]=0;
   for (k=0; k<19; k++) Ndum[k]=0;       
   for (k=1; k<=7; k++) ncodemax[k]=0;        for (i=1; i<=imx; i++) {
           bool=1;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          if  (cptcovn>0) {
     for (i=1; i<=imx; i++) {            for (z1=1; z1<=cptcoveff; z1++) 
       ij=(int)(covar[Tvar[j]][i]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       Ndum[ij]++;                bool=0;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          } 
       if (ij > cptcode) cptcode=ij;          if (bool==1) { 
     }            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
     for (i=0; i<=cptcode; i++) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
       if(Ndum[i]!=0) ncodemax[j]++;                if(agev[m][i]==0) agev[m][i]=agemax+1;
     }                if(agev[m][i]==1) agev[m][i]=agemax+2;
     ij=1;                if (m<lastpass) {
                   if (calagedate>0) 
                     freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
     for (i=1; i<=ncodemax[j]; i++) {                  else
       for (k=0; k<=19; k++) {                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         if (Ndum[k] != 0) {                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
           nbcode[Tvar[j]][ij]=k;                }
                        }
           ij++;            }
         }          }
         if (ij > ncodemax[j]) break;        }
       }          for(i=(int)agemin; i <= (int)agemax+3; i++){ 
     }          for(jk=1; jk <=nlstate ; jk++){
   }              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
  for (k=0; k<19; k++) Ndum[k]=0;          }
           for(jk=1; jk <=nlstate ; jk++){
  for (i=1; i<=ncovmodel-2; i++) {            for(m=-1, pos=0; m <=0 ; m++)
    ij=Tvar[i];              pos += freq[jk][m][i];
    Ndum[ij]++;          }
  }          
           for(jk=1; jk <=nlstate ; jk++){
  ij=1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  for (i=1; i<=10; i++) {              pp[jk] += freq[jk][m][i];
    if((Ndum[i]!=0) && (i<=ncovcol)){          }
      Tvaraff[ij]=i;          
      ij++;          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
    }          
  }          for(jk=1; jk <=nlstate ; jk++){    
              if( i <= (int) agemax){
  cptcoveff=ij-1;              if(pos>=1.e-5){
 }                probs[i][jk][j1]= pp[jk]/pos;
               }
 /*********** Health Expectancies ****************/            }
           }/* end jk */
 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 )        }/* end i */
       } /* end i1 */
 {    } /* end k1 */
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    
   double age, agelim, hf;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   double ***p3mat,***varhe;    free_vector(pp,1,nlstate);
   double **dnewm,**doldm;    
   double *xp;  }  /* End of Freq */
   double **gp, **gm;  
   double ***gradg, ***trgradg;  /************* Waves Concatenation ***************/
   int theta;  
   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)
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  {
   xp=vector(1,npar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   dnewm=matrix(1,nlstate*2,1,npar);       Death is a valid wave (if date is known).
   doldm=matrix(1,nlstate*2,1,nlstate*2);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   fprintf(ficreseij,"# Health expectancies\n");       and mw[mi+1][i]. dh depends on stepm.
   fprintf(ficreseij,"# Age");       */
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    int i, mi, m;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   fprintf(ficreseij,"\n");       double sum=0., jmean=0.;*/
     int first;
   if(estepm < stepm){    int j, k=0,jk, ju, jl;
     printf ("Problem %d lower than %d\n",estepm, stepm);    double sum=0.;
   }    first=0;
   else  hstepm=estepm;      jmin=1e+5;
   /* We compute the life expectancy from trapezoids spaced every estepm months    jmax=-1;
    * This is mainly to measure the difference between two models: for example    jmean=0.;
    * if stepm=24 months pijx are given only every 2 years and by summing them    for(i=1; i<=imx; i++){
    * we are calculating an estimate of the Life Expectancy assuming a linear      mi=0;
    * progression inbetween and thus overestimating or underestimating according      m=firstpass;
    * to the curvature of the survival function. If, for the same date, we      while(s[m][i] <= nlstate){
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        if(s[m][i]>=1)
    * to compare the new estimate of Life expectancy with the same linear          mw[++mi][i]=m;
    * hypothesis. A more precise result, taking into account a more precise        if(m >=lastpass)
    * curvature will be obtained if estepm is as small as stepm. */          break;
         else
   /* For example we decided to compute the life expectancy with the smallest unit */          m++;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      }/* end while */
      nhstepm is the number of hstepm from age to agelim      if (s[m][i] > nlstate){
      nstepm is the number of stepm from age to agelin.        mi++;     /* Death is another wave */
      Look at hpijx to understand the reason of that which relies in memory size        /* if(mi==0)  never been interviewed correctly before death */
      and note for a fixed period like estepm months */           /* Only death is a correct wave */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        mw[mi][i]=m;
      survival function given by stepm (the optimization length). Unfortunately it      }
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      wav[i]=mi;
      results. So we changed our mind and took the option of the best precision.      if(mi==0){
   */        if(first==0){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
           first=1;
   agelim=AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if(first==1){
     /* nhstepm age range expressed in number of stepm */          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      } /* end mi==0 */
     /* if (stepm >= YEARM) hstepm=1;*/    }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=imx; i++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      for(mi=1; mi<wav[i];mi++){
     gp=matrix(0,nhstepm,1,nlstate*2);        if (stepm <=0)
     gm=matrix(0,nhstepm,1,nlstate*2);          dh[mi][i]=1;
         else{
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          if (s[mw[mi+1][i]][i] > nlstate) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            if (agedc[i] < 2*AGESUP) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              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;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
     /* Computing Variances of health expectancies */            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
      for(theta=1; theta <=npar; theta++){            }
       for(i=1; i<=npar; i++){          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              k=k+1;
              if (j >= jmax) jmax=j;
       cptj=0;            else if (j <= jmin)jmin=j;
       for(j=1; j<= nlstate; j++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         for(i=1; i<=nlstate; i++){            sum=sum+j;
           cptj=cptj+1;          }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          jk= j/stepm;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          jl= j -jk*stepm;
           }          ju= j -(jk+1)*stepm;
         }          if(mle <=1){ 
       }            if(jl==0){
                    dh[mi][i]=jk;
                    bh[mi][i]=0;
       for(i=1; i<=npar; i++)            }else{ /* We want a negative bias in order to only have interpolation ie
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                    * at the price of an extra matrix product in likelihood */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                dh[mi][i]=jk+1;
                    bh[mi][i]=ju;
       cptj=0;            }
       for(j=1; j<= nlstate; j++){          }else{
         for(i=1;i<=nlstate;i++){            if(jl <= -ju){
           cptj=cptj+1;              dh[mi][i]=jk;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){              bh[mi][i]=jl;       /* bias is positive if real duration
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                                   * is higher than the multiple of stepm and negative otherwise.
           }                                   */
         }            }
       }            else{
       for(j=1; j<= nlstate*2; j++)              dh[mi][i]=jk+1;
         for(h=0; h<=nhstepm-1; h++){              bh[mi][i]=ju;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            }
         }            if(dh[mi][i]==0){
      }              dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
 /* End theta */              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);
             }
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);            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);
           }
      for(h=0; h<=nhstepm-1; h++)        } /* end if mle */
       for(j=1; j<=nlstate*2;j++)      } /* end wave */
         for(theta=1; theta <=npar; theta++)    }
           trgradg[h][j][theta]=gradg[h][theta][j];    jmean=sum/k;
          printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      for(i=1;i<=nlstate*2;i++)   }
       for(j=1;j<=nlstate*2;j++)  
         varhe[i][j][(int)age] =0.;  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
      printf("%d|",(int)age);fflush(stdout);  {
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    
      for(h=0;h<=nhstepm-1;h++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
       for(k=0;k<=nhstepm-1;k++){    int cptcode=0;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    cptcoveff=0; 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);   
         for(i=1;i<=nlstate*2;i++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
           for(j=1;j<=nlstate*2;j++)    for (k=1; k<=7; k++) ncodemax[k]=0;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     /* Computing expectancies */                                 modality*/ 
     for(i=1; i<=nlstate;i++)        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for(j=1; j<=nlstate;j++)        Ndum[ij]++; /*store the modality */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                                   Tvar[j]. If V=sex and male is 0 and 
 /* 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]);*/                                         female is 1, then  cptcode=1.*/
       }
         }  
       for (i=0; i<=cptcode; i++) {
     fprintf(ficreseij,"%3.0f",age );        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 */
     cptj=0;      }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){      ij=1; 
         cptj++;      for (i=1; i<=ncodemax[j]; i++) {
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        for (k=0; k<= maxncov; k++) {
       }          if (Ndum[k] != 0) {
     fprintf(ficreseij,"\n");            nbcode[Tvar[j]][ij]=k; 
                /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     free_matrix(gm,0,nhstepm,1,nlstate*2);            
     free_matrix(gp,0,nhstepm,1,nlstate*2);            ij++;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          }
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          if (ij > ncodemax[j]) break; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }  
   }      } 
   printf("\n");    }  
   fprintf(ficlog,"\n");  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);   for (i=1; i<=ncovmodel-2; i++) { 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);     ij=Tvar[i];
 }     Ndum[ij]++;
    }
 /************ 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)   ij=1;
 {   for (i=1; i<= maxncov; i++) {
   /* Variance of health expectancies */     if((Ndum[i]!=0) && (i<=ncovcol)){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       Tvaraff[ij]=i; /*For printing */
   /* double **newm;*/       ij++;
   double **dnewm,**doldm;     }
   double **dnewmp,**doldmp;   }
   int i, j, nhstepm, hstepm, h, nstepm ;   
   int k, cptcode;   cptcoveff=ij-1; /*Number of simple covariates*/
   double *xp;  }
   double **gp, **gm;  /* for var eij */  
   double ***gradg, ***trgradg; /*for var eij */  /*********** Health Expectancies ****************/
   double **gradgp, **trgradgp; /* for var p point j */  
   double *gpp, *gmp; /* for var p point j */  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */  
   double ***p3mat;  {
   double age,agelim, hf;    /* Health expectancies */
   int theta;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   char digit[4];    double age, agelim, hf;
   char digitp[16];    double ***p3mat,***varhe;
     double **dnewm,**doldm;
   char fileresprobmorprev[FILENAMELENGTH];    double *xp;
     double **gp, **gm;
   if(popbased==1)    double ***gradg, ***trgradg;
     strcpy(digitp,"-populbased-");    int theta;
   else  
     strcpy(digitp,"-stablbased-");    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     xp=vector(1,npar);
   strcpy(fileresprobmorprev,"prmorprev");    dnewm=matrix(1,nlstate*2,1,npar);
   sprintf(digit,"%-d",ij);    doldm=matrix(1,nlstate*2,1,nlstate*2);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    fprintf(ficreseij,"# Health expectancies\n");
   strcat(fileresprobmorprev,digitp); /* Popbased or not */    fprintf(ficreseij,"# Age");
   strcat(fileresprobmorprev,fileres);    for(i=1; i<=nlstate;i++)
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {      for(j=1; j<=nlstate;j++)
     printf("Problem with resultfile: %s\n", fileresprobmorprev);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);    fprintf(ficreseij,"\n");
   }  
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    if(estepm < stepm){
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);      printf ("Problem %d lower than %d\n",estepm, stepm);
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    }
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    else  hstepm=estepm;   
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    /* We compute the life expectancy from trapezoids spaced every estepm months
     fprintf(ficresprobmorprev," p.%-d SE",j);     * This is mainly to measure the difference between two models: for example
     for(i=1; i<=nlstate;i++)     * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }       * progression in between and thus overestimating or underestimating according
   fprintf(ficresprobmorprev,"\n");     * to the curvature of the survival function. If, for the same date, we 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);     * to compare the new estimate of Life expectancy with the same linear 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);     * hypothesis. A more precise result, taking into account a more precise
     exit(0);     * curvature will be obtained if estepm is as small as stepm. */
   }  
   else{    /* For example we decided to compute the life expectancy with the smallest unit */
     fprintf(ficgp,"\n# Routine varevsij");    /* 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 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with html file: %s\n", optionfilehtm);       Look at hpijx to understand the reason of that which relies in memory size
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);       and note for a fixed period like estepm months */
     exit(0);    /* 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
   else{       means that if the survival funtion is printed only each two years of age and if
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  
   fprintf(ficresvij,"# Age");    agelim=AGESUP;
   for(i=1; i<=nlstate;i++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for(j=1; j<=nlstate;j++)      /* nhstepm age range expressed in number of stepm */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fprintf(ficresvij,"\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   xp=vector(1,npar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   dnewm=matrix(1,nlstate,1,npar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   doldm=matrix(1,nlstate,1,nlstate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      gp=matrix(0,nhstepm,1,nlstate*2);
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      gm=matrix(0,nhstepm,1,nlstate*2);
   
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   gpp=vector(nlstate+1,nlstate+ndeath);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   gmp=vector(nlstate+1,nlstate+ndeath);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/   
    
   if(estepm < stepm){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }      /* Computing Variances of health expectancies */
   else  hstepm=estepm;    
   /* For example we decided to compute the life expectancy with the smallest unit */       for(theta=1; theta <=npar; theta++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for(i=1; i<=npar; i++){ 
      nhstepm is the number of hstepm from age to agelim          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      nstepm is the number of stepm from age to agelin.        }
      Look at hpijx to understand the reason of that which relies in memory size        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      and note for a fixed period like k years */    
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        cptj=0;
      survival function given by stepm (the optimization length). Unfortunately it        for(j=1; j<= nlstate; j++){
      means that if the survival funtion is printed only each two years of age and if          for(i=1; i<=nlstate; i++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            cptj=cptj+1;
      results. So we changed our mind and took the option of the best precision.            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   */              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   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 */        }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */       
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<=npar; i++) 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     gp=matrix(0,nhstepm,1,nlstate);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     gm=matrix(0,nhstepm,1,nlstate);        
         cptj=0;
         for(j=1; j<= nlstate; j++){
     for(theta=1; theta <=npar; theta++){          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, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
         }
       if (popbased==1) {        for(j=1; j<= nlstate*2; j++)
         for(i=1; i<=nlstate;i++)          for(h=0; h<=nhstepm-1; h++){
           prlim[i][i]=probs[(int)age][i][ij];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       }          }
         } 
       for(j=1; j<= nlstate; j++){     
         for(h=0; h<=nhstepm; h++){  /* End theta */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
         }  
       }       for(h=0; h<=nhstepm-1; h++)
       /* This for computing forces of mortality (h=1)as a weighted average */        for(j=1; j<=nlstate*2;j++)
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){          for(theta=1; theta <=npar; theta++)
         for(i=1; i<= nlstate; i++)            trgradg[h][j][theta]=gradg[h][theta][j];
           gpp[j] += prlim[i][i]*p3mat[i][j][1];       
       }      
       /* end force of mortality */       for(i=1;i<=nlstate*2;i++)
         for(j=1;j<=nlstate*2;j++)
       for(i=1; i<=npar; i++) /* Computes gradient */          varhe[i][j][(int)age] =0.;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         printf("%d|",(int)age);fflush(stdout);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
       if (popbased==1) {        for(k=0;k<=nhstepm-1;k++){
         for(i=1; i<=nlstate;i++)          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
           prlim[i][i]=probs[(int)age][i][ij];          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
       }          for(i=1;i<=nlstate*2;i++)
             for(j=1;j<=nlstate*2;j++)
       for(j=1; j<= nlstate; j++){              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         for(h=0; h<=nhstepm; h++){        }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      /* Computing expectancies */
         }      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++)
       /* This for computing force of mortality (h=1)as a weighted average */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         for(i=1; i<= nlstate; i++)            
           gmp[j] += prlim[i][i]*p3mat[i][j][1];  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       }      
       /* end force of mortality */          }
   
       for(j=1; j<= nlstate; j++) /* vareij */      fprintf(ficreseij,"%3.0f",age );
         for(h=0; h<=nhstepm; h++){      cptj=0;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          cptj++;
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       }        }
       fprintf(ficreseij,"\n");
     } /* End theta */     
       free_matrix(gm,0,nhstepm,1,nlstate*2);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */      free_matrix(gp,0,nhstepm,1,nlstate*2);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
     for(h=0; h<=nhstepm; h++) /* veij */      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
       for(j=1; j<=nlstate;j++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(theta=1; theta <=npar; theta++)    }
           trgradg[h][j][theta]=gradg[h][theta][j];    printf("\n");
     fprintf(ficlog,"\n");
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */  
       for(theta=1; theta <=npar; theta++)    free_vector(xp,1,npar);
         trgradgp[j][theta]=gradgp[theta][j];    free_matrix(dnewm,1,nlstate*2,1,npar);
     free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
     for(i=1;i<=nlstate;i++)  }
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;  /************ 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(h=0;h<=nhstepm;h++){  {
       for(k=0;k<=nhstepm;k++){    /* Variance of health expectancies */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    /* double **newm;*/
         for(i=1;i<=nlstate;i++)    double **dnewm,**doldm;
           for(j=1;j<=nlstate;j++)    double **dnewmp,**doldmp;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
     }    double *xp;
     double **gp, **gm;  /* for var eij */
     /* pptj */    double ***gradg, ***trgradg; /*for var eij */
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);    double **gradgp, **trgradgp; /* for var p point j */
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);    double *gpp, *gmp; /* for var p point j */
     for(j=nlstate+1;j<=nlstate+ndeath;j++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       for(i=nlstate+1;i<=nlstate+ndeath;i++)    double ***p3mat;
         varppt[j][i]=doldmp[j][i];    double age,agelim, hf;
     /* end ppptj */    double ***mobaverage;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      int theta;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    char digit[4];
      char digitp[25];
     if (popbased==1) {  
       for(i=1; i<=nlstate;i++)    char fileresprobmorprev[FILENAMELENGTH];
         prlim[i][i]=probs[(int)age][i][ij];  
     }    if(popbased==1){
          if(mobilav!=0)
     /* This for computing force of mortality (h=1)as a weighted average */        strcpy(digitp,"-populbased-mobilav-");
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      else strcpy(digitp,"-populbased-nomobil-");
       for(i=1; i<= nlstate; i++)    }
         gmp[j] += prlim[i][i]*p3mat[i][j][1];    else 
     }          strcpy(digitp,"-stablbased-");
     /* end force of mortality */  
     if (mobilav!=0) {
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       for(i=1; i<=nlstate;i++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);      }
       }    }
     }  
     fprintf(ficresprobmorprev,"\n");    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     fprintf(ficresvij,"%.0f ",age );    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     for(i=1; i<=nlstate;i++)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for(j=1; j<=nlstate;j++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    strcat(fileresprobmorprev,fileres);
       }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fprintf(ficresvij,"\n");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     free_matrix(gp,0,nhstepm,1,nlstate);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     free_matrix(gm,0,nhstepm,1,nlstate);    }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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);
   } /* End age */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   free_vector(gpp,nlstate+1,nlstate+ndeath);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   free_vector(gmp,nlstate+1,nlstate+ndeath);      fprintf(ficresprobmorprev," p.%-d SE",j);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);      for(i=1; i<=nlstate;i++)
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    }  
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);      exit(0);
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    }
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);    else{
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);      fprintf(ficgp,"\n# Routine varevsij");
 */    }
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
   free_vector(xp,1,npar);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   free_matrix(doldm,1,nlstate,1,nlstate);      exit(0);
   free_matrix(dnewm,1,nlstate,1,npar);    }
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    else{
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
   fclose(ficresprobmorprev);    }
   fclose(ficgp);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fclose(fichtm);  
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
 }    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
 /************ Variance of prevlim ******************/      for(j=1; j<=nlstate;j++)
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 {    fprintf(ficresvij,"\n");
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    xp=vector(1,npar);
   double **newm;    dnewm=matrix(1,nlstate,1,npar);
   double **dnewm,**doldm;    doldm=matrix(1,nlstate,1,nlstate);
   int i, j, nhstepm, hstepm;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   int k, cptcode;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double *xp;  
   double *gp, *gm;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   double **gradg, **trgradg;    gpp=vector(nlstate+1,nlstate+ndeath);
   double age,agelim;    gmp=vector(nlstate+1,nlstate+ndeath);
   int theta;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    if(estepm < stepm){
   fprintf(ficresvpl,"# Age");      printf ("Problem %d lower than %d\n",estepm, stepm);
   for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %1d-%1d",i,i);    else  hstepm=estepm;   
   fprintf(ficresvpl,"\n");    /* 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. 
   xp=vector(1,npar);       nhstepm is the number of hstepm from age to agelim 
   dnewm=matrix(1,nlstate,1,npar);       nstepm is the number of stepm from age to agelin. 
   doldm=matrix(1,nlstate,1,nlstate);       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like k years */
   hstepm=1*YEARM; /* Every year of age */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       survival function given by stepm (the optimization length). Unfortunately it
   agelim = AGESUP;       means that if the survival funtion is printed every two years of age and if
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       results. So we changed our mind and took the option of the best precision.
     if (stepm >= YEARM) hstepm=1;    */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     gradg=matrix(1,npar,1,nlstate);    agelim = AGESUP;
     gp=vector(1,nlstate);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     gm=vector(1,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 */
     for(theta=1; theta <=npar; theta++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(i=1; i<=npar; i++){ /* Computes gradient */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      gp=matrix(0,nhstepm,1,nlstate);
       }      gm=matrix(0,nhstepm,1,nlstate);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       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);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(i=1;i<=nlstate;i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         gm[i] = prlim[i][i];  
         if (popbased==1) {
       for(i=1;i<=nlstate;i++)          if(mobilav ==0){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            for(i=1; i<=nlstate;i++)
     } /* End theta */              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
     trgradg =matrix(1,nlstate,1,npar);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)        }
         trgradg[j][theta]=gradg[theta][j];    
         for(j=1; j<= nlstate; j++){
     for(i=1;i<=nlstate;i++)          for(h=0; h<=nhstepm; h++){
       varpl[i][(int)age] =0.;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     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 */        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
     fprintf(ficresvpl,"%.0f ",age );           as a weighted average of prlim.
     for(i=1; i<=nlstate;i++)        */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
     fprintf(ficresvpl,"\n");          for(i=1; i<= nlstate; i++)
     free_vector(gp,1,nlstate);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     free_vector(gm,1,nlstate);        }    
     free_matrix(gradg,1,npar,1,nlstate);        /* end probability of death */
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   free_vector(xp,1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_matrix(doldm,1,nlstate,1,npar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_matrix(dnewm,1,nlstate,1,nlstate);   
         if (popbased==1) {
 }          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
 /************ Variance of one-step probabilities  ******************/              prlim[i][i]=probs[(int)age][i][ij];
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          }else{ /* mobilav */ 
 {            for(i=1; i<=nlstate;i++)
   int i, j=0,  i1, k1, l1, t, tj;              prlim[i][i]=mobaverage[(int)age][i][ij];
   int k2, l2, j1,  z1;          }
   int k=0,l, cptcode;        }
   int first=1, first1;  
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;        for(j=1; j<= nlstate; j++){
   double **dnewm,**doldm;          for(h=0; h<=nhstepm; h++){
   double *xp;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   double *gp, *gm;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   double **gradg, **trgradg;          }
   double **mu;        }
   double age,agelim, cov[NCOVMAX];        /* This for computing probability of death (h=1 means
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */           computed over hstepm matrices product = hstepm*stepm months) 
   int theta;           as a weighted average of prlim.
   char fileresprob[FILENAMELENGTH];        */
   char fileresprobcov[FILENAMELENGTH];        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   char fileresprobcor[FILENAMELENGTH];          for(i=1; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
   double ***varpij;        }    
         /* end probability of death */
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);        for(j=1; j<= nlstate; j++) /* vareij */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with resultfile: %s\n", fileresprob);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);          }
   }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   strcpy(fileresprobcov,"probcov");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   strcat(fileresprobcov,fileres);        }
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcov);      } /* End theta */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  
   }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   strcpy(fileresprobcor,"probcor");  
   strcat(fileresprobcor,fileres);      for(h=0; h<=nhstepm; h++) /* veij */
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        for(j=1; j<=nlstate;j++)
     printf("Problem with resultfile: %s\n", fileresprobcor);          for(theta=1; theta <=npar; theta++)
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);            trgradg[h][j][theta]=gradg[h][theta][j];
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        for(theta=1; theta <=npar; theta++)
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          trgradgp[j][theta]=gradgp[theta][j];
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      for(i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate;j++)
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");          vareij[i][j][(int)age] =0.;
   fprintf(ficresprob,"# Age");  
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      for(h=0;h<=nhstepm;h++){
   fprintf(ficresprobcov,"# Age");        for(k=0;k<=nhstepm;k++){
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficresprobcov,"# Age");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   for(i=1; i<=nlstate;i++)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     for(j=1; j<=(nlstate+ndeath);j++){        }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      }
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      /* pptj */
     }        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fprintf(ficresprob,"\n");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   fprintf(ficresprobcov,"\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   fprintf(ficresprobcor,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   xp=vector(1,npar);          varppt[j][i]=doldmp[j][i];
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      /* end ppptj */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      /*  x centered again */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   first=1;   
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      if (popbased==1) {
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        if(mobilav ==0){
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          for(i=1; i<=nlstate;i++)
     exit(0);            prlim[i][i]=probs[(int)age][i][ij];
   }        }else{ /* mobilav */ 
   else{          for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"\n# Routine varprob");            prlim[i][i]=mobaverage[(int)age][i][ij];
   }        }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      }
     printf("Problem with html file: %s\n", optionfilehtm);      
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      /* This for computing probability of death (h=1 means
     exit(0);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
   else{      */
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     fprintf(fichtm,"\n");        for(i=1; i<= nlstate; i++)
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");      }    
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");      /* end probability of death */
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   cov[1]=1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   tj=cptcoveff;        }
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      } 
   j1=0;      fprintf(ficresprobmorprev,"\n");
   for(t=1; t<=tj;t++){  
     for(i1=1; i1<=ncodemax[t];i1++){      fprintf(ficresvij,"%.0f ",age );
       j1++;      for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++){
       if  (cptcovn>0) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         fprintf(ficresprob, "\n#********** Variable ");        }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      fprintf(ficresvij,"\n");
         fprintf(ficresprob, "**********\n#");      free_matrix(gp,0,nhstepm,1,nlstate);
         fprintf(ficresprobcov, "\n#********** Variable ");      free_matrix(gm,0,nhstepm,1,nlstate);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         fprintf(ficresprobcov, "**********\n#");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficgp, "\n#********** Variable ");    } /* End age */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    free_vector(gpp,nlstate+1,nlstate+ndeath);
         fprintf(ficgp, "**********\n#");    free_vector(gmp,nlstate+1,nlstate+ndeath);
            free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
            free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
            fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
         fprintf(ficresprobcor, "\n#********** Variable ");        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
         fprintf(ficgp, "**********\n#");        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
       }    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,"\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);
       for (age=bage; age<=fage; age ++){  */
         cov[2]=age;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
         for (k=1; k<=cptcovn;k++) {  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,nlstate);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free_matrix(dnewm,1,nlstate,1,npar);
         for (k=1; k<=cptcovprod;k++)    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
            free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    fclose(ficresprobmorprev);
         gp=vector(1,(nlstate)*(nlstate+ndeath));    fclose(ficgp);
         gm=vector(1,(nlstate)*(nlstate+ndeath));    fclose(fichtm);
      }
         for(theta=1; theta <=npar; theta++){  
           for(i=1; i<=npar; i++)  /************ Variance of prevlim ******************/
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  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)
            {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    /* Variance of prevalence limit */
              /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           k=0;    double **newm;
           for(i=1; i<= (nlstate); i++){    double **dnewm,**doldm;
             for(j=1; j<=(nlstate+ndeath);j++){    int i, j, nhstepm, hstepm;
               k=k+1;    int k, cptcode;
               gp[k]=pmmij[i][j];    double *xp;
             }    double *gp, *gm;
           }    double **gradg, **trgradg;
              double age,agelim;
           for(i=1; i<=npar; i++)    int theta;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);     
        fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    fprintf(ficresvpl,"# Age");
           k=0;    for(i=1; i<=nlstate;i++)
           for(i=1; i<=(nlstate); i++){        fprintf(ficresvpl," %1d-%1d",i,i);
             for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficresvpl,"\n");
               k=k+1;  
               gm[k]=pmmij[i][j];    xp=vector(1,npar);
             }    dnewm=matrix(1,nlstate,1,npar);
           }    doldm=matrix(1,nlstate,1,nlstate);
          
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    hstepm=1*YEARM; /* Every year of age */
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         }    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           for(theta=1; theta <=npar; theta++)      if (stepm >= YEARM) hstepm=1;
             trgradg[j][theta]=gradg[theta][j];      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
              gradg=matrix(1,npar,1,nlstate);
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);      gp=vector(1,nlstate);
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);      gm=vector(1,nlstate);
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);      for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++){ /* Computes gradient */
         k=0;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         for(i=1; i<=(nlstate); i++){        }
           for(j=1; j<=(nlstate+ndeath);j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             k=k+1;        for(i=1;i<=nlstate;i++)
             mu[k][(int) age]=pmmij[i][j];          gp[i] = prlim[i][i];
           }      
         }        for(i=1; i<=npar; i++) /* Computes gradient */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             varpij[i][j][(int)age] = doldm[i][j];        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
         /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        for(i=1;i<=nlstate;i++)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      } /* End theta */
      }*/  
       trgradg =matrix(1,nlstate,1,npar);
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);      for(j=1; j<=nlstate;j++)
         fprintf(ficresprobcor,"\n%d ",(int)age);        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
         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;i++)
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        varpl[i][(int)age] =0.;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         }      for(i=1;i<=nlstate;i++)
         i=0;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){      fprintf(ficresvpl,"%.0f ",age );
             i=i++;      for(i=1; i<=nlstate;i++)
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      fprintf(ficresvpl,"\n");
             for (j=1; j<=i;j++){      free_vector(gp,1,nlstate);
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      free_vector(gm,1,nlstate);
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));      free_matrix(gradg,1,npar,1,nlstate);
             }      free_matrix(trgradg,1,nlstate,1,npar);
           }    } /* End age */
         }/* end of loop for state */  
       } /* end of loop for age */    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
       /* Confidence intervalle of pij  */    free_matrix(dnewm,1,nlstate,1,nlstate);
       /*  
       fprintf(ficgp,"\nset noparametric;unset label");  }
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");  
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  /************ Variance of one-step probabilities  ******************/
       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);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);  {
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    int k2, l2, j1,  z1;
       */    int k=0,l, cptcode;
     int first=1, first1;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       first1=1;    double **dnewm,**doldm;
       for (k2=1; k2<=(nlstate);k2++){    double *xp;
         for (l2=1; l2<=(nlstate+ndeath);l2++){    double *gp, *gm;
           if(l2==k2) continue;    double **gradg, **trgradg;
           j=(k2-1)*(nlstate+ndeath)+l2;    double **mu;
           for (k1=1; k1<=(nlstate);k1++){    double age,agelim, cov[NCOVMAX];
             for (l1=1; l1<=(nlstate+ndeath);l1++){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
               if(l1==k1) continue;    int theta;
               i=(k1-1)*(nlstate+ndeath)+l1;    char fileresprob[FILENAMELENGTH];
               if(i<=j) continue;    char fileresprobcov[FILENAMELENGTH];
               for (age=bage; age<=fage; age ++){    char fileresprobcor[FILENAMELENGTH];
                 if ((int)age %5==0){  
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    double ***varpij;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    strcpy(fileresprob,"prob"); 
                   mu1=mu[i][(int) age]/stepm*YEARM ;    strcat(fileresprob,fileres);
                   mu2=mu[j][(int) age]/stepm*YEARM;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   c12=cv12/sqrt(v1*v2);      printf("Problem with resultfile: %s\n", fileresprob);
                   /* Computing eigen value of matrix of covariance */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    }
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    strcpy(fileresprobcov,"probcov"); 
                   /* Eigen vectors */    strcat(fileresprobcov,fileres);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   /*v21=sqrt(1.-v11*v11); *//* error */      printf("Problem with resultfile: %s\n", fileresprobcov);
                   v21=(lc1-v1)/cv12*v11;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   v12=-v21;    }
                   v22=v11;    strcpy(fileresprobcor,"probcor"); 
                   tnalp=v21/v11;    strcat(fileresprobcor,fileres);
                   if(first1==1){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                     first1=0;      printf("Problem with resultfile: %s\n", fileresprobcor);
                     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);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   }    }
                   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("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   /*printf(fignu*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   if(first==1){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                     first=0;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                     fprintf(ficgp,"\nset parametric;unset label");    
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    fprintf(ficresprob,"# Age");
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);    fprintf(ficresprobcov,"# Age");
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    fprintf(ficresprobcov,"# Age");
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);  
                     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",\    for(i=1; i<=nlstate;i++)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\      for(j=1; j<=(nlstate+ndeath);j++){
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   }else{        fprintf(ficresprobcov," p%1d-%1d ",i,j);
                     first=0;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);      }  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    fprintf(ficresprob,"\n");
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    fprintf(ficresprobcov,"\n");
                     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",\    fprintf(ficresprobcor,"\n");
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    xp=vector(1,npar);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   }/* if first */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                 } /* age mod 5 */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               } /* end loop age */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);    first=1;
               first=1;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
             } /*l12 */      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           } /* k12 */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         } /*l1 */      exit(0);
       }/* k1 */    }
     } /* loop covariates */    else{
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);      fprintf(ficgp,"\n# Routine varprob");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      printf("Problem with html file: %s\n", optionfilehtm);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      exit(0);
   }    }
   free_vector(xp,1,npar);    else{
   fclose(ficresprob);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fclose(ficresprobcov);      fprintf(fichtm,"\n");
   fclose(ficresprobcor);  
   fclose(ficgp);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   fclose(fichtm);      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
 }      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   
     }
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    cov[1]=1;
                   int lastpass, int stepm, int weightopt, char model[],\    tj=cptcoveff;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   int popforecast, int estepm ,\    j1=0;
                   double jprev1, double mprev1,double anprev1, \    for(t=1; t<=tj;t++){
                   double jprev2, double mprev2,double anprev2){      for(i1=1; i1<=ncodemax[t];i1++){ 
   int jj1, k1, i1, cpt;        j1++;
   /*char optionfilehtm[FILENAMELENGTH];*/        if  (cptcovn>0) {
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {          fprintf(ficresprob, "\n#********** Variable "); 
     printf("Problem with %s \n",optionfilehtm), exit(0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);          fprintf(ficresprob, "**********\n#");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n          fprintf(ficresprobcov, "**********\n#");
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n          
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n          fprintf(ficgp, "\n#********** Variable "); 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  - Life expectancies by age and initial health status (estepm=%2d months):          fprintf(ficgp, "**********\n#");
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
  m=cptcoveff;          
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  jj1=0;          fprintf(ficgp, "**********\n#");    
  for(k1=1; k1<=m;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){        
      jj1++;        for (age=bage; age<=fage; age ++){ 
      if (cptcovn > 0) {          cov[2]=age;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          for (k=1; k<=cptcovn;k++) {
        for (cpt=1; cpt<=cptcoveff;cpt++)            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      }          for (k=1; k<=cptcovprod;k++)
      /* Pij */            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>          
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
      /* Quasi-incidences */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      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>          gp=vector(1,(nlstate)*(nlstate+ndeath));
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          gm=vector(1,(nlstate)*(nlstate+ndeath));
        /* Stable prevalence in each health state */      
        for(cpt=1; cpt<nlstate;cpt++){          for(theta=1; theta <=npar; theta++){
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            for(i=1; i<=npar; i++)
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }            
      for(cpt=1; cpt<=nlstate;cpt++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>            
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            k=0;
      }            for(i=1; i<= (nlstate); i++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              for(j=1; j<=(nlstate+ndeath);j++){
 health expectancies in states (1) and (2): e%s%d.png<br>                k=k+1;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                gp[k]=pmmij[i][j];
    } /* end i1 */              }
  }/* End k1 */            }
  fprintf(fichtm,"</ul>");            
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:0);
  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            pmij(pmmij,cov,ncovmodel,xp,nlstate);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n            k=0;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n            for(i=1; i<=(nlstate); i++){
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n              for(j=1; j<=(nlstate+ndeath);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                k=k+1;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n                gm[k]=pmmij[i][j];
  - 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       
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
         <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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
  m=cptcoveff;          
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
  jj1=0;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
  for(k1=1; k1<=m;k1++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
    for(i1=1; i1<=ncodemax[k1];i1++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      jj1++;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      if (cptcovn > 0) {  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          pmij(pmmij,cov,ncovmodel,x,nlstate);
        for (cpt=1; cpt<=cptcoveff;cpt++)          
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          k=0;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          for(i=1; i<=(nlstate); i++){
      }            for(j=1; j<=(nlstate+ndeath);j++){
      for(cpt=1; cpt<=nlstate;cpt++) {              k=k+1;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              mu[k][(int) age]=pmmij[i][j];
 interval) in state (%d): v%s%d%d.png <br>            }
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            }
      }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
    } /* end i1 */            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
  }/* End k1 */              varpij[i][j][(int)age] = doldm[i][j];
  fprintf(fichtm,"</ul>");  
 fclose(fichtm);          /*printf("\n%d ",(int)age);
 }            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]));
 /******************* Gnuplot file **************/            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){            }*/
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          fprintf(ficresprob,"\n%d ",(int)age);
   int ng;          fprintf(ficresprobcov,"\n%d ",(int)age);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          fprintf(ficresprobcor,"\n%d ",(int)age);
     printf("Problem with file %s",optionfilegnuplot);  
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);          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++){
 #ifdef windows            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     fprintf(ficgp,"cd \"%s\" \n",pathc);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 #endif          }
 m=pow(2,cptcoveff);          i=0;
            for (k=1; k<=(nlstate);k++){
  /* 1eme*/            for (l=1; l<=(nlstate+ndeath);l++){ 
   for (cpt=1; cpt<= nlstate ; cpt ++) {              i=i++;
    for (k1=1; k1<= m ; k1 ++) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
 #ifdef windows              for (j=1; j<=i;j++){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
      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);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
 #endif              }
 #ifdef unix            }
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          }/* end of loop for state */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        } /* end of loop for age */
 #endif  
         /* Confidence intervalle of pij  */
 for (i=1; i<= nlstate ; i ++) {        /*
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficgp,"\nset noparametric;unset label");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
 }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          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);
     for (i=1; i<= nlstate ; i ++) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
 }        */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        first1=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (k2=1; k2<=(nlstate);k2++){
 }            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            if(l2==k2) continue;
 #ifdef unix            j=(k2-1)*(nlstate+ndeath)+l2;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            for (k1=1; k1<=(nlstate);k1++){
 #endif              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
    }                if(l1==k1) continue;
   }                i=(k1-1)*(nlstate+ndeath)+l1;
   /*2 eme*/                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   for (k1=1; k1<= m ; k1 ++) {                  if ((int)age %5==0){
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                        cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     for (i=1; i<= nlstate+1 ; i ++) {                    mu1=mu[i][(int) age]/stepm*YEARM ;
       k=2*i;                    mu2=mu[j][(int) age]/stepm*YEARM;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                    c12=cv12/sqrt(v1*v2);
       for (j=1; j<= nlstate+1 ; j ++) {                    /* Computing eigen value of matrix of covariance */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 }                      /* Eigen vectors */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                    /*v21=sqrt(1.-v11*v11); *//* error */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                    v21=(lc1-v1)/cv12*v11;
       for (j=1; j<= nlstate+1 ; j ++) {                    v12=-v21;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                    v22=v11;
         else fprintf(ficgp," \%%*lf (\%%*lf)");                    tnalp=v21/v11;
 }                      if(first1==1){
       fprintf(ficgp,"\" t\"\" w l 0,");                      first1=0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
       for (j=1; j<= nlstate+1 ; j ++) {                    }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                    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);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                    /*printf(fignu*/
 }                      /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       else fprintf(ficgp,"\" t\"\" w l 0,");                    if(first==1){
     }                      first=0;
   }                      fprintf(ficgp,"\nset parametric;unset label");
                        fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   /*3eme*/                      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);
   for (k1=1; k1<= m ; k1 ++) {                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     for (cpt=1; cpt<= nlstate ; cpt ++) {                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       k=2+nlstate*(2*cpt-2);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       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,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);                    }else{
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");                      first=0;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       for (i=1; i< nlstate ; i ++) {                      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",\
         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);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       }                    }/* if first */
     }                  } /* age mod 5 */
   }                } /* end loop age */
                  fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   /* CV preval stat */                first=1;
     for (k1=1; k1<= m ; k1 ++) {              } /*l12 */
     for (cpt=1; cpt<nlstate ; cpt ++) {            } /* k12 */
       k=3;          } /*l1 */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }/* k1 */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      } /* loop covariates */
     }
       for (i=1; i< nlstate ; i ++)    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         fprintf(ficgp,"+$%d",k+i+1);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    free_vector(xp,1,npar);
          fclose(ficresprob);
       l=3+(nlstate+ndeath)*cpt;    fclose(ficresprobcov);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fclose(ficresprobcor);
       for (i=1; i< nlstate ; i ++) {    fclose(ficgp);
         l=3+(nlstate+ndeath)*cpt;    fclose(fichtm);
         fprintf(ficgp,"+$%d",l+i+1);  }
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
     }  /******************* Printing html file ***********/
   }    void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                      int lastpass, int stepm, int weightopt, char model[],\
   /* proba elementaires */                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
    for(i=1,jk=1; i <=nlstate; i++){                    int popforecast, int estepm ,\
     for(k=1; k <=(nlstate+ndeath); k++){                    double jprev1, double mprev1,double anprev1, \
       if (k != i) {                    double jprev2, double mprev2,double anprev2){
         for(j=1; j <=ncovmodel; j++){    int jj1, k1, i1, cpt;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    /*char optionfilehtm[FILENAMELENGTH];*/
           jk++;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           fprintf(ficgp,"\n");      printf("Problem with %s \n",optionfilehtm), exit(0);
         }      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
       }    }
     }  
    }     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
    - 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
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
      for(jk=1; jk <=m; jk++) {   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);   - Life expectancies by age and initial health status (estepm=%2d months): 
        if (ng==2)     <a href=\"e%s\">e%s</a> <br>\n</li>", \
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
        else  
          fprintf(ficgp,"\nset title \"Probability\"\n");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);  
        i=1;   m=cptcoveff;
        for(k2=1; k2<=nlstate; k2++) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
          k3=i;  
          for(k=1; k<=(nlstate+ndeath); k++) {   jj1=0;
            if (k != k2){   for(k1=1; k1<=m;k1++){
              if(ng==2)     for(i1=1; i1<=ncodemax[k1];i1++){
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);       jj1++;
              else       if (cptcovn > 0) {
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
              ij=1;         for (cpt=1; cpt<=cptcoveff;cpt++) 
              for(j=3; j <=ncovmodel; j++) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       }
                  ij++;       /* Pij */
                }       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>
                else  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       /* 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>
              fprintf(ficgp,")/(1");  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
                       /* Stable prevalence in each health state */
              for(k1=1; k1 <=nlstate; k1++){           for(cpt=1; cpt<nlstate;cpt++){
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
                ij=1;  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
                for(j=3; j <=ncovmodel; j++){         }
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       for(cpt=1; cpt<=nlstate;cpt++) {
                    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>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
                    ij++;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
                  }       }
                  else       fprintf(fichtm,"\n<br>- Total life expectancy by age and
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  health expectancies in states (1) and (2): e%s%d.png<br>
                }  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
                fprintf(ficgp,")");     } /* end i1 */
              }   }/* End k1 */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);   fprintf(fichtm,"</ul>");
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
              i=i+ncovmodel;  
            }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
          } /* end k */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
        } /* end k2 */   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
      } /* end jk */   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    } /* end ng */   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    fclose(ficgp);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
 }  /* end gnuplot */   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
 /*************** Moving average **************/   if(popforecast==1) fprintf(fichtm,"\n
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){   - 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
   int i, cpt, cptcod;          <br>",fileres,fileres,fileres,fileres);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)   else 
       for (i=1; i<=nlstate;i++)     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           mobaverage[(int)agedeb][i][cptcod]=0.;  
       m=cptcoveff;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   jj1=0;
           for (cpt=0;cpt<=4;cpt++){   for(k1=1; k1<=m;k1++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];     for(i1=1; i1<=ncodemax[k1];i1++){
           }       jj1++;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;       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<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
 /************** Forecasting ******************/  interval) in state (%d): v%s%d%d.png <br>
 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){  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
         }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;     } /* end i1 */
   int *popage;   }/* End k1 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   fprintf(fichtm,"</ul>");
   double *popeffectif,*popcount;  fclose(fichtm);
   double ***p3mat;  }
   char fileresf[FILENAMELENGTH];  
   /******************* Gnuplot file **************/
  agelim=AGESUP;  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    int ng;
      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        printf("Problem with file %s",optionfilegnuplot);
   strcpy(fileresf,"f");      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   strcat(fileresf,fileres);    }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);    /*#ifdef windows */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   printf("Computing forecasting: result on file '%s' \n", fileresf);  m=pow(2,cptcoveff);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    
    /* 1eme*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   if (mobilav==1) {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       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);
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   stepsize=(int) (stepm+YEARM-1)/YEARM;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   if (stepm<=12) stepsize=1;       }
         fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
   agelim=AGESUP;       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   hstepm=1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   hstepm=hstepm/stepm;       } 
   yp1=modf(dateintmean,&yp);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
   anprojmean=yp;       for (i=1; i<= nlstate ; i ++) {
   yp2=modf((yp1*12),&yp);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   mprojmean=yp;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   yp1=modf((yp2*30.5),&yp);       }  
   jprojmean=yp;       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   if(jprojmean==0) jprojmean=1;     }
   if(mprojmean==0) jprojmean=1;    }
      /*2 eme*/
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    
      for (k1=1; k1<= m ; k1 ++) { 
   for(cptcov=1;cptcov<=i2;cptcov++){      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       k=k+1;      
       fprintf(ficresf,"\n#******");      for (i=1; i<= nlstate+1 ; i ++) {
       for(j=1;j<=cptcoveff;j++) {        k=2*i;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       }        for (j=1; j<= nlstate+1 ; j ++) {
       fprintf(ficresf,"******\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficresf,"# StartingAge FinalAge");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }   
              if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
              else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         fprintf(ficresf,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }   
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficgp,"\" t\"\" w l 0,");
           nhstepm = nhstepm/hstepm;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
                  for (j=1; j<= nlstate+1 ; j ++) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           oldm=oldms;savm=savms;          else fprintf(ficgp," \%%*lf (\%%*lf)");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }   
                if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           for (h=0; h<=nhstepm; h++){        else fprintf(ficgp,"\" t\"\" w l 0,");
             if (h==(int) (calagedate+YEARM*cpt)) {      }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    }
             }    
             for(j=1; j<=nlstate+ndeath;j++) {    /*3eme*/
               kk1=0.;kk2=0;    
               for(i=1; i<=nlstate;i++) {                  for (k1=1; k1<= m ; k1 ++) { 
                 if (mobilav==1)      for (cpt=1; cpt<= nlstate ; cpt ++) {
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        k=2+nlstate*(2*cpt-2);
                 else {        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
                 }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
               }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               if (h==(int)(calagedate+12*cpt)){          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                 fprintf(ficresf," %.3f", kk1);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                                  fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
               }          
             }        */
           }        for (i=1; i< nlstate ; i ++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
         }          
       }        } 
     }      }
   }    }
            
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
   fclose(ficresf);      for (cpt=1; cpt<nlstate ; cpt ++) {
 }        k=3;
 /************** Forecasting ******************/        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        fprintf(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);
          
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for (i=1; i< nlstate ; i ++)
   int *popage;          fprintf(ficgp,"+$%d",k+i+1);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   double *popeffectif,*popcount;        
   double ***p3mat,***tabpop,***tabpopprev;        l=3+(nlstate+ndeath)*cpt;
   char filerespop[FILENAMELENGTH];        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          l=3+(nlstate+ndeath)*cpt;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"+$%d",l+i+1);
   agelim=AGESUP;        }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
        } 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }  
      
      /* proba elementaires */
   strcpy(filerespop,"pop");    for(i=1,jk=1; i <=nlstate; i++){
   strcat(filerespop,fileres);      for(k=1; k <=(nlstate+ndeath); k++){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        if (k != i) {
     printf("Problem with forecast resultfile: %s\n", filerespop);          for(j=1; j <=ncovmodel; j++){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   }            jk++; 
   printf("Computing forecasting: result on file '%s' \n", filerespop);            fprintf(ficgp,"\n");
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          }
         }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      }
      }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);       for(jk=1; jk <=m; jk++) {
   }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
   stepsize=(int) (stepm+YEARM-1)/YEARM;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   if (stepm<=12) stepsize=1;         else
             fprintf(ficgp,"\nset title \"Probability\"\n");
   agelim=AGESUP;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           i=1;
   hstepm=1;         for(k2=1; k2<=nlstate; k2++) {
   hstepm=hstepm/stepm;           k3=i;
             for(k=1; k<=(nlstate+ndeath); k++) {
   if (popforecast==1) {             if (k != k2){
     if((ficpop=fopen(popfile,"r"))==NULL) {               if(ng==2)
       printf("Problem with population file : %s\n",popfile);exit(0);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);               else
     }                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     popage=ivector(0,AGESUP);               ij=1;
     popeffectif=vector(0,AGESUP);               for(j=3; j <=ncovmodel; j++) {
     popcount=vector(0,AGESUP);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                       fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     i=1;                     ij++;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                 }
                     else
     imx=i;                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];               }
   }               fprintf(ficgp,")/(1");
                
   for(cptcov=1;cptcov<=i2;cptcov++){               for(k1=1; k1 <=nlstate; k1++){   
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       k=k+1;                 ij=1;
       fprintf(ficrespop,"\n#******");                 for(j=3; j <=ncovmodel; j++){
       for(j=1;j<=cptcoveff;j++) {                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       }                     ij++;
       fprintf(ficrespop,"******\n");                   }
       fprintf(ficrespop,"# Age");                   else
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       if (popforecast==1)  fprintf(ficrespop," [Population]");                 }
                       fprintf(ficgp,")");
       for (cpt=0; cpt<=0;cpt++) {               }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                 fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                       if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){               i=i+ncovmodel;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);             }
           nhstepm = nhstepm/hstepm;           } /* end k */
                   } /* end k2 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       } /* end jk */
           oldm=oldms;savm=savms;     } /* end ng */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       fclose(ficgp); 
          }  /* end gnuplot */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*************** Moving average **************/
             }  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    int i, cpt, cptcod;
               for(i=1; i<=nlstate;i++) {                  int modcovmax =1;
                 if (mobilav==1)    int mobilavrange, mob;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double age;
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                 }                             a covariate has 2 modalities */
               }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   /*fprintf(ficrespop," %.3f", kk1);      if(mobilav==1) mobilavrange=5; /* default */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      else mobilavrange=mobilav;
               }      for (age=bage; age<=fage; age++)
             }        for (i=1; i<=nlstate;i++)
             for(i=1; i<=nlstate;i++){          for (cptcod=1;cptcod<=modcovmax;cptcod++)
               kk1=0.;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                 for(j=1; j<=nlstate;j++){      /* We keep the original values on the extreme ages bage, fage and for 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];         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. 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      */ 
             }      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          for (i=1; i<=nlstate;i++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
           }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
         }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                  }
   /******/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          }/* end age */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      }/* end mob */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    }else return -1;
           nhstepm = nhstepm/hstepm;    return 0;
            }/* End movingaverage */
           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);    /************** Forecasting ******************/
           for (h=0; h<=nhstepm; h++){  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 (h==(int) (calagedate+YEARM*cpt)) {    
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
             }    int *popage;
             for(j=1; j<=nlstate+ndeath;j++) {    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
               kk1=0.;kk2=0;    double *popeffectif,*popcount;
               for(i=1; i<=nlstate;i++) {                  double ***p3mat;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double ***mobaverage;
               }    char fileresf[FILENAMELENGTH];
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }   agelim=AGESUP;
           }   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
       }   
    }   
   }    strcpy(fileresf,"f"); 
      strcat(fileresf,fileres);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
   if (popforecast==1) {      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     free_vector(popcount,0,AGESUP);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);    if (mobilav!=0) {
 }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
 /***********************************************/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 /**************** Main Program *****************/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 /***********************************************/      }
     }
 int main(int argc, char *argv[])  
 {    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    
   double agedeb, agefin,hf;    agelim=AGESUP;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    
     hstepm=1;
   double fret;    hstepm=hstepm/stepm; 
   double **xi,tmp,delta;    yp1=modf(dateintmean,&yp);
     anprojmean=yp;
   double dum; /* Dummy variable */    yp2=modf((yp1*12),&yp);
   double ***p3mat;    mprojmean=yp;
   int *indx;    yp1=modf((yp2*30.5),&yp);
   char line[MAXLINE], linepar[MAXLINE];    jprojmean=yp;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    if(jprojmean==0) jprojmean=1;
   int firstobs=1, lastobs=10;    if(mprojmean==0) jprojmean=1;
   int sdeb, sfin; /* Status at beginning and end */    
   int c,  h , cpt,l;    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
   int ju,jl, mi;    
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    for(cptcov=1;cptcov<=i2;cptcov++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   int mobilav=0,popforecast=0;        k=k+1;
   int hstepm, nhstepm;        fprintf(ficresf,"\n#******");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;        fprintf(ficresf,"******\n");
   double **prlim;        fprintf(ficresf,"# StartingAge FinalAge");
   double *severity;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
   double ***param; /* Matrix of parameters */        
   double  *p;        
   double **matcov; /* Matrix of covariance */        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
   double ***delti3; /* Scale */          fprintf(ficresf,"\n");
   double *delti; /* Scale */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   double *epj, vepp;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   double kk1, kk2;            nhstepm = nhstepm/hstepm; 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            
              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   char *alph[]={"a","a","b","c","d","e"}, str[4];            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
   char z[1]="c", occ;              if (h==(int) (calagedate+YEARM*cpt)) {
 #include <sys/time.h>                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
 #include <time.h>              } 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              for(j=1; j<=nlstate+ndeath;j++) {
                  kk1=0.;kk2=0;
   /* long total_usecs;                for(i=1; i<=nlstate;i++) {              
   struct timeval start_time, end_time;                  if (mobilav==1) 
                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                  else {
   getcwd(pathcd, size);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
   printf("\n%s",version);                  
   if(argc <=1){                }
     printf("\nEnter the parameter file name: ");                if (h==(int)(calagedate+12*cpt)){
     scanf("%s",pathtot);                  fprintf(ficresf," %.3f", kk1);
   }                          
   else{                }
     strcpy(pathtot,argv[1]);              }
   }            }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*cygwin_split_path(pathtot,path,optionfile);          }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        }
   /* cutv(path,optionfile,pathtot,'\\');*/      }
     }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);         
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   chdir(path);  
   replace(pathc,path);    fclose(ficresf);
   }
 /*-------- arguments in the command line --------*/  /************** 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){
   /* Log file */    
   strcat(filelog, optionfilefiname);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   strcat(filelog,".log");    /* */    int *popage;
   if((ficlog=fopen(filelog,"w"))==NULL)    {    double calagedate, agelim, kk1, kk2;
     printf("Problem with logfile %s\n",filelog);    double *popeffectif,*popcount;
     goto end;    double ***p3mat,***tabpop,***tabpopprev;
   }    double ***mobaverage;
   fprintf(ficlog,"Log filename:%s\n",filelog);    char filerespop[FILENAMELENGTH];
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fflush(ficlog);    agelim=AGESUP;
     calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   /* */    
   strcpy(fileres,"r");    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   strcat(fileres, optionfilefiname);    
   strcat(fileres,".txt");    /* Other files have txt extension */    
     strcpy(filerespop,"pop"); 
   /*---------arguments file --------*/    strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      printf("Problem with forecast resultfile: %s\n", filerespop);
     printf("Problem with optionfile %s\n",optionfile);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    }
     goto end;    printf("Computing forecasting: result on file '%s' \n", filerespop);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
   strcpy(filereso,"o");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    if (mobilav!=0) {
     printf("Problem with Output resultfile: %s\n", filereso);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     goto end;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     fgets(line, MAXLINE, ficpar);    if (stepm<=12) stepsize=1;
     puts(line);    
     fputs(line,ficparo);    agelim=AGESUP;
   }    
   ungetc(c,ficpar);    hstepm=1;
     hstepm=hstepm/stepm; 
   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);    if (popforecast==1) {
   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);      if((ficpop=fopen(popfile,"r"))==NULL) {
 while((c=getc(ficpar))=='#' && c!= EOF){        printf("Problem with population file : %s\n",popfile);exit(0);
     ungetc(c,ficpar);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);      popage=ivector(0,AGESUP);
     fputs(line,ficparo);      popeffectif=vector(0,AGESUP);
   }      popcount=vector(0,AGESUP);
   ungetc(c,ficpar);      
        i=1;   
          while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   covar=matrix(0,NCOVMAX,1,n);     
   cptcovn=0;      imx=i;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for(cptcov=1;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /* Read guess parameters */        k=k+1;
   /* Reads comments: lines beginning with '#' */        fprintf(ficrespop,"\n#******");
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1;j<=cptcoveff;j++) {
     ungetc(c,ficpar);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        fprintf(ficrespop,"******\n");
     fputs(line,ficparo);        fprintf(ficrespop,"# Age");
   }        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   ungetc(c,ficpar);        if (popforecast==1)  fprintf(ficrespop," [Population]");
          
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for (cpt=0; cpt<=0;cpt++) { 
     for(i=1; i <=nlstate; i++)          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     for(j=1; j <=nlstate+ndeath-1; j++){          
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
       fprintf(ficparo,"%1d%1d",i1,j1);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       if(mle==1)            nhstepm = nhstepm/hstepm; 
         printf("%1d%1d",i,j);            
       fprintf(ficlog,"%1d%1d",i,j);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(k=1; k<=ncovmodel;k++){            oldm=oldms;savm=savms;
         fscanf(ficpar," %lf",&param[i][j][k]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         if(mle==1){          
           printf(" %lf",param[i][j][k]);            for (h=0; h<=nhstepm; h++){
           fprintf(ficlog," %lf",param[i][j][k]);              if (h==(int) (calagedate+YEARM*cpt)) {
         }                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         else              } 
           fprintf(ficlog," %lf",param[i][j][k]);              for(j=1; j<=nlstate+ndeath;j++) {
         fprintf(ficparo," %lf",param[i][j][k]);                kk1=0.;kk2=0;
       }                for(i=1; i<=nlstate;i++) {              
       fscanf(ficpar,"\n");                  if (mobilav==1) 
       if(mle==1)                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         printf("\n");                  else {
       fprintf(ficlog,"\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       fprintf(ficparo,"\n");                  }
     }                }
                  if (h==(int)(calagedate+12*cpt)){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
   p=param[1][1];                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                  }
   /* Reads comments: lines beginning with '#' */              }
   while((c=getc(ficpar))=='#' && c!= EOF){              for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);                kk1=0.;
     fgets(line, MAXLINE, ficpar);                  for(j=1; j<=nlstate;j++){
     puts(line);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     fputs(line,ficparo);                  }
   }                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
   ungetc(c,ficpar);              }
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   for(i=1; i <=nlstate; i++){            }
     for(j=1; j <=nlstate+ndeath-1; j++){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       printf("%1d%1d",i,j);        }
       fprintf(ficparo,"%1d%1d",i1,j1);   
       for(k=1; k<=ncovmodel;k++){    /******/
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficparo," %le",delti3[i][j][k]);          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--){ 
       fscanf(ficpar,"\n");            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       printf("\n");            nhstepm = nhstepm/hstepm; 
       fprintf(ficparo,"\n");            
     }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }            oldm=oldms;savm=savms;
   delti=delti3[1][1];            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
              for (h=0; h<=nhstepm; h++){
   /* Reads comments: lines beginning with '#' */              if (h==(int) (calagedate+YEARM*cpt)) {
   while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     ungetc(c,ficpar);              } 
     fgets(line, MAXLINE, ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
     puts(line);                kk1=0.;kk2=0;
     fputs(line,ficparo);                for(i=1; i<=nlstate;i++) {              
   }                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   ungetc(c,ficpar);                }
                  if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
   matcov=matrix(1,npar,1,npar);              }
   for(i=1; i <=npar; i++){            }
     fscanf(ficpar,"%s",&str);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if(mle==1)          }
       printf("%s",str);        }
     fprintf(ficlog,"%s",str);     } 
     fprintf(ficparo,"%s",str);    }
     for(j=1; j <=i; j++){   
       fscanf(ficpar," %le",&matcov[i][j]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if(mle==1){  
         printf(" %.5le",matcov[i][j]);    if (popforecast==1) {
         fprintf(ficlog," %.5le",matcov[i][j]);      free_ivector(popage,0,AGESUP);
       }      free_vector(popeffectif,0,AGESUP);
       else      free_vector(popcount,0,AGESUP);
         fprintf(ficlog," %.5le",matcov[i][j]);    }
       fprintf(ficparo," %.5le",matcov[i][j]);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fscanf(ficpar,"\n");    fclose(ficrespop);
     if(mle==1)  }
       printf("\n");  
     fprintf(ficlog,"\n");  /***********************************************/
     fprintf(ficparo,"\n");  /**************** Main Program *****************/
   }  /***********************************************/
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  int main(int argc, char *argv[])
       matcov[i][j]=matcov[j][i];  {
        int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   if(mle==1)    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     printf("\n");    double agedeb, agefin,hf;
   fprintf(ficlog,"\n");    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     /*-------- Rewriting paramater file ----------*/    double **xi,tmp,delta;
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    double dum; /* Dummy variable */
      strcat(rfileres,".");    /* */    double ***p3mat;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    double ***mobaverage;
     if((ficres =fopen(rfileres,"w"))==NULL) {    int *indx;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    char line[MAXLINE], linepar[MAXLINE];
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     }    int firstobs=1, lastobs=10;
     fprintf(ficres,"#%s\n",version);    int sdeb, sfin; /* Status at beginning and end */
        int c,  h , cpt,l;
     /*-------- data file ----------*/    int ju,jl, mi;
     if((fic=fopen(datafile,"r"))==NULL)    {    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       printf("Problem with datafile: %s\n", datafile);goto end;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;    int mobilav=0,popforecast=0;
     }    int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
     n= lastobs;  
     severity = vector(1,maxwav);    double bage, fage, age, agelim, agebase;
     outcome=imatrix(1,maxwav+1,1,n);    double ftolpl=FTOL;
     num=ivector(1,n);    double **prlim;
     moisnais=vector(1,n);    double *severity;
     annais=vector(1,n);    double ***param; /* Matrix of parameters */
     moisdc=vector(1,n);    double  *p;
     andc=vector(1,n);    double **matcov; /* Matrix of covariance */
     agedc=vector(1,n);    double ***delti3; /* Scale */
     cod=ivector(1,n);    double *delti; /* Scale */
     weight=vector(1,n);    double ***eij, ***vareij;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **varpl; /* Variances of prevalence limits by age */
     mint=matrix(1,maxwav,1,n);    double *epj, vepp;
     anint=matrix(1,maxwav,1,n);    double kk1, kk2;
     s=imatrix(1,maxwav+1,1,n);    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);    char *alph[]={"a","a","b","c","d","e"}, str[4];
     ncodemax=ivector(1,8);  
   
     i=1;    char z[1]="c", occ;
     while (fgets(line, MAXLINE, fic) != NULL)    {  #include <sys/time.h>
       if ((i >= firstobs) && (i <=lastobs)) {  #include <time.h>
            char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
         for (j=maxwav;j>=1;j--){   
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    /* long total_usecs;
           strcpy(line,stra);       struct timeval start_time, end_time;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         }    getcwd(pathcd, size);
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    printf("\n%s",version);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    if(argc <=1){
       printf("\nEnter the parameter file name: ");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      scanf("%s",pathtot);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     else{
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      strcpy(pathtot,argv[1]);
         for (j=ncovcol;j>=1;j--){    }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
         }    /*cygwin_split_path(pathtot,path,optionfile);
         num[i]=atol(stra);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
            /* cutv(path,optionfile,pathtot,'\\');*/
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
         i=i+1;    chdir(path);
       }    replace(pathc,path);
     }  
     /* printf("ii=%d", ij);    /*-------- arguments in the command line --------*/
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */    /* Log file */
     strcat(filelog, optionfilefiname);
   /* for (i=1; i<=imx; i++){    strcat(filelog,".log");    /* */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    if((ficlog=fopen(filelog,"w"))==NULL)    {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      printf("Problem with logfile %s\n",filelog);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      goto end;
     }*/    }
    /*  for (i=1; i<=imx; i++){    fprintf(ficlog,"Log filename:%s\n",filelog);
      if (s[4][i]==9)  s[4][i]=-1;    fprintf(ficlog,"\n%s",version);
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/    fprintf(ficlog,"\nEnter the parameter file name: ");
      fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
      fflush(ficlog);
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */    /* */
   Tprod=ivector(1,15);    strcpy(fileres,"r");
   Tvaraff=ivector(1,15);    strcat(fileres, optionfilefiname);
   Tvard=imatrix(1,15,1,2);    strcat(fileres,".txt");    /* Other files have txt extension */
   Tage=ivector(1,15);        
        /*---------arguments file --------*/
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     j=nbocc(model,'+');      printf("Problem with optionfile %s\n",optionfile);
     j1=nbocc(model,'*');      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     cptcovn=j+1;      goto end;
     cptcovprod=j1;    }
      
     strcpy(modelsav,model);    strcpy(filereso,"o");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    strcat(filereso,fileres);
       printf("Error. Non available option model=%s ",model);    if((ficparo=fopen(filereso,"w"))==NULL) {
       fprintf(ficlog,"Error. Non available option model=%s ",model);      printf("Problem with Output resultfile: %s\n", filereso);
       goto end;      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
     }      goto end;
        }
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    /* Reads comments: lines beginning with '#' */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    while((c=getc(ficpar))=='#' && c!= EOF){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      ungetc(c,ficpar);
       /*scanf("%d",i);*/      fgets(line, MAXLINE, ficpar);
       if (strchr(strb,'*')) {  /* Model includes a product */      puts(line);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/      fputs(line,ficparo);
         if (strcmp(strc,"age")==0) { /* Vn*age */    }
           cptcovprod--;    ungetc(c,ficpar);
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    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);
           cptcovage++;    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);
             Tage[cptcovage]=i;    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);
             /*printf("stre=%s ", stre);*/    while((c=getc(ficpar))=='#' && c!= EOF){
         }      ungetc(c,ficpar);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      fgets(line, MAXLINE, ficpar);
           cptcovprod--;      puts(line);
           cutv(strb,stre,strc,'V');      fputs(line,ficparo);
           Tvar[i]=atoi(stre);    }
           cptcovage++;    ungetc(c,ficpar);
           Tage[cptcovage]=i;    
         }     
         else {  /* Age is not in the model */    covar=matrix(0,NCOVMAX,1,n); 
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
           Tvar[i]=ncovcol+k1;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */  
           Tprod[k1]=i;    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
           Tvard[k1][1]=atoi(strc); /* m*/    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
           Tvard[k1][2]=atoi(stre); /* n */    
           Tvar[cptcovn+k2]=Tvard[k1][1];    /* Read guess parameters */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    /* Reads comments: lines beginning with '#' */
           for (k=1; k<=lastobs;k++)    while((c=getc(ficpar))=='#' && c!= EOF){
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      ungetc(c,ficpar);
           k1++;      fgets(line, MAXLINE, ficpar);
           k2=k2+2;      puts(line);
         }      fputs(line,ficparo);
       }    }
       else { /* no more sum */    ungetc(c,ficpar);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    
        /*  scanf("%d",i);*/    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       cutv(strd,strc,strb,'V');    for(i=1; i <=nlstate; i++)
       Tvar[i]=atoi(strc);      for(j=1; j <=nlstate+ndeath-1; j++){
       }        fscanf(ficpar,"%1d%1d",&i1,&j1);
       strcpy(modelsav,stra);          fprintf(ficparo,"%1d%1d",i1,j1);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        if(mle==1)
         scanf("%d",i);*/          printf("%1d%1d",i,j);
     } /* end of loop + */        fprintf(ficlog,"%1d%1d",i,j);
   } /* end model */        for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar," %lf",&param[i][j][k]);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          if(mle==1){
   printf("cptcovprod=%d ", cptcovprod);            printf(" %lf",param[i][j][k]);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);            fprintf(ficlog," %lf",param[i][j][k]);
   scanf("%d ",i);*/          }
     fclose(fic);          else
             fprintf(ficlog," %lf",param[i][j][k]);
     /*  if(mle==1){*/          fprintf(ficparo," %lf",param[i][j][k]);
     if (weightopt != 1) { /* Maximisation without weights*/        }
       for(i=1;i<=n;i++) weight[i]=1.0;        fscanf(ficpar,"\n");
     }        if(mle==1)
     /*-calculation of age at interview from date of interview and age at death -*/          printf("\n");
     agev=matrix(1,maxwav,1,imx);        fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
     for (i=1; i<=imx; i++) {      }
       for(m=2; (m<= maxwav); m++) {    
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
          anint[m][i]=9999;  
          s[m][i]=-1;    p=param[1][1];
        }    
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    /* Reads comments: lines beginning with '#' */
       }    while((c=getc(ficpar))=='#' && c!= EOF){
     }      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
     for (i=1; i<=imx; i++)  {      puts(line);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      fputs(line,ficparo);
       for(m=1; (m<= maxwav); m++){    }
         if(s[m][i] >0){    ungetc(c,ficpar);
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
               if(moisdc[i]!=99 && andc[i]!=9999)    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
                 agev[m][i]=agedc[i];    for(i=1; i <=nlstate; i++){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      for(j=1; j <=nlstate+ndeath-1; j++){
            else {        fscanf(ficpar,"%1d%1d",&i1,&j1);
               if (andc[i]!=9999){        printf("%1d%1d",i,j);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        fprintf(ficparo,"%1d%1d",i1,j1);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);        for(k=1; k<=ncovmodel;k++){
               agev[m][i]=-1;          fscanf(ficpar,"%le",&delti3[i][j][k]);
               }          printf(" %le",delti3[i][j][k]);
             }          fprintf(ficparo," %le",delti3[i][j][k]);
           }        }
           else if(s[m][i] !=9){ /* Should no more exist */        fscanf(ficpar,"\n");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        printf("\n");
             if(mint[m][i]==99 || anint[m][i]==9999)        fprintf(ficparo,"\n");
               agev[m][i]=1;      }
             else if(agev[m][i] <agemin){    }
               agemin=agev[m][i];    delti=delti3[1][1];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    
             }    /* Reads comments: lines beginning with '#' */
             else if(agev[m][i] >agemax){    while((c=getc(ficpar))=='#' && c!= EOF){
               agemax=agev[m][i];      ungetc(c,ficpar);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fgets(line, MAXLINE, ficpar);
             }      puts(line);
             /*agev[m][i]=anint[m][i]-annais[i];*/      fputs(line,ficparo);
             /*   agev[m][i] = age[i]+2*m;*/    }
           }    ungetc(c,ficpar);
           else { /* =9 */    
             agev[m][i]=1;    matcov=matrix(1,npar,1,npar);
             s[m][i]=-1;    for(i=1; i <=npar; i++){
           }      fscanf(ficpar,"%s",&str);
         }      if(mle==1)
         else /*= 0 Unknown */        printf("%s",str);
           agev[m][i]=1;      fprintf(ficlog,"%s",str);
       }      fprintf(ficparo,"%s",str);
          for(j=1; j <=i; j++){
     }        fscanf(ficpar," %le",&matcov[i][j]);
     for (i=1; i<=imx; i++)  {        if(mle==1){
       for(m=1; (m<= maxwav); m++){          printf(" %.5le",matcov[i][j]);
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(ficlog," %.5le",matcov[i][j]);
           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);          else
           goto end;          fprintf(ficlog," %.5le",matcov[i][j]);
         }        fprintf(ficparo," %.5le",matcov[i][j]);
       }      }
     }      fscanf(ficpar,"\n");
       if(mle==1)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        printf("\n");
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     free_vector(severity,1,maxwav);    }
     free_imatrix(outcome,1,maxwav+1,1,n);    for(i=1; i <=npar; i++)
     free_vector(moisnais,1,n);      for(j=i+1;j<=npar;j++)
     free_vector(annais,1,n);        matcov[i][j]=matcov[j][i];
     /* free_matrix(mint,1,maxwav,1,n);     
        free_matrix(anint,1,maxwav,1,n);*/    if(mle==1)
     free_vector(moisdc,1,n);      printf("\n");
     free_vector(andc,1,n);    fprintf(ficlog,"\n");
   
      
     wav=ivector(1,imx);    /*-------- Rewriting paramater file ----------*/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    strcpy(rfileres,"r");    /* "Rparameterfile */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
        strcat(rfileres,".");    /* */
     /* Concatenates waves */    strcat(rfileres,optionfilext);    /* Other files have txt extension */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       Tcode=ivector(1,100);    }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficres,"#%s\n",version);
       ncodemax[1]=1;      
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    /*-------- data file ----------*/
          if((fic=fopen(datafile,"r"))==NULL)    {
    codtab=imatrix(1,100,1,10);      printf("Problem with datafile: %s\n", datafile);goto end;
    h=0;      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
    m=pow(2,cptcoveff);    }
    
    for(k=1;k<=cptcoveff; k++){    n= lastobs;
      for(i=1; i <=(m/pow(2,k));i++){    severity = vector(1,maxwav);
        for(j=1; j <= ncodemax[k]; j++){    outcome=imatrix(1,maxwav+1,1,n);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    num=ivector(1,n);
            h++;    moisnais=vector(1,n);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    annais=vector(1,n);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    moisdc=vector(1,n);
          }    andc=vector(1,n);
        }    agedc=vector(1,n);
      }    cod=ivector(1,n);
    }    weight=vector(1,n);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
       codtab[1][2]=1;codtab[2][2]=2; */    mint=matrix(1,maxwav,1,n);
    /* for(i=1; i <=m ;i++){    anint=matrix(1,maxwav,1,n);
       for(k=1; k <=cptcovn; k++){    s=imatrix(1,maxwav+1,1,n);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    tab=ivector(1,NCOVMAX);
       }    ncodemax=ivector(1,8);
       printf("\n");  
       }    i=1;
       scanf("%d",i);*/    while (fgets(line, MAXLINE, fic) != NULL)    {
          if ((i >= firstobs) && (i <=lastobs)) {
    /* Calculates basic frequencies. Computes observed prevalence at single age          
        and prints on file fileres'p'. */        for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
              strcpy(line,stra);
              cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
     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 */        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
        
     /* For Powell, parameters are in a vector p[] starting at p[1]        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
     if(mle==1){        for (j=ncovcol;j>=1;j--){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
     }        } 
            num[i]=atol(stra);
     /*--------- 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((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
            printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
    jk=1;        i=i+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");    /* printf("ii=%d", ij);
    for(i=1,jk=1; i <=nlstate; i++){       scanf("%d",i);*/
      for(k=1; k <=(nlstate+ndeath); k++){    imx=i-1; /* Number of individuals */
        if (k != i)  
          {    /* for (i=1; i<=imx; i++){
            printf("%d%d ",i,k);      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
            fprintf(ficlog,"%d%d ",i,k);      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
            fprintf(ficres,"%1d%1d ",i,k);      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
            for(j=1; j <=ncovmodel; j++){      }*/
              printf("%f ",p[jk]);     /*  for (i=1; i<=imx; i++){
              fprintf(ficlog,"%f ",p[jk]);       if (s[4][i]==9)  s[4][i]=-1; 
              fprintf(ficres,"%f ",p[jk]);       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]));}*/
              jk++;    
            }   
            printf("\n");    /* Calculation of the number of parameter from char model*/
            fprintf(ficlog,"\n");    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
            fprintf(ficres,"\n");    Tprod=ivector(1,15); 
          }    Tvaraff=ivector(1,15); 
      }    Tvard=imatrix(1,15,1,2);
    }    Tage=ivector(1,15);      
    if(mle==1){     
      /* Computing hessian and covariance matrix */    if (strlen(model) >1){ /* If there is at least 1 covariate */
      ftolhess=ftol; /* Usually correct */      j=0, j1=0, k1=1, k2=1;
      hesscov(matcov, p, npar, delti, ftolhess, func);      j=nbocc(model,'+'); /* j=Number of '+' */
    }      j1=nbocc(model,'*'); /* j1=Number of '*' */
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      cptcovn=j+1; 
    printf("# Scales (for hessian or gradient estimation)\n");      cptcovprod=j1; /*Number of products */
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      
    for(i=1,jk=1; i <=nlstate; i++){      strcpy(modelsav,model); 
      for(j=1; j <=nlstate+ndeath; j++){      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
        if (j!=i) {        printf("Error. Non available option model=%s ",model);
          fprintf(ficres,"%1d%1d",i,j);        fprintf(ficlog,"Error. Non available option model=%s ",model);
          printf("%1d%1d",i,j);        goto end;
          fprintf(ficlog,"%1d%1d",i,j);      }
          for(k=1; k<=ncovmodel;k++){      
            printf(" %.5e",delti[jk]);      /* This loop fills the array Tvar from the string 'model'.*/
            fprintf(ficlog," %.5e",delti[jk]);  
            fprintf(ficres," %.5e",delti[jk]);      for(i=(j+1); i>=1;i--){
            jk++;        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
          }        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
          printf("\n");        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
          fprintf(ficlog,"\n");        /*scanf("%d",i);*/
          fprintf(ficres,"\n");        if (strchr(strb,'*')) {  /* Model includes a product */
        }          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
      }          if (strcmp(strc,"age")==0) { /* Vn*age */
    }            cptcovprod--;
                cutv(strb,stre,strd,'V');
    k=1;            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
    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");            cptcovage++;
    if(mle==1)              Tage[cptcovage]=i;
      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");              /*printf("stre=%s ", stre);*/
    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;i<=npar;i++){          else if (strcmp(strd,"age")==0) { /* or age*Vn */
      /*  if (k>nlstate) k=1;            cptcovprod--;
          i1=(i-1)/(ncovmodel*nlstate)+1;            cutv(strb,stre,strc,'V');
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            Tvar[i]=atoi(stre);
          printf("%s%d%d",alph[k],i1,tab[i]);*/            cptcovage++;
      fprintf(ficres,"%3d",i);            Tage[cptcovage]=i;
      if(mle==1)          }
        printf("%3d",i);          else {  /* Age is not in the model */
      fprintf(ficlog,"%3d",i);            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
      for(j=1; j<=i;j++){            Tvar[i]=ncovcol+k1;
        fprintf(ficres," %.5e",matcov[i][j]);            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
        if(mle==1)            Tprod[k1]=i;
          printf(" %.5e",matcov[i][j]);            Tvard[k1][1]=atoi(strc); /* m*/
        fprintf(ficlog," %.5e",matcov[i][j]);            Tvard[k1][2]=atoi(stre); /* n */
      }            Tvar[cptcovn+k2]=Tvard[k1][1];
      fprintf(ficres,"\n");            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
      if(mle==1)            for (k=1; k<=lastobs;k++) 
        printf("\n");              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
      fprintf(ficlog,"\n");            k1++;
      k++;            k2=k2+2;
    }          }
            }
    while((c=getc(ficpar))=='#' && c!= EOF){        else { /* no more sum */
      ungetc(c,ficpar);          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
      fgets(line, MAXLINE, ficpar);         /*  scanf("%d",i);*/
      puts(line);        cutv(strd,strc,strb,'V');
      fputs(line,ficparo);        Tvar[i]=atoi(strc);
    }        }
    ungetc(c,ficpar);        strcpy(modelsav,stra);  
    estepm=0;        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);          scanf("%d",i);*/
    if (estepm==0 || estepm < stepm) estepm=stepm;      } /* end of loop + */
    if (fage <= 2) {    } /* end model */
      bage = ageminpar;    
      fage = agemaxpar;    /*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*/
      
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    printf("cptcovprod=%d ", cptcovprod);
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
      
    while((c=getc(ficpar))=='#' && c!= EOF){    scanf("%d ",i);
      ungetc(c,ficpar);    fclose(fic);*/
      fgets(line, MAXLINE, ficpar);  
      puts(line);      /*  if(mle==1){*/
      fputs(line,ficparo);    if (weightopt != 1) { /* Maximisation without weights*/
    }      for(i=1;i<=n;i++) weight[i]=1.0;
    ungetc(c,ficpar);    }
        /*-calculation of age at interview from date of interview and age at death -*/
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    agev=matrix(1,maxwav,1,imx);
    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);    for (i=1; i<=imx; i++) {
          for(m=2; (m<= maxwav); m++) {
    while((c=getc(ficpar))=='#' && c!= EOF){        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
      ungetc(c,ficpar);          anint[m][i]=9999;
      fgets(line, MAXLINE, ficpar);          s[m][i]=-1;
      puts(line);        }
      fputs(line,ficparo);        if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
    }      }
    ungetc(c,ficpar);    }
    
     for (i=1; i<=imx; i++)  {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
   fscanf(ficpar,"pop_based=%d\n",&popbased);          if (s[m][i] >= nlstate+1) {
   fprintf(ficparo,"pop_based=%d\n",popbased);              if(agedc[i]>0)
   fprintf(ficres,"pop_based=%d\n",popbased);                if(moisdc[i]!=99 && andc[i]!=9999)
                  agev[m][i]=agedc[i];
   while((c=getc(ficpar))=='#' && c!= EOF){            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
     ungetc(c,ficpar);              else {
     fgets(line, MAXLINE, ficpar);                if (andc[i]!=9999){
     puts(line);                  printf("Warning negative age at death: %d line:%d\n",num[i],i);
     fputs(line,ficparo);                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
   }                  agev[m][i]=-1;
   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);          }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          else if(s[m][i] !=9){ /* Should no more exist */
 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);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
 while((c=getc(ficpar))=='#' && c!= EOF){            else if(agev[m][i] <agemin){ 
     ungetc(c,ficpar);              agemin=agev[m][i];
     fgets(line, MAXLINE, ficpar);              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
     puts(line);            }
     fputs(line,ficparo);            else if(agev[m][i] >agemax){
   }              agemax=agev[m][i];
   ungetc(c,ficpar);              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            /*agev[m][i]=anint[m][i]-annais[i];*/
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            /*     agev[m][i] = age[i]+2*m;*/
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          }
           else { /* =9 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            agev[m][i]=1;
             s[m][i]=-1;
 /*------------ gnuplot -------------*/          }
   strcpy(optionfilegnuplot,optionfilefiname);        }
   strcat(optionfilegnuplot,".gp");        else /*= 0 Unknown */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          agev[m][i]=1;
     printf("Problem with file %s",optionfilegnuplot);      }
   }      
   fclose(ficgp);    }
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    for (i=1; i<=imx; i++)  {
 /*--------- index.htm --------*/      for(m=1; (m<= maxwav); m++){
         if (s[m][i] > (nlstate+ndeath)) {
   strcpy(optionfilehtm,optionfile);          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);     
   strcat(optionfilehtm,".htm");          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);     
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          goto end;
     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    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
 \n    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    free_vector(severity,1,maxwav);
 <hr  size=\"2\" color=\"#EC5E5E\">    free_imatrix(outcome,1,maxwav+1,1,n);
  <ul><li><h4>Parameter files</h4>\n    free_vector(moisnais,1,n);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    free_vector(annais,1,n);
  - Log file of the run: <a href=\"%s\">%s</a><br>\n    /* free_matrix(mint,1,maxwav,1,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);       free_matrix(anint,1,maxwav,1,n);*/
   fclose(fichtm);    free_vector(moisdc,1,n);
     free_vector(andc,1,n);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
       
 /*------------ free_vector  -------------*/    wav=ivector(1,imx);
  chdir(path);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
      bh=imatrix(1,lastpass-firstpass+1,1,imx);
  free_ivector(wav,1,imx);    mw=imatrix(1,lastpass-firstpass+1,1,imx);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);     
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      /* Concatenates waves */
  free_ivector(num,1,n);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
  fclose(ficparo);  
  fclose(ficres);    Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
   /*--------------- Prevalence limit --------------*/    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
          
   strcpy(filerespl,"pl");    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
   strcat(filerespl,fileres);                                   the estimations*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    h=0;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    m=pow(2,cptcoveff);
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;   
   }    for(k=1;k<=cptcoveff; k++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      for(i=1; i <=(m/pow(2,k));i++){
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);        for(j=1; j <= ncodemax[k]; j++){
   fprintf(ficrespl,"#Prevalence limit\n");          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
   fprintf(ficrespl,"#Age ");            h++;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
   fprintf(ficrespl,"\n");            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
            } 
   prlim=matrix(1,nlstate,1,nlstate);        }
   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 */    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       codtab[1][2]=1;codtab[2][2]=2; */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /* for(i=1; i <=m ;i++){ 
   k=0;       for(k=1; k <=cptcovn; k++){
   agebase=ageminpar;       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
   agelim=agemaxpar;       }
   ftolpl=1.e-10;       printf("\n");
   i1=cptcoveff;       }
   if (cptcovn < 1){i1=1;}       scanf("%d",i);*/
       
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Calculates basic frequencies. Computes observed prevalence at single age
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       and prints on file fileres'p'. */
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         fprintf(ficrespl,"\n#******");      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         printf("\n#******");      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         fprintf(ficlog,"\n#******");      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         for(j=1;j<=cptcoveff;j++) {      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
           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]]);    /* 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] */
         fprintf(ficrespl,"******\n");    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
         printf("******\n");  
         fprintf(ficlog,"******\n");    if(mle>=1){ /* Could be 1 or 2 */
              mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
         for (age=agebase; age<=agelim; age++){    }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      
           fprintf(ficrespl,"%.0f",age );    /*--------- results files --------------*/
           for(i=1; i<=nlstate;i++)    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
           fprintf(ficrespl," %.5f", prlim[i][i]);    
           fprintf(ficrespl,"\n");  
         }    jk=1;
       }    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     }    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   fclose(ficrespl);    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
   /*------------- h Pij x at various ages ------------*/      for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            printf("%d%d ",i,k);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            fprintf(ficlog,"%d%d ",i,k);
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;            fprintf(ficres,"%1d%1d ",i,k);
   }            for(j=1; j <=ncovmodel; j++){
   printf("Computing pij: result on file '%s' \n", filerespij);              printf("%f ",p[jk]);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);              fprintf(ficlog,"%f ",p[jk]);
                fprintf(ficres,"%f ",p[jk]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;              jk++; 
   /*if (stepm<=24) stepsize=2;*/            }
             printf("\n");
   agelim=AGESUP;            fprintf(ficlog,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */            fprintf(ficres,"\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          }
       }
   /* hstepm=1;   aff par mois*/    }
     if(mle==1){
   k=0;      /* Computing hessian and covariance matrix */
   for(cptcov=1;cptcov<=i1;cptcov++){      ftolhess=ftol; /* Usually correct */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      hesscov(matcov, p, npar, delti, ftolhess, func);
       k=k+1;    }
         fprintf(ficrespij,"\n#****** ");    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
         for(j=1;j<=cptcoveff;j++)    printf("# Scales (for hessian or gradient estimation)\n");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
         fprintf(ficrespij,"******\n");    for(i=1,jk=1; i <=nlstate; i++){
              for(j=1; j <=nlstate+ndeath; j++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        if (j!=i) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficres,"%1d%1d",i,j);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog," %.5e",delti[jk]);
           oldm=oldms;savm=savms;            fprintf(ficres," %.5e",delti[jk]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              jk++;
           fprintf(ficrespij,"# Age");          }
           for(i=1; i<=nlstate;i++)          printf("\n");
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficlog,"\n");
               fprintf(ficrespij," %1d-%1d",i,j);          fprintf(ficres,"\n");
           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(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    if(mle==1)
             fprintf(ficrespij,"\n");      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
              }    fprintf(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");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1,k=1;i<=npar;i++){
           fprintf(ficrespij,"\n");      /*  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]);
       */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      fprintf(ficres,"%3d",i);
       if(mle==1)
   fclose(ficrespij);        printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
   /*---------- Forecasting ------------------*/        fprintf(ficres," %.5e",matcov[i][j]);
   if((stepm == 1) && (strcmp(model,".")==0)){        if(mle==1)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          printf(" %.5e",matcov[i][j]);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        fprintf(ficlog," %.5e",matcov[i][j]);
   }      }
   else{      fprintf(ficres,"\n");
     erreur=108;      if(mle==1)
     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);        printf("\n");
     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);      fprintf(ficlog,"\n");
   }      k++;
      }
      
   /*---------- Health expectancies and variances ------------*/    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
   strcpy(filerest,"t");      fgets(line, MAXLINE, ficpar);
   strcat(filerest,fileres);      puts(line);
   if((ficrest=fopen(filerest,"w"))==NULL) {      fputs(line,ficparo);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    }
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    ungetc(c,ficpar);
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    estepm=0;
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    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) {
   strcpy(filerese,"e");      bage = ageminpar;
   strcat(filerese,fileres);      fage = agemaxpar;
   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);    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);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);     
     while((c=getc(ficpar))=='#' && c!= EOF){
   strcpy(fileresv,"v");      ungetc(c,ficpar);
   strcat(fileresv,fileres);      fgets(line, MAXLINE, ficpar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      puts(line);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      fputs(line,ficparo);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }    ungetc(c,ficpar);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    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);
   calagedate=-1;    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);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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);
      
   k=0;    while((c=getc(ficpar))=='#' && c!= EOF){
   for(cptcov=1;cptcov<=i1;cptcov++){      ungetc(c,ficpar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fgets(line, MAXLINE, ficpar);
       k=k+1;      puts(line);
       fprintf(ficrest,"\n#****** ");      fputs(line,ficparo);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    ungetc(c,ficpar);
       fprintf(ficrest,"******\n");   
   
       fprintf(ficreseij,"\n#****** ");    dateprev1=anprev1+mprev1/12.+jprev1/365.;
       for(j=1;j<=cptcoveff;j++)    dateprev2=anprev2+mprev2/12.+jprev2/365.;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficresvij,"\n#****** ");    fprintf(ficres,"pop_based=%d\n",popbased);   
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficresvij,"******\n");      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      puts(line);
       oldm=oldms;savm=savms;      fputs(line,ficparo);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      }
      ungetc(c,ficpar);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
       if(popbased==1){    fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }  
     while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      fgets(line, MAXLINE, ficpar);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      puts(line);
       fprintf(ficrest,"\n");      fputs(line,ficparo);
     }
       epj=vector(1,nlstate+1);    ungetc(c,ficpar);
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
         if (popbased==1) {    fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
           for(i=1; i<=nlstate;i++)    fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
             prlim[i][i]=probs[(int)age][i][k];  
         }    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
          
         fprintf(ficrest," %4.0f",age);    /*------------ gnuplot -------------*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    strcpy(optionfilegnuplot,optionfilefiname);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    strcat(optionfilegnuplot,".gp");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      printf("Problem with file %s",optionfilegnuplot);
           }    }
           epj[nlstate+1] +=epj[j];    else{
         }      fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
         for(i=1, vepp=0.;i <=nlstate;i++)      fprintf(ficgp,"set missing 'NaNq'\n");
           for(j=1;j <=nlstate;j++)    }
             vepp += vareij[i][j][(int)age];    fclose(ficgp);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
         for(j=1;j <=nlstate;j++){    /*--------- index.htm --------*/
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  
         }    strcpy(optionfilehtm,optionfile);
         fprintf(ficrest,"\n");    strcat(optionfilehtm,".htm");
       }    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     }      printf("Problem with %s \n",optionfilehtm), exit(0);
   }    }
 free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
     free_vector(weight,1,n);  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   fclose(ficreseij);  \n
   fclose(ficresvij);  Total number of observations=%d <br>\n
   fclose(ficrest);  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   fclose(ficpar);  <hr  size=\"2\" color=\"#EC5E5E\">
   free_vector(epj,1,nlstate+1);   <ul><li><h4>Parameter files</h4>\n
     - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
   /*------- Variance limit prevalence------*/     - 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);
   strcpy(fileresvpl,"vpl");    fclose(fichtm);
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   
     exit(0);    /*------------ free_vector  -------------*/
   }    chdir(path);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   
     free_ivector(wav,1,imx);
   k=0;    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       k=k+1;    free_ivector(num,1,n);
       fprintf(ficresvpl,"\n#****** ");    free_vector(agedc,1,n);
       for(j=1;j<=cptcoveff;j++)    /*free_matrix(covar,0,NCOVMAX,1,n);*/
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fprintf(ficresvpl,"******\n");    fclose(ficparo);
          fclose(ficres);
       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);    /*--------------- Prevalence limit  (stable prevalence) --------------*/
     }    
  }    strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
   fclose(ficresvpl);    if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
   /*---------- End : free ----------------*/      fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    }
      printf("Computing stable prevalence: result on file '%s' \n", filerespl);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficrespl,"#Stable prevalence \n");
      fprintf(ficrespl,"#Age ");
      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficrespl,"\n");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    prlim=matrix(1,nlstate,1,nlstate);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      agebase=ageminpar;
   free_matrix(matcov,1,npar,1,npar);    agelim=agemaxpar;
   free_vector(delti,1,npar);    ftolpl=1.e-10;
   free_matrix(agev,1,maxwav,1,imx);    i1=cptcoveff;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if (cptcovn < 1){i1=1;}
   
   fprintf(fichtm,"\n</body>");    for(cptcov=1,k=0;cptcov<=i1;cptcov++){
   fclose(fichtm);      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
   fclose(ficgp);        k=k+1;
          /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
   if(erreur >0){        printf("\n#******");
     printf("End of Imach with error or warning %d\n",erreur);        fprintf(ficlog,"\n#******");
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);        for(j=1;j<=cptcoveff;j++) {
   }else{          fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    printf("End of Imach\n");          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    fprintf(ficlog,"End of Imach\n");          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   }        }
   printf("See log file on %s\n",filelog);        fprintf(ficrespl,"******\n");
   fclose(ficlog);        printf("******\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        fprintf(ficlog,"******\n");
            
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        for (age=agebase; age<=agelim; age++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
   /*------ End -----------*/          fprintf(ficrespl,"%.0f",age );
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
  end:          fprintf(ficrespl,"\n");
 #ifdef windows        }
   /* chdir(pathcd);*/      }
 #endif    }
  /*system("wgnuplot graph.plt");*/    fclose(ficrespl);
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/    /*------------- h Pij x at various ages ------------*/
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    
  strcpy(plotcmd,GNUPLOTPROGRAM);    strcpy(filerespij,"pij");  strcat(filerespij,fileres);
  strcat(plotcmd," ");    if((ficrespij=fopen(filerespij,"w"))==NULL) {
  strcat(plotcmd,optionfilegnuplot);      printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
  system(plotcmd);      fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
 #ifdef windows    printf("Computing pij: result on file '%s' \n", filerespij);
   while (z[0] != 'q') {    fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     /* chdir(path); */    
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    stepsize=(int) (stepm+YEARM-1)/YEARM;
     scanf("%s",z);    /*if (stepm<=24) stepsize=2;*/
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    agelim=AGESUP;
     else if (z[0] == 'g') system(plotcmd);    hstepm=stepsize*YEARM; /* Every year of age */
     else if (z[0] == 'q') exit(0);    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   }  
 #endif    /* 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.1.52  
changed lines
  Added in v.1.66


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