Diff for /imach/src/imach.c between versions 1.36 and 1.71

version 1.36, 2002/03/29 15:27:27 version 1.71, 2003/03/28 13:32:54
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.92, February 2003, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   char fileresv[FILENAMELENGTH];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  FILE  *ficresvpl;  double jmean; /* Mean space between 2 waves */
   char fileresvpl[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define NR_END 1  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FREE_ARG char*  FILE *ficlog;
 #define FTOL 1.0e-10  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define NRANSI  FILE *fichtm; /* Html File */
 #define ITMAX 200  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define CGOLD 0.3819660  FILE  *ficresvpl;
 #define ZEPS 1.0e-10  char fileresvpl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GOLD 1.618034  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 static double maxarg1,maxarg2;  char filerest[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  
   #define NR_END 1
 static double sqrarg;  #define FREE_ARG char*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FTOL 1.0e-10
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NRANSI 
 int imx;  #define ITMAX 200 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define TOL 2.0e-4 
   
 int estepm;  #define CGOLD 0.3819660 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GOLD 1.618034 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GLIMIT 100.0 
 double **pmmij, ***probs, ***mobaverage;  #define TINY 1.0e-20 
 double dateintmean=0;  
   static double maxarg1,maxarg2;
 double *weight;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 int **s; /* Status */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /**************** split *************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  int imx; 
    char *s;                             /* pointer */  int stepm;
    int  l1, l2;                         /* length counters */  /* Stepm, step in month: minimum step interpolation*/
   
    l1 = strlen( path );                 /* length of path */  int estepm;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  int m,nb;
 #else  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    s = strrchr( path, '/' );            /* find last / */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #endif  double **pmmij, ***probs;
    if ( s == NULL ) {                   /* no directory, so use current */  double dateintmean=0;
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  double *weight;
   int **s; /* Status */
       if ( getwd( dirc ) == NULL ) {  double *agedc, **covar, idx;
 #else  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       extern char       *getcwd( );  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double ftolhess; /* Tolerance for computing hessian */
 #endif  
          return( GLOCK_ERROR_GETCWD );  /**************** split *************************/
       }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       strcpy( name, path );             /* we've got it */  {
    } else {                             /* strip direcotry from path */    char  *ss;                            /* pointer */
       s++;                              /* after this, the filename */    int   l1, l2;                         /* length counters */
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    l1 = strlen(path );                   /* length of path */
       strcpy( name, s );                /* save file name */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       dirc[l1-l2] = 0;                  /* add zero */    if ( ss == NULL ) {                   /* no directory, so use current */
    }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
    l1 = strlen( dirc );                 /* length of directory */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #ifdef windows  #if     defined(__bsd__)                /* get current working directory */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      extern char *getwd( );
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      if ( getwd( dirc ) == NULL ) {
 #endif  #else
    s = strrchr( name, '.' );            /* find last / */      extern char *getcwd( );
    s++;  
    strcpy(ext,s);                       /* save extension */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    l1= strlen( name);  #endif
    l2= strlen( s)+1;        return( GLOCK_ERROR_GETCWD );
    strncpy( finame, name, l1-l2);      }
    finame[l1-l2]= 0;      strcpy( name, path );               /* we've got it */
    return( 0 );                         /* we're done */    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /******************************************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void replace(char *s, char*t)      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   int i;    l1 = strlen( dirc );                  /* length of directory */
   int lg=20;  #ifdef windows
   i=0;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   lg=strlen(t);  #else
   for(i=0; i<= lg; i++) {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     (s[i] = t[i]);  #endif
     if (t[i]== '\\') s[i]='/';    ss = strrchr( name, '.' );            /* find last / */
   }    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 int nbocc(char *s, char occ)    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   int i,j=0;    finame[l1-l2]= 0;
   int lg=20;    return( 0 );                          /* we're done */
   i=0;  }
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  /******************************************/
   }  
   return j;  void replace(char *s, char*t)
 }  {
     int i;
 void cutv(char *u,char *v, char*t, char occ)    int lg=20;
 {    i=0;
   int i,lg,j,p=0;    lg=strlen(t);
   i=0;    for(i=0; i<= lg; i++) {
   for(j=0; j<=strlen(t)-1; j++) {      (s[i] = t[i]);
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      if (t[i]== '\\') s[i]='/';
   }    }
   }
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int nbocc(char *s, char occ)
     (u[j] = t[j]);  {
   }    int i,j=0;
      u[p]='\0';    int lg=20;
     i=0;
    for(j=0; j<= lg; j++) {    lg=strlen(s);
     if (j>=(p+1))(v[j-p-1] = t[j]);    for(i=0; i<= lg; i++) {
   }    if  (s[i] == occ ) j++;
 }    }
     return j;
 /********************** nrerror ********************/  }
   
 void nrerror(char error_text[])  void cutv(char *u,char *v, char*t, char occ)
 {  {
   fprintf(stderr,"ERREUR ...\n");    /* cuts string t into u and v where u is ended by char occ excluding it
   fprintf(stderr,"%s\n",error_text);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   exit(1);       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
 /*********************** vector *******************/    i=0;
 double *vector(int nl, int nh)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double *v;    }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /************************ free vector ******************/       u[p]='\0';
 void free_vector(double*v, int nl, int nh)  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(v+nl-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /********************** nrerror ********************/
 {  
   int *v;  void nrerror(char error_text[])
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    fprintf(stderr,"ERREUR ...\n");
   return v-nl+NR_END;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /******************free ivector **************************/  /*********************** vector *******************/
 void free_ivector(int *v, long nl, long nh)  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /******************* imatrix *******************************/    return v-nl+NR_END;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  /************************ free vector ******************/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  void free_vector(double*v, int nl, int nh)
   int **m;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
      int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* allocate rows and set pointers to them */    if (!v) nrerror("allocation failure in ivector");
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    return v-nl+NR_END;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* return pointer to array of pointers to rows */  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /****************** free_imatrix *************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_imatrix(m,nrl,nrh,ncl,nch)  { 
       int **m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       long nch,ncl,nrh,nrl;    int **m; 
      /* free an int matrix allocated by imatrix() */    
 {    /* allocate pointers to rows */ 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   free((FREE_ARG) (m+nrl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /******************* matrix *******************************/    
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    /* allocate rows and set pointers to them */ 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double **m;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl] -= ncl; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m -= nrl;    
     /* return pointer to array of pointers to rows */ 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  } 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;        int **m;
   return m;        long nch,ncl,nrh,nrl; 
 }       /* free an int matrix allocated by imatrix() */ 
   { 
 /*************************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));  /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 /******************* ma3x *******************************/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+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;    return m;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /*************************free matrix ************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m[nrl][ncl] -= nll;    free((FREE_ARG)(m+nrl-NR_END));
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  
    /******************* ma3x *******************************/
   for (i=nrl+1; i<=nrh; i++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  {
     for (j=ncl+1; j<=nch; j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       m[i][j]=m[i][j-1]+nlay;    double ***m;
   }  
   return m;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free ma3x ************************/    m -= nrl;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] += NR_END;
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /***************** f1dim *************************/  
 extern int ncom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 extern double (*nrfunc)(double []);    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
 double f1dim(double x)    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   int j;    
   double f;    for (i=nrl+1; i<=nrh; i++) {
   double *xt;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
        for (j=ncl+1; j<=nch; j++) 
   xt=vector(1,ncom);        m[i][j]=m[i][j-1]+nlay;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    }
   f=(*nrfunc)(xt);    return m;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int iter;    free((FREE_ARG)(m+nrl-NR_END));
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /***************** f1dim *************************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern int ncom; 
   double e=0.0;  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
   a=(ax < cx ? ax : cx);   
   b=(ax > cx ? ax : cx);  double f1dim(double x) 
   x=w=v=bx;  { 
   fw=fv=fx=(*f)(x);    int j; 
   for (iter=1;iter<=ITMAX;iter++) {    double f;
     xm=0.5*(a+b);    double *xt; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);   
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    xt=vector(1,ncom); 
     printf(".");fflush(stdout);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #ifdef DEBUG    f=(*nrfunc)(xt); 
     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);    free_vector(xt,1,ncom); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return f; 
 #endif  } 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /*****************brent *************************/
       return fx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     ftemp=fu;    int iter; 
     if (fabs(e) > tol1) {    double a,b,d,etemp;
       r=(x-w)*(fx-fv);    double fu,fv,fw,fx;
       q=(x-v)*(fx-fw);    double ftemp;
       p=(x-v)*q-(x-w)*r;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       q=2.0*(q-r);    double e=0.0; 
       if (q > 0.0) p = -p;   
       q=fabs(q);    a=(ax < cx ? ax : cx); 
       etemp=e;    b=(ax > cx ? ax : cx); 
       e=d;    x=w=v=bx; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    fw=fv=fx=(*f)(x); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (iter=1;iter<=ITMAX;iter++) { 
       else {      xm=0.5*(a+b); 
         d=p/q;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         u=x+d;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         if (u-a < tol2 || b-u < tol2)      printf(".");fflush(stdout);
           d=SIGN(tol1,xm-x);      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
     } else {      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);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #endif
     fu=(*f)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     if (fu <= fx) {        *xmin=x; 
       if (u >= x) a=x; else b=x;        return fx; 
       SHFT(v,w,x,u)      } 
         SHFT(fv,fw,fx,fu)      ftemp=fu;
         } else {      if (fabs(e) > tol1) { 
           if (u < x) a=u; else b=u;        r=(x-w)*(fx-fv); 
           if (fu <= fw || w == x) {        q=(x-v)*(fx-fw); 
             v=w;        p=(x-v)*q-(x-w)*r; 
             w=u;        q=2.0*(q-r); 
             fv=fw;        if (q > 0.0) p = -p; 
             fw=fu;        q=fabs(q); 
           } else if (fu <= fv || v == x || v == w) {        etemp=e; 
             v=u;        e=d; 
             fv=fu;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         }        else { 
   }          d=p/q; 
   nrerror("Too many iterations in brent");          u=x+d; 
   *xmin=x;          if (u-a < tol2 || b-u < tol2) 
   return fx;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /****************** mnbrak ***********************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             double (*func)(double))      fu=(*f)(u); 
 {      if (fu <= fx) { 
   double ulim,u,r,q, dum;        if (u >= x) a=x; else b=x; 
   double fu;        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
   *fa=(*func)(*ax);          } else { 
   *fb=(*func)(*bx);            if (u < x) a=u; else b=u; 
   if (*fb > *fa) {            if (fu <= fw || w == x) { 
     SHFT(dum,*ax,*bx,dum)              v=w; 
       SHFT(dum,*fb,*fa,dum)              w=u; 
       }              fv=fw; 
   *cx=(*bx)+GOLD*(*bx-*ax);              fw=fu; 
   *fc=(*func)(*cx);            } else if (fu <= fv || v == x || v == w) { 
   while (*fb > *fc) {              v=u; 
     r=(*bx-*ax)*(*fb-*fc);              fv=fu; 
     q=(*bx-*cx)*(*fb-*fa);            } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/          } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    nrerror("Too many iterations in brent"); 
     if ((*bx-u)*(u-*cx) > 0.0) {    *xmin=x; 
       fu=(*func)(u);    return fx; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  } 
       fu=(*func)(u);  
       if (fu < *fc) {  /****************** mnbrak ***********************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           }              double (*func)(double)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  { 
       u=ulim;    double ulim,u,r,q, dum;
       fu=(*func)(u);    double fu; 
     } else {   
       u=(*cx)+GOLD*(*cx-*bx);    *fa=(*func)(*ax); 
       fu=(*func)(u);    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     SHFT(*ax,*bx,*cx,u)      SHFT(dum,*ax,*bx,dum) 
       SHFT(*fa,*fb,*fc,fu)        SHFT(dum,*fb,*fa,dum) 
       }        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /*************** linmin ************************/    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 int ncom;      q=(*bx-*cx)*(*fb-*fa); 
 double *pcom,*xicom;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 double (*nrfunc)(double []);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
        ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double brent(double ax, double bx, double cx,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
                double (*f)(double), double tol, double *xmin);        fu=(*func)(u); 
   double f1dim(double x);        if (fu < *fc) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
               double *fc, double (*func)(double));            SHFT(*fb,*fc,fu,(*func)(u)) 
   int j;            } 
   double xx,xmin,bx,ax;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double fx,fb,fa;        u=ulim; 
          fu=(*func)(u); 
   ncom=n;      } else { 
   pcom=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   xicom=vector(1,n);        fu=(*func)(u); 
   nrfunc=func;      } 
   for (j=1;j<=n;j++) {      SHFT(*ax,*bx,*cx,u) 
     pcom[j]=p[j];        SHFT(*fa,*fb,*fc,fu) 
     xicom[j]=xi[j];        } 
   }  } 
   ax=0.0;  
   xx=1.0;  /*************** linmin ************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int ncom; 
 #ifdef DEBUG  double *pcom,*xicom;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double (*nrfunc)(double []); 
 #endif   
   for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     xi[j] *= xmin;  { 
     p[j] += xi[j];    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
   free_vector(xicom,1,n);    double f1dim(double x); 
   free_vector(pcom,1,n);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 }                double *fc, double (*func)(double)); 
     int j; 
 /*************** powell ************************/    double xx,xmin,bx,ax; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double fx,fb,fa;
             double (*func)(double []))   
 {    ncom=n; 
   void linmin(double p[], double xi[], int n, double *fret,    pcom=vector(1,n); 
               double (*func)(double []));    xicom=vector(1,n); 
   int i,ibig,j;    nrfunc=func; 
   double del,t,*pt,*ptt,*xit;    for (j=1;j<=n;j++) { 
   double fp,fptt;      pcom[j]=p[j]; 
   double *xits;      xicom[j]=xi[j]; 
   pt=vector(1,n);    } 
   ptt=vector(1,n);    ax=0.0; 
   xit=vector(1,n);    xx=1.0; 
   xits=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   *fret=(*func)(p);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (j=1;j<=n;j++) pt[j]=p[j];  #ifdef DEBUG
   for (*iter=1;;++(*iter)) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fp=(*fret);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     ibig=0;  #endif
     del=0.0;    for (j=1;j<=n;j++) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      xi[j] *= xmin; 
     for (i=1;i<=n;i++)      p[j] += xi[j]; 
       printf(" %d %.12f",i, p[i]);    } 
     printf("\n");    free_vector(xicom,1,n); 
     for (i=1;i<=n;i++) {    free_vector(pcom,1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  } 
       fptt=(*fret);  
 #ifdef DEBUG  /*************** powell ************************/
       printf("fret=%lf \n",*fret);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 #endif              double (*func)(double [])) 
       printf("%d",i);fflush(stdout);  { 
       linmin(p,xit,n,fret,func);    void linmin(double p[], double xi[], int n, double *fret, 
       if (fabs(fptt-(*fret)) > del) {                double (*func)(double [])); 
         del=fabs(fptt-(*fret));    int i,ibig,j; 
         ibig=i;    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
 #ifdef DEBUG    double *xits;
       printf("%d %.12e",i,(*fret));    pt=vector(1,n); 
       for (j=1;j<=n;j++) {    ptt=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xit=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xits=vector(1,n); 
       }    *fret=(*func)(p); 
       for(j=1;j<=n;j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(" p=%.12e",p[j]);    for (*iter=1;;++(*iter)) { 
       printf("\n");      fp=(*fret); 
 #endif      ibig=0; 
     }      del=0.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       int k[2],l;      for (i=1;i<=n;i++) 
       k[0]=1;        printf(" %d %.12f",i, p[i]);
       k[1]=-1;      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("Max: %.12e",(*func)(p));      printf("\n");
       for (j=1;j<=n;j++)      fprintf(ficlog,"\n");
         printf(" %.12e",p[j]);      for (i=1;i<=n;i++) { 
       printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for(l=0;l<=1;l++) {        fptt=(*fret); 
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        printf("fret=%lf \n",*fret);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        fprintf(ficlog,"fret=%lf \n",*fret);
         }  #endif
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
       free_vector(xit,1,n);          ibig=i; 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);  #ifdef DEBUG
       free_vector(pt,1,n);        printf("%d %.12e",i,(*fret));
       return;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=n;j++) {          printf(" x(%d)=%.12e",j,xit[j]);
       ptt[j]=2.0*p[j]-pt[j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       xit[j]=p[j]-pt[j];        }
       pt[j]=p[j];        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
     fptt=(*func)(ptt);          fprintf(ficlog," p=%.12e",p[j]);
     if (fptt < fp) {        }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf("\n");
       if (t < 0.0) {        fprintf(ficlog,"\n");
         linmin(p,xit,n,fret,func);  #endif
         for (j=1;j<=n;j++) {      } 
           xi[j][ibig]=xi[j][n];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           xi[j][n]=xit[j];  #ifdef DEBUG
         }        int k[2],l;
 #ifdef DEBUG        k[0]=1;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        k[1]=-1;
         for(j=1;j<=n;j++)        printf("Max: %.12e",(*func)(p));
           printf(" %.12e",xit[j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         printf("\n");        for (j=1;j<=n;j++) {
 #endif          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /**** Prevalence limit ****************/          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[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]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          }
      matrix by transitions matrix until convergence is reached */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, ii,j,k;        }
   double min, max, maxmin, maxmax,sumnew=0.;  #endif
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;        free_vector(xit,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(pt,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        return; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
    cov[1]=1.;        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        pt[j]=p[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      } 
     newm=savm;      fptt=(*func)(ptt); 
     /* Covariates have to be included here again */      if (fptt < fp) { 
      cov[2]=agefin;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
       for (k=1; k<=cptcovn;k++) {          linmin(p,xit,n,fret,func); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          for (j=1;j<=n;j++) { 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/            xi[j][ibig]=xi[j][n]; 
       }            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
       for (k=1; k<=cptcovprod;k++)  #ifdef DEBUG
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          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);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          for(j=1;j<=n;j++){
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            printf(" %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            fprintf(ficlog," %.12e",xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          }
           printf("\n");
     savm=oldm;          fprintf(ficlog,"\n");
     oldm=newm;  #endif
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){      } 
       min=1.;    } 
       max=0.;  } 
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /**** Prevalence limit (stable prevalence)  ****************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
     if(maxmax < ftolpl){    double **matprod2();
       return prlim;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /*************** transition probabilities ***************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      }
 {  
   double s1, s2;     cov[1]=1.;
   /*double t34;*/   
   int i,j,j1, nc, ii, jj;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(i=1; i<= nlstate; i++){      newm=savm;
     for(j=1; j<i;j++){      /* Covariates have to be included here again */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       cov[2]=agefin;
         /*s2 += param[i][j][nc]*cov[nc];*/    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (k=1; k<=cptcovn;k++) {
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          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]]);*/
       ps[i][j]=s2;        }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     for(j=i+1; j<=nlstate+ndeath;j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*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]);*/
       ps[i][j]=s2;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     }  
   }      savm=oldm;
     /*ps[3][2]=1;*/      oldm=newm;
       maxmax=0.;
   for(i=1; i<= nlstate; i++){      for(j=1;j<=nlstate;j++){
      s1=0;        min=1.;
     for(j=1; j<i; j++)        max=0.;
       s1+=exp(ps[i][j]);        for(i=1; i<=nlstate; i++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          sumnew=0;
       s1+=exp(ps[i][j]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     ps[i][i]=1./(s1+1.);          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(j=1; j<i; j++)          max=FMAX(max,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          min=FMIN(min,prlim[i][j]);
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmin=max-min;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        maxmax=FMAX(maxmax,maxmin);
   } /* end i */      }
       if(maxmax < ftolpl){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        return prlim;
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;  }
     }  
   }  /*************** transition probabilities ***************/ 
   
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    double s1, s2;
      printf("%lf ",ps[ii][jj]);    /*double t34;*/
    }    int i,j,j1, nc, ii, jj;
     printf("\n ");  
     }      for(i=1; i<= nlstate; i++){
     printf("\n ");printf("%lf ",cov[2]);*/      for(j=1; j<i;j++){
 /*        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          /*s2 += param[i][j][nc]*cov[nc];*/
   goto end;*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     return ps;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 }        }
         ps[i][j]=s2;
 /**************** Product of 2 matrices ******************/        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      for(j=i+1; j<=nlstate+ndeath;j++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /* in, b, out are matrice of pointers which should have been initialized        }
      before: only the contents of out is modified. The function returns        ps[i][j]=s2;
      a pointer to pointers identical to out */      }
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)      /*ps[3][2]=1;*/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(i=1; i<= nlstate; i++){
         out[i][k] +=in[i][j]*b[j][k];       s1=0;
       for(j=1; j<i; j++)
   return out;        s1+=exp(ps[i][j]);
 }      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
 /************* Higher Matrix Product ***************/      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for(j=i+1; j<=nlstate+ndeath; j++)
 {        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      duration (i.e. until    } /* end i */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      (typically every 2 years instead of every month which is too big).      for(jj=1; jj<= nlstate+ndeath; jj++){
      Model is determined by parameters x and covariates have to be        ps[ii][jj]=0;
      included manually here.        ps[ii][ii]=1;
       }
      */    }
   
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double **newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
   /* Hstepm could be zero and should return the unit matrix */     }
   for (i=1;i<=nlstate+ndeath;i++)      printf("\n ");
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*
     }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    goto end;*/
   for(h=1; h <=nhstepm; h++){      return ps;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /**************** Product of 2 matrices ******************/
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (k=1; k<=cptcovprod;k++)    /* in, b, out are matrice of pointers which should have been initialized 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     long i, j, k;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(i=nrl; i<= nrh; i++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for(k=ncolol; k<=ncoloh; k++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          out[i][k] +=in[i][j]*b[j][k];
       savm=oldm;  
       oldm=newm;    return out;
     }  }
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /************* Higher Matrix Product ***************/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
   } /* end h */    /* Computes the transition matrix starting at age 'age' over 
   return po;       'nhstepm*hstepm*stepm' months (i.e. until
 }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /*************** log-likelihood *************/       (typically every 2 years instead of every month which is too big 
 double func( double *x)       for the memory).
 {       Model is determined by parameters x and covariates have to be 
   int i, ii, j, k, mi, d, kk;       included manually here. 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;       */
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    int i, j, d, h, k;
   long ipmx;    double **out, cov[NCOVMAX];
   /*extern weight */    double **newm;
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* Hstepm could be zero and should return the unit matrix */
   /*for(i=1;i<imx;i++)    for (i=1;i<=nlstate+ndeath;i++)
     printf(" %d\n",s[4][i]);      for (j=1;j<=nlstate+ndeath;j++){
   */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   cov[1]=1.;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for(k=1; k<=nlstate; k++) ll[k]=0.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for(h=1; h <=nhstepm; h++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for(d=1; d <=hstepm; d++){
     for(mi=1; mi<= wav[i]-1; mi++){        newm=savm;
       for (ii=1;ii<=nlstate+ndeath;ii++)        /* Covariates have to be included here again */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        cov[1]=1.;
       for(d=0; d<dh[mi][i]; d++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         newm=savm;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovage;k++)
         for (kk=1; kk<=cptcovage;kk++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        for (k=1; k<=cptcovprod;k++)
         }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         savm=oldm;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         oldm=newm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                             pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       } /* end mult */        oldm=newm;
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      for(i=1; i<=nlstate+ndeath; i++)
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for(j=1;j<=nlstate+ndeath;j++) {
       ipmx +=1;          po[i][j][h]=newm[i][j];
       sw += weight[i];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;           */
     } /* end of wave */        }
   } /* end of individual */    } /* end h */
     return po;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  /*************** log-likelihood *************/
 }  double func( double *x)
   {
     int i, ii, j, k, mi, d, kk;
 /*********** Maximum Likelihood Estimation ***************/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double sw; /* Sum of weights */
 {    double lli; /* Individual log likelihood */
   int i,j, iter;    int s1, s2;
   double **xi,*delti;    double bbh, survp;
   double fret;    long ipmx;
   xi=matrix(1,npar,1,npar);    /*extern weight */
   for (i=1;i<=npar;i++)    /* We are differentiating ll according to initial status */
     for (j=1;j<=npar;j++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       xi[i][j]=(i==j ? 1.0 : 0.0);    /*for(i=1;i<imx;i++) 
   printf("Powell\n");      printf(" %d\n",s[4][i]);
   powell(p,xi,npar,ftol,&iter,&fret,func);    */
     cov[1]=1.;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /**** Computes Hessian and covariance matrix ***/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   double  **a,**y,*x,pd;            for (j=1;j<=nlstate+ndeath;j++){
   double **hess;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j,jk;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int *indx;            }
           for(d=0; d<dh[mi][i]; d++){
   double hessii(double p[], double delta, int theta, double delti[]);            newm=savm;
   double hessij(double p[], double delti[], int i, int j);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   void lubksb(double **a, int npar, int *indx, double b[]) ;            for (kk=1; kk<=cptcovage;kk++) {
   void ludcmp(double **a, int npar, int *indx, double *d) ;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   hess=matrix(1,npar,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\nCalculation of the hessian matrix. Wait...\n");            savm=oldm;
   for (i=1;i<=npar;i++){            oldm=newm;
     printf("%d",i);fflush(stdout);          } /* end mult */
     hess[i][i]=hessii(p,ftolhess,i,delti);        
     /*printf(" %f ",p[i]);*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     /*printf(" %lf ",hess[i][i]);*/          /* 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 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
   for (i=1;i<=npar;i++) {           * the nearest (and in case of equal distance, to the lowest) interval but now
     for (j=1;j<=npar;j++)  {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if (j>i) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         printf(".%d%d",i,j);fflush(stdout);           * probability in order to take into account the bias as a fraction of the way
         hess[i][j]=hessij(p,delti,i,j);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         hess[j][i]=hess[i][j];               * -stepm/2 to stepm/2 .
         /*printf(" %lf ",hess[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. 
     }           */
   }          s1=s[mw[mi][i]][i];
   printf("\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
             * is higher than the multiple of stepm and negative otherwise.
   a=matrix(1,npar,1,npar);           */
   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);          if( s2 > nlstate){ 
   indx=ivector(1,npar);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for (i=1;i<=npar;i++)               to the likelihood is the probability to die between last step unit time and current 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];               step unit time, which is also the differences between probability to die before dh 
   ludcmp(a,npar,indx,&pd);               and probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   for (j=1;j<=npar;j++) {          as if date of death was unknown. Death was treated as any other
     for (i=1;i<=npar;i++) x[i]=0;          health state: the date of the interview describes the actual state
     x[j]=1;          and not the date of a change in health state. The former idea was
     lubksb(a,npar,indx,x);          to consider that at each interview the state was recorded
     for (i=1;i<=npar;i++){          (healthy, disable or death) and IMaCh was corrected; but when we
       matcov[i][j]=x[i];          introduced the exact date of death then we should have modified
     }          the contribution of an exact death to the likelihood. This new
   }          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
   printf("\n#Hessian matrix#\n");          and month of death but the probability to survive from last
   for (i=1;i<=npar;i++) {          interview up to one month before death multiplied by the
     for (j=1;j<=npar;j++) {          probability to die within a month. Thanks to Chris
       printf("%.3e ",hess[i][j]);          Jackson for correcting this bug.  Former versions increased
     }          mortality artificially. The bad side is that we add another loop
     printf("\n");          which slows down the processing. The difference can be up to 10%
   }          lower mortality.
             */
   /* Recompute Inverse */            lli=log(out[s1][s2] - savm[s1][s2]);
   for (i=1;i<=npar;i++)          }else{
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   ludcmp(a,npar,indx,&pd);            /*  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#Hessian matrix recomputed#\n");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   for (j=1;j<=npar;j++) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for (i=1;i<=npar;i++) x[i]=0;          ipmx +=1;
     x[j]=1;          sw += weight[i];
     lubksb(a,npar,indx,x);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++){        } /* end of wave */
       y[i][j]=x[i];      } /* end of individual */
       printf("%.3e ",y[i][j]);    }  else if(mle==2){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf("\n");        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++){
   free_matrix(a,1,npar,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(y,1,npar,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(x,1,npar);            }
   free_ivector(indx,1,npar);          for(d=0; d<=dh[mi][i]; d++){
   free_matrix(hess,1,npar,1,npar);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /*************** hessian matrix ****************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 double hessii( double x[], double delta, int theta, double delti[])                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   int i;            oldm=newm;
   int l=1, lmax=20;          } /* end mult */
   double k1,k2;        
   double p2[NPARMAX+1];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double res;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double fx;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   int k=0,kmax=10;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double l1;           * 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
   fx=func(x);           * probability in order to take into account the bias as a fraction of the way
   for (i=1;i<=npar;i++) p2[i]=x[i];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for(l=0 ; l <=lmax; l++){           * -stepm/2 to stepm/2 .
     l1=pow(10,l);           * For stepm=1 the results are the same as for previous versions of Imach.
     delts=delt;           * For stepm > 1 the results are less biased than in previous versions. 
     for(k=1 ; k <kmax; k=k+1){           */
       delt = delta*(l1*k);          s1=s[mw[mi][i]][i];
       p2[theta]=x[theta] +delt;          s2=s[mw[mi+1][i]][i];
       k1=func(p2)-fx;          bbh=(double)bh[mi][i]/(double)stepm; 
       p2[theta]=x[theta]-delt;          /* bias is positive if real duration
       k2=func(p2)-fx;           * is higher than the multiple of stepm and negative otherwise.
       /*res= (k1-2.0*fx+k2)/delt/delt; */           */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 #ifdef DEBUG          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
       printf("%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);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 #endif          /*if(lli ==000.0)*/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*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); */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          ipmx +=1;
         k=kmax;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        } /* end of wave */
         k=kmax; l=lmax*10.;      } /* end of individual */
       }    }  else if(mle==3){  /* exponential inter-extrapolation */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         delts=delt;        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++){
   delti[theta]=delts;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 double hessij( double x[], double delti[], int thetai,int thetaj)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   int i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int l=1, l1, lmax=20;            }
   double k1,k2,k3,k4,res,fx;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double p2[NPARMAX+1];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int k;            savm=oldm;
             oldm=newm;
   fx=func(x);          } /* end mult */
   for (k=1; k<=2; k++) {        
     for (i=1;i<=npar;i++) p2[i]=x[i];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetai]=x[thetai]+delti[thetai]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     k1=func(p2)-fx;           * (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
     p2[thetai]=x[thetai]+delti[thetai]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     k2=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * -stepm/2 to stepm/2 .
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * For stepm=1 the results are the same as for previous versions of Imach.
     k3=func(p2)-fx;           * For stepm > 1 the results are less biased than in previous versions. 
             */
     p2[thetai]=x[thetai]-delti[thetai]/k;          s1=s[mw[mi][i]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          s2=s[mw[mi+1][i]][i];
     k4=func(p2)-fx;          bbh=(double)bh[mi][i]/(double)stepm; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          /* bias is positive if real duration
 #ifdef DEBUG           * is higher than the multiple of stepm and negative otherwise.
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);           */
 #endif          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   return res;          /*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); */
 /************** Inverse of matrix **************/          ipmx +=1;
 void ludcmp(double **a, int n, int *indx, double *d)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i,imax,j,k;        } /* end of wave */
   double big,dum,sum,temp;      } /* end of individual */
   double *vv;    }else{  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   vv=vector(1,n);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   *d=1.0;        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=n;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     big=0.0;            for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=n;j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if ((temp=fabs(a[i][j])) > big) big=temp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            }
     vv[i]=1.0/big;          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   for (j=1;j<=n;j++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (i=1;i<j;i++) {            for (kk=1; kk<=cptcovage;kk++) {
       sum=a[i][j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            }
       a[i][j]=sum;          
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     big=0.0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=j;i<=n;i++) {            savm=oldm;
       sum=a[i][j];            oldm=newm;
       for (k=1;k<j;k++)          } /* end mult */
         sum -= a[i][k]*a[k][j];        
       a[i][j]=sum;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          ipmx +=1;
         big=dum;          sw += weight[i];
         imax=i;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
     }      } /* end of individual */
     if (j != imax) {    } /* End of if */
       for (k=1;k<=n;k++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         dum=a[imax][k];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         a[imax][k]=a[j][k];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         a[j][k]=dum;    return -l;
       }  }
       *d = -(*d);  
       vv[imax]=vv[j];  
     }  /*********** Maximum Likelihood Estimation ***************/
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     if (j != n) {  {
       dum=1.0/(a[j][j]);    int i,j, iter;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double **xi,*delti;
     }    double fret;
   }    xi=matrix(1,npar,1,npar);
   free_vector(vv,1,n);  /* Doesn't work */    for (i=1;i<=npar;i++)
 ;      for (j=1;j<=npar;j++)
 }        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
 void lubksb(double **a, int n, int *indx, double b[])    powell(p,xi,npar,ftol,&iter,&fret,func);
 {  
   int i,ii=0,ip,j;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double sum;    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));
   for (i=1;i<=n;i++) {  
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /**** Computes Hessian and covariance matrix ***/
     if (ii)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  {
     else if (sum) ii=i;    double  **a,**y,*x,pd;
     b[i]=sum;    double **hess;
   }    int i, j,jk;
   for (i=n;i>=1;i--) {    int *indx;
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    double hessii(double p[], double delta, int theta, double delti[]);
     b[i]=sum/a[i][i];    double hessij(double p[], double delti[], int i, int j);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
 }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   
 /************ Frequencies ********************/    hess=matrix(1,npar,1,npar);
 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 */    printf("\nCalculation of the hessian matrix. Wait...\n");
      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    for (i=1;i<=npar;i++){
   double ***freq; /* Frequencies */      printf("%d",i);fflush(stdout);
   double *pp;      fprintf(ficlog,"%d",i);fflush(ficlog);
   double pos, k2, dateintsum=0,k2cpt=0;      hess[i][i]=hessii(p,ftolhess,i,delti);
   FILE *ficresp;      /*printf(" %f ",p[i]);*/
   char fileresp[FILENAMELENGTH];      /*printf(" %lf ",hess[i][i]);*/
      }
   pp=vector(1,nlstate);    
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=1;i<=npar;i++) {
   strcpy(fileresp,"p");      for (j=1;j<=npar;j++)  {
   strcat(fileresp,fileres);        if (j>i) { 
   if((ficresp=fopen(fileresp,"w"))==NULL) {          printf(".%d%d",i,j);fflush(stdout);
     printf("Problem with prevalence resultfile: %s\n", fileresp);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     exit(0);          hess[i][j]=hessij(p,delti,i,j);
   }          hess[j][i]=hess[i][j];    
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          /*printf(" %lf ",hess[i][j]);*/
   j1=0;        }
        }
   j=cptcoveff;    }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    printf("\n");
      fprintf(ficlog,"\n");
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       j1++;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    
         scanf("%d", i);*/    a=matrix(1,npar,1,npar);
       for (i=-1; i<=nlstate+ndeath; i++)      y=matrix(1,npar,1,npar);
         for (jk=-1; jk<=nlstate+ndeath; jk++)      x=vector(1,npar);
           for(m=agemin; m <= agemax+3; m++)    indx=ivector(1,npar);
             freq[i][jk][m]=0;    for (i=1;i<=npar;i++)
            for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       dateintsum=0;    ludcmp(a,npar,indx,&pd);
       k2cpt=0;  
       for (i=1; i<=imx; i++) {    for (j=1;j<=npar;j++) {
         bool=1;      for (i=1;i<=npar;i++) x[i]=0;
         if  (cptcovn>0) {      x[j]=1;
           for (z1=1; z1<=cptcoveff; z1++)      lubksb(a,npar,indx,x);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (i=1;i<=npar;i++){ 
               bool=0;        matcov[i][j]=x[i];
         }      }
         if (bool==1) {    }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);    printf("\n#Hessian matrix#\n");
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    fprintf(ficlog,"\n#Hessian matrix#\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;    for (i=1;i<=npar;i++) { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      for (j=1;j<=npar;j++) { 
               if (m<lastpass) {        printf("%.3e ",hess[i][j]);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        fprintf(ficlog,"%.3e ",hess[i][j]);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      }
               }      printf("\n");
                    fprintf(ficlog,"\n");
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    }
                 dateintsum=dateintsum+k2;  
                 k2cpt++;    /* Recompute Inverse */
               }    for (i=1;i<=npar;i++)
             }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           }    ludcmp(a,npar,indx,&pd);
         }  
       }    /*  printf("\n#Hessian matrix recomputed#\n");
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
       if  (cptcovn>0) {      x[j]=1;
         fprintf(ficresp, "\n#********** Variable ");      lubksb(a,npar,indx,x);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for (i=1;i<=npar;i++){ 
         fprintf(ficresp, "**********\n#");        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
       for(i=1; i<=nlstate;i++)        fprintf(ficlog,"%.3e ",y[i][j]);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
       fprintf(ficresp, "\n");      printf("\n");
            fprintf(ficlog,"\n");
       for(i=(int)agemin; i <= (int)agemax+3; i++){    }
         if(i==(int)agemax+3)    */
           printf("Total");  
         else    free_matrix(a,1,npar,1,npar);
           printf("Age %d", i);    free_matrix(y,1,npar,1,npar);
         for(jk=1; jk <=nlstate ; jk++){    free_vector(x,1,npar);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    free_ivector(indx,1,npar);
             pp[jk] += freq[jk][m][i];    free_matrix(hess,1,npar,1,npar);
         }  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  }
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10)  /*************** hessian matrix ****************/
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  double hessii( double x[], double delta, int theta, double delti[])
           else  {
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    int i;
         }    int l=1, lmax=20;
     double k1,k2;
         for(jk=1; jk <=nlstate ; jk++){    double p2[NPARMAX+1];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double res;
             pp[jk] += freq[jk][m][i];    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         }    double fx;
     int k=0,kmax=10;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double l1;
           pos += pp[jk];  
         for(jk=1; jk <=nlstate ; jk++){    fx=func(x);
           if(pos>=1.e-5)    for (i=1;i<=npar;i++) p2[i]=x[i];
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for(l=0 ; l <=lmax; l++){
           else      l1=pow(10,l);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      delts=delt;
           if( i <= (int) agemax){      for(k=1 ; k <kmax; k=k+1){
             if(pos>=1.e-5){        delt = delta*(l1*k);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        p2[theta]=x[theta] +delt;
               probs[i][jk][j1]= pp[jk]/pos;        k1=func(p2)-fx;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        p2[theta]=x[theta]-delt;
             }        k2=func(p2)-fx;
             else        /*res= (k1-2.0*fx+k2)/delt/delt; */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           }        
         }  #ifdef DEBUG
                printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(jk=-1; jk <=nlstate+ndeath; jk++)        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           for(m=-1; m <=nlstate+ndeath; m++)  #endif
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if(i <= (int) agemax)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           fprintf(ficresp,"\n");          k=kmax;
         printf("\n");        }
       }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     }          k=kmax; l=lmax*10.;
   }        }
   dateintmean=dateintsum/k2cpt;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            delts=delt;
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);    }
      delti[theta]=delts;
   /* End of Freq */    return res; 
 }    
   }
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  double hessij( double x[], double delti[], int thetai,int thetaj)
 {  /* Some frequencies */  {
      int i;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int l=1, l1, lmax=20;
   double ***freq; /* Frequencies */    double k1,k2,k3,k4,res,fx;
   double *pp;    double p2[NPARMAX+1];
   double pos, k2;    int k;
   
   pp=vector(1,nlstate);    fx=func(x);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      p2[thetai]=x[thetai]+delti[thetai]/k;
   j1=0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k1=func(p2)-fx;
   j=cptcoveff;    
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  for(k1=1; k1<=j;k1++){      k2=func(p2)-fx;
     for(i1=1; i1<=ncodemax[k1];i1++){    
       j1++;      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for (i=-1; i<=nlstate+ndeath; i++)        k3=func(p2)-fx;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      
           for(m=agemin; m <= agemax+3; m++)      p2[thetai]=x[thetai]-delti[thetai]/k;
             freq[i][jk][m]=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            k4=func(p2)-fx;
       for (i=1; i<=imx; i++) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         bool=1;  #ifdef DEBUG
         if  (cptcovn>0) {      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 (z1=1; z1<=cptcoveff; z1++)      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 (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  #endif
               bool=0;    }
         }    return res;
         if (bool==1) {  }
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  /************** Inverse of matrix **************/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  void ludcmp(double **a, int n, int *indx, double *d) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int i,imax,j,k; 
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double big,dum,sum,temp; 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    double *vv; 
             }   
           }    vv=vector(1,n); 
         }    *d=1.0; 
       }    for (i=1;i<=n;i++) { 
         for(i=(int)agemin; i <= (int)agemax+3; i++){      big=0.0; 
           for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=n;j++) 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
               pp[jk] += freq[jk][m][i];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           }      vv[i]=1.0/big; 
           for(jk=1; jk <=nlstate ; jk++){    } 
             for(m=-1, pos=0; m <=0 ; m++)    for (j=1;j<=n;j++) { 
             pos += freq[jk][m][i];      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
                for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          for(jk=1; jk <=nlstate ; jk++){        a[i][j]=sum; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } 
              pp[jk] += freq[jk][m][i];      big=0.0; 
          }      for (i=j;i<=n;i++) { 
                  sum=a[i][j]; 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
          for(jk=1; jk <=nlstate ; jk++){                  a[i][j]=sum; 
            if( i <= (int) agemax){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
              if(pos>=1.e-5){          big=dum; 
                probs[i][jk][j1]= pp[jk]/pos;          imax=i; 
              }        } 
            }      } 
          }      if (j != imax) { 
                  for (k=1;k<=n;k++) { 
         }          dum=a[imax][k]; 
     }          a[imax][k]=a[j][k]; 
   }          a[j][k]=dum; 
          } 
          *d = -(*d); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        vv[imax]=vv[j]; 
   free_vector(pp,1,nlstate);      } 
        indx[j]=imax; 
 }  /* End of Freq */      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
 /************* Waves Concatenation ***************/        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      } 
 {    } 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    free_vector(vv,1,n);  /* Doesn't work */
      Death is a valid wave (if date is known).  ;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  } 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.  void lubksb(double **a, int n, int *indx, double b[]) 
      */  { 
     int i,ii=0,ip,j; 
   int i, mi, m;    double sum; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;   
      double sum=0., jmean=0.;*/    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
   int j, k=0,jk, ju, jl;      sum=b[ip]; 
   double sum=0.;      b[ip]=b[i]; 
   jmin=1e+5;      if (ii) 
   jmax=-1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   jmean=0.;      else if (sum) ii=i; 
   for(i=1; i<=imx; i++){      b[i]=sum; 
     mi=0;    } 
     m=firstpass;    for (i=n;i>=1;i--) { 
     while(s[m][i] <= nlstate){      sum=b[i]; 
       if(s[m][i]>=1)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         mw[++mi][i]=m;      b[i]=sum/a[i][i]; 
       if(m >=lastpass)    } 
         break;  } 
       else  
         m++;  /************ Frequencies ********************/
     }/* end while */  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)
     if (s[m][i] > nlstate){  {  /* Some frequencies */
       mi++;     /* Death is another wave */    
       /* if(mi==0)  never been interviewed correctly before death */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
          /* Only death is a correct wave */    int first;
       mw[mi][i]=m;    double ***freq; /* Frequencies */
     }    double *pp;
     double pos, k2, dateintsum=0,k2cpt=0;
     wav[i]=mi;    FILE *ficresp;
     if(mi==0)    char fileresp[FILENAMELENGTH];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    
   }    pp=vector(1,nlstate);
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(i=1; i<=imx; i++){    strcpy(fileresp,"p");
     for(mi=1; mi<wav[i];mi++){    strcat(fileresp,fileres);
       if (stepm <=0)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         dh[mi][i]=1;      printf("Problem with prevalence resultfile: %s\n", fileresp);
       else{      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         if (s[mw[mi+1][i]][i] > nlstate) {      exit(0);
           if (agedc[i] < 2*AGESUP) {    }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           if(j==0) j=1;  /* Survives at least one month after exam */    j1=0;
           k=k+1;    
           if (j >= jmax) jmax=j;    j=cptcoveff;
           if (j <= jmin) jmin=j;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           sum=sum+j;  
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    first=1;
           }  
         }    for(k1=1; k1<=j;k1++){
         else{      for(i1=1; i1<=ncodemax[k1];i1++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        j1++;
           k=k+1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           if (j >= jmax) jmax=j;          scanf("%d", i);*/
           else if (j <= jmin)jmin=j;        for (i=-1; i<=nlstate+ndeath; i++)  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           sum=sum+j;            for(m=agemin; m <= agemax+3; m++)
         }              freq[i][jk][m]=0;
         jk= j/stepm;        
         jl= j -jk*stepm;        dateintsum=0;
         ju= j -(jk+1)*stepm;        k2cpt=0;
         if(jl <= -ju)        for (i=1; i<=imx; i++) {
           dh[mi][i]=jk;          bool=1;
         else          if  (cptcovn>0) {
           dh[mi][i]=jk+1;            for (z1=1; z1<=cptcoveff; z1++) 
         if(dh[mi][i]==0)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           dh[mi][i]=1; /* At least one step */                bool=0;
       }          }
     }          if (bool==1){
   }            for(m=firstpass; m<=lastpass; m++){
   jmean=sum/k;              k2=anint[m][i]+(mint[m][i]/12.);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              if ((k2>=dateprev1) && (k2<=dateprev2)) {
  }                if(agev[m][i]==0) agev[m][i]=agemax+1;
 /*********** Tricode ****************************/                if(agev[m][i]==1) agev[m][i]=agemax+2;
 void tricode(int *Tvar, int **nbcode, int imx)                if (m<lastpass) {
 {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   int Ndum[20],ij=1, k, j, i;                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
   int cptcode=0;                }
   cptcoveff=0;                
                  if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
   for (k=0; k<19; k++) Ndum[k]=0;                  dateintsum=dateintsum+k2;
   for (k=1; k<=7; k++) ncodemax[k]=0;                  k2cpt++;
                 }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              }
     for (i=1; i<=imx; i++) {            }
       ij=(int)(covar[Tvar[j]][i]);          }
       Ndum[ij]++;        }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/         
       if (ij > cptcode) cptcode=ij;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     }  
         if  (cptcovn>0) {
     for (i=0; i<=cptcode; i++) {          fprintf(ficresp, "\n#********** Variable "); 
       if(Ndum[i]!=0) ncodemax[j]++;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresp, "**********\n#");
     ij=1;        }
         for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     for (i=1; i<=ncodemax[j]; i++) {        fprintf(ficresp, "\n");
       for (k=0; k<=19; k++) {        
         if (Ndum[k] != 0) {        for(i=(int)agemin; i <= (int)agemax+3; i++){
           nbcode[Tvar[j]][ij]=k;          if(i==(int)agemax+3){
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/            fprintf(ficlog,"Total");
           ij++;          }else{
         }            if(first==1){
         if (ij > ncodemax[j]) break;              first=0;
       }                printf("See log file for details...\n");
     }            }
   }              fprintf(ficlog,"Age %d", i);
           }
  for (k=0; k<19; k++) Ndum[k]=0;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
  for (i=1; i<=ncovmodel-2; i++) {              pp[jk] += freq[jk][m][i]; 
       ij=Tvar[i];          }
       Ndum[ij]++;          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
  ij=1;            if(pp[jk]>=1.e-10){
  for (i=1; i<=10; i++) {              if(first==1){
    if((Ndum[i]!=0) && (i<=ncovcol)){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      Tvaraff[ij]=i;              }
      ij++;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    }            }else{
  }              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     cptcoveff=ij-1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }            }
           }
 /*********** Health Expectancies ****************/  
           for(jk=1; jk <=nlstate ; 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)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 {              pp[jk] += freq[jk][m][i];
   /* Health expectancies */          }
   int i, j, nhstepm, hstepm, h, nstepm;  
   double age, agelim, hf;          for(jk=1,pos=0; jk <=nlstate ; jk++)
   double ***p3mat;            pos += pp[jk];
            for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficreseij,"# Health expectancies\n");            if(pos>=1.e-5){
   fprintf(ficreseij,"# Age");              if(first==1)
   for(i=1; i<=nlstate;i++)                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(j=1; j<=nlstate;j++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficreseij," %1d-%1d",i,j);            }else{
   fprintf(ficreseij,"\n");              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if(estepm < stepm){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     printf ("Problem %d lower than %d\n",estepm, stepm);            }
   }            if( i <= (int) agemax){
   else  hstepm=estepm;                if(pos>=1.e-5){
   /* We compute the life expectancy from trapezoids spaced every estepm months                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
    * This is mainly to measure the difference between two models: for example                probs[i][jk][j1]= pp[jk]/pos;
    * if stepm=24 months pijx are given only every 2 years and by summing them                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
    * we are calculating an estimate of the Life Expectancy assuming a linear              }
    * progression inbetween and thus overestimating or underestimating according              else
    * to the curvature of the survival function. If, for the same date, we                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            }
    * to compare the new estimate of Life expectancy with the same linear          }
    * hypothesis. A more precise result, taking into account a more precise          
    * curvature will be obtained if estepm is as small as stepm. */          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
   /* For example we decided to compute the life expectancy with the smallest unit */              if(freq[jk][m][i] !=0 ) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              if(first==1)
      nhstepm is the number of hstepm from age to agelim                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      nstepm is the number of stepm from age to agelin.                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      Look at hpijx to understand the reason of that which relies in memory size              }
      and note for a fixed period like estepm months */          if(i <= (int) agemax)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            fprintf(ficresp,"\n");
      survival function given by stepm (the optimization length). Unfortunately it          if(first==1)
      means that if the survival funtion is printed only each two years of age and if            printf("Others in log...\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          fprintf(ficlog,"\n");
      results. So we changed our mind and took the option of the best precision.        }
   */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    }
     dateintmean=dateintsum/k2cpt; 
   agelim=AGESUP;   
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fclose(ficresp);
     /* nhstepm age range expressed in number of stepm */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    free_vector(pp,1,nlstate);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    
     /* if (stepm >= YEARM) hstepm=1;*/    /* End of Freq */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  /************ Prevalence ********************/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  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, int firstpass, int lastpass)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    {  
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     for(i=1; i<=nlstate;i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
       for(j=1; j<=nlstate;j++)       We still use firstpass and lastpass as another selection.
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;   
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         }    double ***freq; /* Frequencies */
     fprintf(ficreseij,"%3.0f",age );    double *pp;
     for(i=1; i<=nlstate;i++)    double pos; 
       for(j=1; j<=nlstate;j++){    double  y2; /* in fractional years */
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  
       }    pp=vector(1,nlstate);
     fprintf(ficreseij,"\n");    
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   }    j1=0;
 }    
     j=cptcoveff;
 /************ Variance ******************/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    
 {    for(k1=1; k1<=j;k1++){
   /* Variance of health expectancies */      for(i1=1; i1<=ncodemax[k1];i1++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        j1++;
   double **newm;        
   double **dnewm,**doldm;        for (i=-1; i<=nlstate+ndeath; i++)  
   int i, j, nhstepm, hstepm, h, nstepm ;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   int k, cptcode;            for(m=agemin; m <= agemax+3; m++)
   double *xp;              freq[i][jk][m]=0;
   double **gp, **gm;       
   double ***gradg, ***trgradg;        for (i=1; i<=imx; i++) { /* Each individual */
   double ***p3mat;          bool=1;
   double age,agelim, hf;          if  (cptcovn>0) {
   int theta;            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    fprintf(ficresvij,"# Covariances of life expectancies\n");                bool=0;
   fprintf(ficresvij,"# Age");          } 
   for(i=1; i<=nlstate;i++)          if (bool==1) { 
     for(j=1; j<=nlstate;j++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   fprintf(ficresvij,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
   xp=vector(1,npar);                if(agev[m][i]==1) agev[m][i]=agemax+2;
   dnewm=matrix(1,nlstate,1,npar);                if (m<lastpass) {
   doldm=matrix(1,nlstate,1,nlstate);                  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]; 
   if(estepm < stepm){                }
     printf ("Problem %d lower than %d\n",estepm, stepm);              }
   }            } /* end selection of waves */
   else  hstepm=estepm;            }
   /* For example we decided to compute the life expectancy with the smallest unit */        }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
      nhstepm is the number of hstepm from age to agelim          for(jk=1; jk <=nlstate ; jk++){
      nstepm is the number of stepm from age to agelin.            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      Look at hpijx to understand the reason of that which relies in memory size              pp[jk] += freq[jk][m][i]; 
      and note for a fixed period like k years */          }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(jk=1; jk <=nlstate ; jk++){
      survival function given by stepm (the optimization length). Unfortunately it            for(m=-1, pos=0; m <=0 ; m++)
      means that if the survival funtion is printed only each two years of age and if              pos += freq[jk][m][i];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          }
      results. So we changed our mind and took the option of the best precision.          
   */          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   agelim = AGESUP;              pp[jk] += freq[jk][m][i];
   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 */          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){    
     gp=matrix(0,nhstepm,1,nlstate);            if( i <= (int) agemax){
     gm=matrix(0,nhstepm,1,nlstate);              if(pos>=1.e-5){
                 probs[i][jk][j1]= pp[jk]/pos;
     for(theta=1; theta <=npar; theta++){              }
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }/* end jk */
       }        }/* end i */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* end i1 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } /* end k1 */
   
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
           prlim[i][i]=probs[(int)age][i][ij];    free_vector(pp,1,nlstate);
       }    
    }  /* End of Freq */
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  /************* Waves Concatenation ***************/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  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)
         }  {
       }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           Death is a valid wave (if date is known).
       for(i=1; i<=npar; i++) /* Computes gradient */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         and mw[mi+1][i]. dh depends on stepm.
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       */
    
       if (popbased==1) {    int i, mi, m;
         for(i=1; i<=nlstate;i++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           prlim[i][i]=probs[(int)age][i][ij];       double sum=0., jmean=0.;*/
       }    int first;
     int j, k=0,jk, ju, jl;
       for(j=1; j<= nlstate; j++){    double sum=0.;
         for(h=0; h<=nhstepm; h++){    first=0;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    jmin=1e+5;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    jmax=-1;
         }    jmean=0.;
       }    for(i=1; i<=imx; i++){
       mi=0;
       for(j=1; j<= nlstate; j++)      m=firstpass;
         for(h=0; h<=nhstepm; h++){      while(s[m][i] <= nlstate){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        if(s[m][i]>=1)
         }          mw[++mi][i]=m;
     } /* End theta */        if(m >=lastpass)
           break;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        else
           m++;
     for(h=0; h<=nhstepm; h++)      }/* end while */
       for(j=1; j<=nlstate;j++)      if (s[m][i] > nlstate){
         for(theta=1; theta <=npar; theta++)        mi++;     /* Death is another wave */
           trgradg[h][j][theta]=gradg[h][theta][j];        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        mw[mi][i]=m;
     for(i=1;i<=nlstate;i++)      }
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;      wav[i]=mi;
       if(mi==0){
     for(h=0;h<=nhstepm;h++){        if(first==0){
       for(k=0;k<=nhstepm;k++){          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          first=1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        }
         for(i=1;i<=nlstate;i++)        if(first==1){
           for(j=1;j<=nlstate;j++)          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        }
       }      } /* end mi==0 */
     }    }
   
     fprintf(ficresvij,"%.0f ",age );    for(i=1; i<=imx; i++){
     for(i=1; i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
       for(j=1; j<=nlstate;j++){        if (stepm <=0)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          dh[mi][i]=1;
       }        else{
     fprintf(ficresvij,"\n");          if (s[mw[mi+1][i]][i] > nlstate) {
     free_matrix(gp,0,nhstepm,1,nlstate);            if (agedc[i] < 2*AGESUP) {
     free_matrix(gm,0,nhstepm,1,nlstate);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            if(j==0) j=1;  /* Survives at least one month after exam */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            k=k+1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if (j >= jmax) jmax=j;
   } /* End age */            if (j <= jmin) jmin=j;
              sum=sum+j;
   free_vector(xp,1,npar);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   free_matrix(doldm,1,nlstate,1,npar);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   free_matrix(dnewm,1,nlstate,1,nlstate);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             }
 }          }
           else{
 /************ Variance of prevlim ******************/            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 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)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 {            k=k+1;
   /* Variance of prevalence limit */            if (j >= jmax) jmax=j;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            else if (j <= jmin)jmin=j;
   double **newm;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   double **dnewm,**doldm;            sum=sum+j;
   int i, j, nhstepm, hstepm;          }
   int k, cptcode;          jk= j/stepm;
   double *xp;          jl= j -jk*stepm;
   double *gp, *gm;          ju= j -(jk+1)*stepm;
   double **gradg, **trgradg;          if(mle <=1){ 
   double age,agelim;            if(jl==0){
   int theta;              dh[mi][i]=jk;
                  bh[mi][i]=0;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            }else{ /* We want a negative bias in order to only have interpolation ie
   fprintf(ficresvpl,"# Age");                    * at the price of an extra matrix product in likelihood */
   for(i=1; i<=nlstate;i++)              dh[mi][i]=jk+1;
       fprintf(ficresvpl," %1d-%1d",i,i);              bh[mi][i]=ju;
   fprintf(ficresvpl,"\n");            }
           }else{
   xp=vector(1,npar);            if(jl <= -ju){
   dnewm=matrix(1,nlstate,1,npar);              dh[mi][i]=jk;
   doldm=matrix(1,nlstate,1,nlstate);              bh[mi][i]=jl;       /* bias is positive if real duration
                                     * is higher than the multiple of stepm and negative otherwise.
   hstepm=1*YEARM; /* Every year of age */                                   */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
   agelim = AGESUP;            else{
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              dh[mi][i]=jk+1;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              bh[mi][i]=ju;
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            if(dh[mi][i]==0){
     gradg=matrix(1,npar,1,nlstate);              dh[mi][i]=1; /* At least one step */
     gp=vector(1,nlstate);              bh[mi][i]=ju; /* At least one step */
     gm=vector(1,nlstate);              /*  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);*/
             }
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */        } /* end if mle */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      } /* end wave */
       }    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    jmean=sum/k;
       for(i=1;i<=nlstate;i++)    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         gp[i] = prlim[i][i];    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*********** Tricode ****************************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  void tricode(int *Tvar, int **nbcode, int imx)
       for(i=1;i<=nlstate;i++)  {
         gm[i] = prlim[i][i];    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
       for(i=1;i<=nlstate;i++)    int cptcode=0;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    cptcoveff=0; 
     } /* End theta */   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
     trgradg =matrix(1,nlstate,1,npar);    for (k=1; k<=7; k++) ncodemax[k]=0;
   
     for(j=1; j<=nlstate;j++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for(theta=1; theta <=npar; theta++)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         trgradg[j][theta]=gradg[theta][j];                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     for(i=1;i<=nlstate;i++)        Ndum[ij]++; /*store the modality */
       varpl[i][(int)age] =0.;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);                                         Tvar[j]. If V=sex and male is 0 and 
     for(i=1;i<=nlstate;i++)                                         female is 1, then  cptcode=1.*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      }
   
     fprintf(ficresvpl,"%.0f ",age );      for (i=0; i<=cptcode; i++) {
     for(i=1; i<=nlstate;i++)        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);      ij=1; 
     free_vector(gm,1,nlstate);      for (i=1; i<=ncodemax[j]; i++) {
     free_matrix(gradg,1,npar,1,nlstate);        for (k=0; k<= maxncov; k++) {
     free_matrix(trgradg,1,nlstate,1,npar);          if (Ndum[k] != 0) {
   } /* End age */            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_vector(xp,1,npar);            
   free_matrix(doldm,1,nlstate,1,npar);            ij++;
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           if (ij > ncodemax[j]) break; 
 }        }  
       } 
 /************ Variance of one-step probabilities  ******************/    }  
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {   for (k=0; k< maxncov; k++) Ndum[k]=0;
   int i, j;  
   int k=0, cptcode;   for (i=1; i<=ncovmodel-2; i++) { 
   double **dnewm,**doldm;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double *xp;     ij=Tvar[i];
   double *gp, *gm;     Ndum[ij]++;
   double **gradg, **trgradg;   }
   double age,agelim, cov[NCOVMAX];  
   int theta;   ij=1;
   char fileresprob[FILENAMELENGTH];   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
   strcpy(fileresprob,"prob");       Tvaraff[ij]=i; /*For printing */
   strcat(fileresprob,fileres);       ij++;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {     }
     printf("Problem with resultfile: %s\n", fileresprob);   }
   }   
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);   cptcoveff=ij-1; /*Number of simple covariates*/
    }
   
   xp=vector(1,npar);  /*********** Health Expectancies ****************/
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  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 )
    
   cov[1]=1;  {
   for (age=bage; age<=fage; age ++){    /* Health expectancies */
     cov[2]=age;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     gradg=matrix(1,npar,1,9);    double age, agelim, hf;
     trgradg=matrix(1,9,1,npar);    double ***p3mat,***varhe;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double **dnewm,**doldm;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double *xp;
        double **gp, **gm;
     for(theta=1; theta <=npar; theta++){    double ***gradg, ***trgradg;
       for(i=1; i<=npar; i++)    int theta;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
          varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    xp=vector(1,npar);
        dnewm=matrix(1,nlstate*2,1,npar);
       k=0;    doldm=matrix(1,nlstate*2,1,nlstate*2);
       for(i=1; i<= (nlstate+ndeath); i++){    
         for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficreseij,"# Health expectancies\n");
            k=k+1;    fprintf(ficreseij,"# Age");
           gp[k]=pmmij[i][j];    for(i=1; i<=nlstate;i++)
         }      for(j=1; j<=nlstate;j++)
       }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
     }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    else  hstepm=estepm;   
       k=0;    /* We compute the life expectancy from trapezoids spaced every estepm months
       for(i=1; i<=(nlstate+ndeath); i++){     * This is mainly to measure the difference between two models: for example
         for(j=1; j<=(nlstate+ndeath);j++){     * if stepm=24 months pijx are given only every 2 years and by summing them
           k=k+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
           gm[k]=pmmij[i][j];     * progression in between and thus overestimating or underestimating according
         }     * to the curvature of the survival function. If, for the same date, we 
       }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           * to compare the new estimate of Life expectancy with the same linear 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)     * hypothesis. A more precise result, taking into account a more precise
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];       * curvature will be obtained if estepm is as small as stepm. */
     }  
     /* For example we decided to compute the life expectancy with the smallest unit */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(theta=1; theta <=npar; theta++)       nhstepm is the number of hstepm from age to agelim 
       trgradg[j][theta]=gradg[theta][j];       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);       and note for a fixed period like estepm months */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    /* 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
      pmij(pmmij,cov,ncovmodel,x,nlstate);       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 
      k=0;       results. So we changed our mind and took the option of the best precision.
      for(i=1; i<=(nlstate+ndeath); i++){    */
        for(j=1; j<=(nlstate+ndeath);j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          k=k+1;  
          gm[k]=pmmij[i][j];    agelim=AGESUP;
         }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      }      /* nhstepm age range expressed in number of stepm */
            nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      /*printf("\n%d ",(int)age);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      /* 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);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
      }*/      gp=matrix(0,nhstepm,1,nlstate*2);
       gm=matrix(0,nhstepm,1,nlstate*2);
   fprintf(ficresprob,"\n%d ",(int)age);  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);   
   }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      /* Computing Variances of health expectancies */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       for(theta=1; theta <=npar; theta++){
 }        for(i=1; i<=npar; i++){ 
  free_vector(xp,1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 fclose(ficresprob);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 }    
         cptj=0;
 /******************* Printing html file ***********/        for(j=1; j<= nlstate; j++){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          for(i=1; i<=nlstate; i++){
  int lastpass, int stepm, int weightopt, char model[],\            cptj=cptj+1;
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  char version[], int popforecast, int estepm ){            }
   int jj1, k1, i1, cpt;          }
   FILE *fichtm;        }
   /*char optionfilehtm[FILENAMELENGTH];*/       
        
   strcpy(optionfilehtm,optionfile);        for(i=1; i<=npar; i++) 
   strcat(optionfilehtm,".htm");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with %s \n",optionfilehtm), exit(0);        
   }        cptj=0;
         for(j=1; j<= nlstate; j++){
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          for(i=1;i<=nlstate;i++){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            cptj=cptj+1;
 \n            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 Total number of observations=%d <br>\n              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            }
 <hr  size=\"2\" color=\"#EC5E5E\">          }
  <ul><li>Outputs files<br>\n        }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        for(j=1; j<= nlstate*2; j++)
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n          for(h=0; h<=nhstepm-1; h++){
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          }
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n       } 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);     
   /* End theta */
  fprintf(fichtm,"\n  
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n       for(h=0; h<=nhstepm-1; h++)
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        for(j=1; j<=nlstate*2;j++)
           for(theta=1; theta <=npar; theta++)
  if(popforecast==1) fprintf(fichtm,"\n            trgradg[h][j][theta]=gradg[h][theta][j];
  - 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  
         <br>",fileres,fileres,fileres,fileres);       for(i=1;i<=nlstate*2;i++)
  else        for(j=1;j<=nlstate*2;j++)
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);          varhe[i][j][(int)age] =0.;
 fprintf(fichtm," <li>Graphs</li><p>");  
        printf("%d|",(int)age);fflush(stdout);
  m=cptcoveff;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
  jj1=0;          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
  for(k1=1; k1<=m;k1++){          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
    for(i1=1; i1<=ncodemax[k1];i1++){          for(i=1;i<=nlstate*2;i++)
        jj1++;            for(j=1;j<=nlstate*2;j++)
        if (cptcovn > 0) {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
          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]]);      /* Computing expectancies */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      for(i=1; i<=nlstate;i++)
        }        for(j=1; j<=nlstate;j++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
        for(cpt=1; cpt<nlstate;cpt++){            
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  /* 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]);*/
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }          }
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      fprintf(ficreseij,"%3.0f",age );
 interval) in state (%d): v%s%d%d.gif <br>      cptj=0;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i=1; i<=nlstate;i++)
      }        for(j=1; j<=nlstate;j++){
      for(cpt=1; cpt<=nlstate;cpt++) {          cptj++;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
      }      fprintf(ficreseij,"\n");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     
 health expectancies in states (1) and (2): e%s%d.gif<br>      free_matrix(gm,0,nhstepm,1,nlstate*2);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      free_matrix(gp,0,nhstepm,1,nlstate*2);
 fprintf(fichtm,"\n</body>");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
    }      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
    }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fclose(fichtm);    }
 }    printf("\n");
     fprintf(ficlog,"\n");
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*2,1,npar);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   strcpy(optionfilegnuplot,optionfilefiname);  }
   strcat(optionfilegnuplot,".gp.txt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  /************ Variance ******************/
     printf("Problem with file %s",optionfilegnuplot);  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)
   }  {
     /* Variance of health expectancies */
 #ifdef windows    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     fprintf(ficgp,"cd \"%s\" \n",pathc);    /* double **newm;*/
 #endif    double **dnewm,**doldm;
 m=pow(2,cptcoveff);    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
  /* 1eme*/    int k, cptcode;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double *xp;
    for (k1=1; k1<= m ; k1 ++) {    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
 #ifdef windows    double **gradgp, **trgradgp; /* for var p point j */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    double *gpp, *gmp; /* for var p point j */
 #endif    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 #ifdef unix    double ***p3mat;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    double age,agelim, hf;
 #endif    double ***mobaverage;
     int theta;
 for (i=1; i<= nlstate ; i ++) {    char digit[4];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    char digitp[25];
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    char fileresprobmorprev[FILENAMELENGTH];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {    if(popbased==1){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if(mobilav!=0)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        strcpy(digitp,"-populbased-mobilav-");
 }      else strcpy(digitp,"-populbased-nomobil-");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
      for (i=1; i<= nlstate ; i ++) {    else 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      strcpy(digitp,"-stablbased-");
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      if (mobilav!=0) {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #ifdef unix      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 fprintf(ficgp,"\nset ter gif small size 400,300");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 #endif        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
    }    }
   }  
   /*2 eme*/    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   for (k1=1; k1<= m ; k1 ++) {    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
        strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for (i=1; i<= nlstate+1 ; i ++) {    strcat(fileresprobmorprev,fileres);
       k=2*i;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 }      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    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);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficresprobmorprev," p.%-d SE",j);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
         else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 }      }  
       fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(ficresprobmorprev,"\n");
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       for (j=1; j<= nlstate+1 ; j ++) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      exit(0);
 }      }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    else{
       else fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficgp,"\n# Routine varevsij");
     }    }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   }      printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   /*3eme*/      exit(0);
     }
   for (k1=1; k1<= m ; k1 ++) {    else{
     for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
       k=2+nlstate*(cpt-1);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    }
       for (i=1; i< nlstate ; i ++) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  
       }    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(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresvij,"# Age");
     }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   /* CV preval stat */    fprintf(ficresvij,"\n");
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    xp=vector(1,npar);
       k=3;    dnewm=matrix(1,nlstate,1,npar);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for (i=1; i< nlstate ; i ++)    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
          gpp=vector(nlstate+1,nlstate+ndeath);
       l=3+(nlstate+ndeath)*cpt;    gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for (i=1; i< nlstate ; i ++) {    
         l=3+(nlstate+ndeath)*cpt;    if(estepm < stepm){
         fprintf(ficgp,"+$%d",l+i+1);      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      else  hstepm=estepm;   
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* For example we decided to compute the life expectancy with the smallest unit */
     }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   }         nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   /* proba elementaires */       Look at hpijx to understand the reason of that which relies in memory size
    for(i=1,jk=1; i <=nlstate; i++){       and note for a fixed period like k years */
     for(k=1; k <=(nlstate+ndeath); k++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       if (k != i) {       survival function given by stepm (the optimization length). Unfortunately it
         for(j=1; j <=ncovmodel; j++){       means that if the survival funtion is printed every two years of age and if
               you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);       results. So we changed our mind and took the option of the best precision.
           jk++;    */
           fprintf(ficgp,"\n");    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(jk=1; jk <=m; jk++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      gp=matrix(0,nhstepm,1,nlstate);
    i=1;      gm=matrix(0,nhstepm,1,nlstate);
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {      for(theta=1; theta <=npar; theta++){
        if (k != k2){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 ij=1;        }
         for(j=3; j <=ncovmodel; j++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;        if (popbased==1) {
           }          if(mobilav ==0){
           else            for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              prlim[i][i]=probs[(int)age][i][ij];
         }          }else{ /* mobilav */ 
           fprintf(ficgp,")/(1");            for(i=1; i<=nlstate;i++)
                      prlim[i][i]=mobaverage[(int)age][i][ij];
         for(k1=1; k1 <=nlstate; k1++){            }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        }
 ij=1;    
           for(j=3; j <=ncovmodel; j++){        for(j=1; j<= nlstate; j++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for(h=0; h<=nhstepm; h++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
             ij++;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }          }
           else        }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        /* This for computing probability of death (h=1 means
           }           computed over hstepm matrices product = hstepm*stepm months) 
           fprintf(ficgp,")");           as a weighted average of prlim.
         }        */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         i=i+ncovmodel;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }        }    
      }        /* end probability of death */
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
    }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fclose(ficgp);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 }  /* end gnuplot */   
         if (popbased==1) {
           if(mobilav ==0){
 /*************** Moving average **************/            for(i=1; i<=nlstate;i++)
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   int i, cpt, cptcod;            for(i=1; i<=nlstate;i++)
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)              prlim[i][i]=mobaverage[(int)age][i][ij];
       for (i=1; i<=nlstate;i++)          }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
            for(j=1; j<= nlstate; j++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          for(h=0; h<=nhstepm; h++){
       for (i=1; i<=nlstate;i++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }        /* This for computing probability of death (h=1 means
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;           computed over hstepm matrices product = hstepm*stepm months) 
         }           as a weighted average of prlim.
       }        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gmp[j]=0.; i<= nlstate; i++)
 }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   double ***p3mat;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   char fileresf[FILENAMELENGTH];        }
   
  agelim=AGESUP;      } /* End theta */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
        for(h=0; h<=nhstepm; h++) /* veij */
          for(j=1; j<=nlstate;j++)
   strcpy(fileresf,"f");          for(theta=1; theta <=npar; theta++)
   strcat(fileresf,fileres);            trgradg[h][j][theta]=gradg[h][theta][j];
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   }        for(theta=1; theta <=npar; theta++)
   printf("Computing forecasting: result on file '%s' \n", fileresf);          trgradgp[j][theta]=gradgp[theta][j];
     
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (mobilav==1) {      for(i=1;i<=nlstate;i++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1;j<=nlstate;j++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);          vareij[i][j][(int)age] =0.;
   }  
       for(h=0;h<=nhstepm;h++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(k=0;k<=nhstepm;k++){
   if (stepm<=12) stepsize=1;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   agelim=AGESUP;          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
   hstepm=1;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   hstepm=hstepm/stepm;        }
   yp1=modf(dateintmean,&yp);      }
   anprojmean=yp;    
   yp2=modf((yp1*12),&yp);      /* pptj */
   mprojmean=yp;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   yp1=modf((yp2*30.5),&yp);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   jprojmean=yp;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if(jprojmean==0) jprojmean=1;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if(mprojmean==0) jprojmean=1;          varppt[j][i]=doldmp[j][i];
        /* end ppptj */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      /*  x centered again */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   for(cptcov=1;cptcov<=i2;cptcov++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   
       k=k+1;      if (popbased==1) {
       fprintf(ficresf,"\n#******");        if(mobilav ==0){
       for(j=1;j<=cptcoveff;j++) {          for(i=1; i<=nlstate;i++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            prlim[i][i]=probs[(int)age][i][ij];
       }        }else{ /* mobilav */ 
       fprintf(ficresf,"******\n");          for(i=1; i<=nlstate;i++)
       fprintf(ficresf,"# StartingAge FinalAge");            prlim[i][i]=mobaverage[(int)age][i][ij];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }
            }
                     
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      /* This for computing probability of death (h=1 means
         fprintf(ficresf,"\n");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);           as a weighted average of prlim.
       */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           nhstepm = nhstepm/hstepm;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                }    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* end probability of death */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
              for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for (h=0; h<=nhstepm; h++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
             if (h==(int) (calagedate+YEARM*cpt)) {        for(i=1; i<=nlstate;i++){
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             }        }
             for(j=1; j<=nlstate+ndeath;j++) {      } 
               kk1=0.;kk2=0;      fprintf(ficresprobmorprev,"\n");
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)      fprintf(ficresvij,"%.0f ",age );
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(i=1; i<=nlstate;i++)
                 else {        for(j=1; j<=nlstate;j++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                 }        }
                      fprintf(ficresvij,"\n");
               }      free_matrix(gp,0,nhstepm,1,nlstate);
               if (h==(int)(calagedate+12*cpt)){      free_matrix(gm,0,nhstepm,1,nlstate);
                 fprintf(ficresf," %.3f", kk1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                              free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
               }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }    } /* End age */
           }    free_vector(gpp,nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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(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(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fclose(ficresf);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
 }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
 /************** Forecasting ******************/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
 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,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
   int *popage;    /*  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);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  */
   double *popeffectif,*popcount;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewm,1,nlstate,1,npar);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   agelim=AGESUP;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fclose(ficresprobmorprev);
      fclose(ficgp);
      fclose(fichtm);
   strcpy(filerespop,"pop");  }  
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /************ Variance of prevlim ******************/
     printf("Problem with forecast resultfile: %s\n", filerespop);  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)
   }  {
   printf("Computing forecasting: result on file '%s' \n", filerespop);    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double **newm;
     double **dnewm,**doldm;
   if (mobilav==1) {    int i, j, nhstepm, hstepm;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int k, cptcode;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double *xp;
   }    double *gp, *gm;
     double **gradg, **trgradg;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double age,agelim;
   if (stepm<=12) stepsize=1;    int theta;
       
   agelim=AGESUP;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
      fprintf(ficresvpl,"# Age");
   hstepm=1;    for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm;        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficresvpl,"\n");
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {    xp=vector(1,npar);
       printf("Problem with population file : %s\n",popfile);exit(0);    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     popage=ivector(0,AGESUP);    
     popeffectif=vector(0,AGESUP);    hstepm=1*YEARM; /* Every year of age */
     popcount=vector(0,AGESUP);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
        agelim = AGESUP;
     i=1;      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          if (stepm >= YEARM) hstepm=1;
     imx=i;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      gradg=matrix(1,npar,1,nlstate);
   }      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(theta=1; theta <=npar; theta++){
       k=k+1;        for(i=1; i<=npar; i++){ /* Computes gradient */
       fprintf(ficrespop,"\n#******");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(j=1;j<=cptcoveff;j++) {        }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }        for(i=1;i<=nlstate;i++)
       fprintf(ficrespop,"******\n");          gp[i] = prlim[i][i];
       fprintf(ficrespop,"# Age");      
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        for(i=1; i<=npar; i++) /* Computes gradient */
       if (popforecast==1)  fprintf(ficrespop," [Population]");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
              prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       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);            gm[i] = prlim[i][i];
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=1;i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           nhstepm = nhstepm/hstepm;      } /* End theta */
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      trgradg =matrix(1,nlstate,1,npar);
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(j=1; j<=nlstate;j++)
                for(theta=1; theta <=npar; theta++)
           for (h=0; h<=nhstepm; h++){          trgradg[j][theta]=gradg[theta][j];
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for(i=1;i<=nlstate;i++)
             }        varpl[i][(int)age] =0.;
             for(j=1; j<=nlstate+ndeath;j++) {      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               kk1=0.;kk2=0;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
               for(i=1; i<=nlstate;i++) {                    for(i=1;i<=nlstate;i++)
                 if (mobilav==1)        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {      fprintf(ficresvpl,"%.0f ",age );
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(i=1; i<=nlstate;i++)
                 }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
               }      fprintf(ficresvpl,"\n");
               if (h==(int)(calagedate+12*cpt)){      free_vector(gp,1,nlstate);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      free_vector(gm,1,nlstate);
                   /*fprintf(ficrespop," %.3f", kk1);      free_matrix(gradg,1,npar,1,nlstate);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      free_matrix(trgradg,1,nlstate,1,npar);
               }    } /* End age */
             }  
             for(i=1; i<=nlstate;i++){    free_vector(xp,1,npar);
               kk1=0.;    free_matrix(doldm,1,nlstate,1,npar);
                 for(j=1; j<=nlstate;j++){    free_matrix(dnewm,1,nlstate,1,nlstate);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }  }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  {
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    int i, j=0,  i1, k1, l1, t, tj;
           }    int k2, l2, j1,  z1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int k=0,l, cptcode;
         }    int first=1, first1;
       }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
   /******/    double *xp;
     double *gp, *gm;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    double **gradg, **trgradg;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double **mu;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double age,agelim, cov[NCOVMAX];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           nhstepm = nhstepm/hstepm;    int theta;
              char fileresprob[FILENAMELENGTH];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresprobcov[FILENAMELENGTH];
           oldm=oldms;savm=savms;    char fileresprobcor[FILENAMELENGTH];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           for (h=0; h<=nhstepm; h++){    double ***varpij;
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    strcpy(fileresprob,"prob"); 
             }    strcat(fileresprob,fileres);
             for(j=1; j<=nlstate+ndeath;j++) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
               kk1=0.;kk2=0;      printf("Problem with resultfile: %s\n", fileresprob);
               for(i=1; i<=nlstate;i++) {                    fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        }
               }    strcpy(fileresprobcov,"probcov"); 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    strcat(fileresprobcov,fileres);
             }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           }      printf("Problem with resultfile: %s\n", fileresprobcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         }    }
       }    strcpy(fileresprobcor,"probcor"); 
    }    strcat(fileresprobcor,fileres);
   }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   if (popforecast==1) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     free_ivector(popage,0,AGESUP);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     free_vector(popeffectif,0,AGESUP);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     free_vector(popcount,0,AGESUP);    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);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   fclose(ficrespop);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 }    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 /***********************************************/    fprintf(ficresprobcov,"# Age");
 /**************** Main Program *****************/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 /***********************************************/    fprintf(ficresprobcov,"# Age");
   
 int main(int argc, char *argv[])  
 {    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   double agedeb, agefin,hf;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
   double fret;   /* fprintf(ficresprob,"\n");
   double **xi,tmp,delta;    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
   double dum; /* Dummy variable */   */
   double ***p3mat;   xp=vector(1,npar);
   int *indx;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   char line[MAXLINE], linepar[MAXLINE];    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   char title[MAXLINE];    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    first=1;
      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   char filerest[FILENAMELENGTH];      exit(0);
   char fileregp[FILENAMELENGTH];    }
   char popfile[FILENAMELENGTH];    else{
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      fprintf(ficgp,"\n# Routine varprob");
   int firstobs=1, lastobs=10;    }
   int sdeb, sfin; /* Status at beginning and end */    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   int c,  h , cpt,l;      printf("Problem with html file: %s\n", optionfilehtm);
   int ju,jl, mi;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      exit(0);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    }
   int mobilav=0,popforecast=0;    else{
   int hstepm, nhstepm;      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;      fprintf(fichtm,"\n");
   
   double bage, fage, age, agelim, agebase;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   double ftolpl=FTOL;      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");
   double **prlim;      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");
   double *severity;  
   double ***param; /* Matrix of parameters */    }
   double  *p;  
   double **matcov; /* Matrix of covariance */    cov[1]=1;
   double ***delti3; /* Scale */    tj=cptcoveff;
   double *delti; /* Scale */    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   double ***eij, ***vareij;    j1=0;
   double **varpl; /* Variances of prevalence limits by age */    for(t=1; t<=tj;t++){
   double *epj, vepp;      for(i1=1; i1<=ncodemax[t];i1++){ 
   double kk1, kk2;        j1++;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";          fprintf(ficresprob, "**********\n#\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
   char z[1]="c", occ;          
 #include <sys/time.h>          fprintf(ficgp, "\n#********** Variable "); 
 #include <time.h>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          fprintf(ficgp, "**********\n#\n");
            
   /* long total_usecs;          
   struct timeval start_time, end_time;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   getcwd(pathcd, size);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   printf("\n%s",version);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if(argc <=1){          fprintf(ficresprobcor, "**********\n#");    
     printf("\nEnter the parameter file name: ");        }
     scanf("%s",pathtot);        
   }        for (age=bage; age<=fage; age ++){ 
   else{          cov[2]=age;
     strcpy(pathtot,argv[1]);          for (k=1; k<=cptcovn;k++) {
   }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          }
   /*cygwin_split_path(pathtot,path,optionfile);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for (k=1; k<=cptcovprod;k++)
   /* cutv(path,optionfile,pathtot,'\\');*/            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   chdir(path);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   replace(pathc,path);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
 /*-------- arguments in the command line --------*/          for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
   strcpy(fileres,"r");              xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcat(fileres, optionfilefiname);            
   strcat(fileres,".txt");    /* Other files have txt extension */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
   /*---------arguments file --------*/            k=0;
             for(i=1; i<= (nlstate); i++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              for(j=1; j<=(nlstate+ndeath);j++){
     printf("Problem with optionfile %s\n",optionfile);                k=k+1;
     goto end;                gp[k]=pmmij[i][j];
   }              }
             }
   strcpy(filereso,"o");            
   strcat(filereso,fileres);            for(i=1; i<=npar; i++)
   if((ficparo=fopen(filereso,"w"))==NULL) {              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=(nlstate); i++){
   while((c=getc(ficpar))=='#' && c!= EOF){              for(j=1; j<=(nlstate+ndeath);j++){
     ungetc(c,ficpar);                k=k+1;
     fgets(line, MAXLINE, ficpar);                gm[k]=pmmij[i][j];
     puts(line);              }
     fputs(line,ficparo);            }
   }       
   ungetc(c,ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);  
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 while((c=getc(ficpar))=='#' && c!= EOF){            for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);              trgradg[j][theta]=gradg[theta][j];
     fgets(line, MAXLINE, ficpar);          
     puts(line);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   ungetc(c,ficpar);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
              free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          
           k=0;
   ncovmodel=2+cptcovn;          for(i=1; i<=(nlstate); i++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
   /* Read guess parameters */              mu[k][(int) age]=pmmij[i][j];
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     fgets(line, MAXLINE, ficpar);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     puts(line);              varpij[i][j][(int)age] = doldm[i][j];
     fputs(line,ficparo);  
   }          /*printf("\n%d ",(int)age);
   ungetc(c,ficpar);            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]));
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     for(i=1; i <=nlstate; i++)            }*/
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficresprob,"\n%d ",(int)age);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficresprobcov,"\n%d ",(int)age);
       printf("%1d%1d",i,j);          fprintf(ficresprobcor,"\n%d ",(int)age);
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         printf(" %lf",param[i][j][k]);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         fprintf(ficparo," %lf",param[i][j][k]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       fscanf(ficpar,"\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       printf("\n");          }
       fprintf(ficparo,"\n");          i=0;
     }          for (k=1; k<=(nlstate);k++){
              for (l=1; l<=(nlstate+ndeath);l++){ 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   p=param[1][1];              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
   /* Reads comments: lines beginning with '#' */                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }/* end of loop for state */
     fputs(line,ficparo);        } /* end of loop for age */
   }  
   ungetc(c,ficpar);        /* Confidence intervalle of pij  */
         /*
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          fprintf(ficgp,"\nset noparametric;unset label");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   for(i=1; i <=nlstate; i++){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       printf("%1d%1d",i,j);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       for(k=1; k<=ncovmodel;k++){        */
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         fprintf(ficparo," %le",delti3[i][j][k]);        first1=1;
       }        for (k2=1; k2<=(nlstate);k2++){
       fscanf(ficpar,"\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       printf("\n");            if(l2==k2) continue;
       fprintf(ficparo,"\n");            j=(k2-1)*(nlstate+ndeath)+l2;
     }            for (k1=1; k1<=(nlstate);k1++){
   }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   delti=delti3[1][1];                if(l1==k1) continue;
                  i=(k1-1)*(nlstate+ndeath)+l1;
   /* Reads comments: lines beginning with '#' */                if(i<=j) continue;
   while((c=getc(ficpar))=='#' && c!= EOF){                for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);                  if ((int)age %5==0){
     fgets(line, MAXLINE, ficpar);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     puts(line);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fputs(line,ficparo);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    mu1=mu[i][(int) age]/stepm*YEARM ;
   ungetc(c,ficpar);                    mu2=mu[j][(int) age]/stepm*YEARM;
                      c12=cv12/sqrt(v1*v2);
   matcov=matrix(1,npar,1,npar);                    /* Computing eigen value of matrix of covariance */
   for(i=1; i <=npar; i++){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fscanf(ficpar,"%s",&str);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     printf("%s",str);                    /* Eigen vectors */
     fprintf(ficparo,"%s",str);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     for(j=1; j <=i; j++){                    /*v21=sqrt(1.-v11*v11); *//* error */
       fscanf(ficpar," %le",&matcov[i][j]);                    v21=(lc1-v1)/cv12*v11;
       printf(" %.5le",matcov[i][j]);                    v12=-v21;
       fprintf(ficparo," %.5le",matcov[i][j]);                    v22=v11;
     }                    tnalp=v21/v11;
     fscanf(ficpar,"\n");                    if(first1==1){
     printf("\n");                      first1=0;
     fprintf(ficparo,"\n");                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   }                    }
   for(i=1; i <=npar; i++)                    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);
     for(j=i+1;j<=npar;j++)                    /*printf(fignu*/
       matcov[i][j]=matcov[j][i];                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                        /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   printf("\n");                    if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
     /*-------- Rewriting paramater file ----------*/                      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);
      strcpy(rfileres,"r");    /* "Rparameterfile */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                      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);
      strcat(rfileres,".");    /* */                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     if((ficres =fopen(rfileres,"w"))==NULL) {                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                      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(ficres,"#%s\n",version);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                  mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     /*-------- data file ----------*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     if((fic=fopen(datafile,"r"))==NULL)    {                    }else{
       printf("Problem with datafile: %s\n", datafile);goto end;                      first=0;
     }                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     n= lastobs;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     severity = vector(1,maxwav);                      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",\
     outcome=imatrix(1,maxwav+1,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     num=ivector(1,n);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     moisnais=vector(1,n);                    }/* if first */
     annais=vector(1,n);                  } /* age mod 5 */
     moisdc=vector(1,n);                } /* end loop age */
     andc=vector(1,n);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
     agedc=vector(1,n);                first=1;
     cod=ivector(1,n);              } /*l12 */
     weight=vector(1,n);            } /* k12 */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          } /*l1 */
     mint=matrix(1,maxwav,1,n);        }/* k1 */
     anint=matrix(1,maxwav,1,n);      } /* loop covariates */
     s=imatrix(1,maxwav+1,1,n);    }
     adl=imatrix(1,maxwav+1,1,n);        free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     tab=ivector(1,NCOVMAX);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     ncodemax=ivector(1,8);    free_vector(xp,1,npar);
     fclose(ficresprob);
     i=1;    fclose(ficresprobcov);
     while (fgets(line, MAXLINE, fic) != NULL)    {    fclose(ficresprobcor);
       if ((i >= firstobs) && (i <=lastobs)) {    fclose(ficgp);
            fclose(fichtm);
         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);  /******************* Printing html file ***********/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         }                    int lastpass, int stepm, int weightopt, char model[],\
                            int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    int popforecast, int estepm ,\
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    int jj1, k1, i1, cpt;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      printf("Problem with %s \n",optionfilehtm), exit(0);
         for (j=ncovcol;j>=1;j--){      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    }
         }  
         num[i]=atol(stra);     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
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
         i=i+1;     <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);
     }  
     /* printf("ii=%d", ij);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;   jj1=0;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;   for(k1=1; k1<=m;k1++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;     for(i1=1; i1<=ncodemax[k1];i1++){
     }*/       jj1++;
         if (cptcovn > 0) {
   /* for (i=1; i<=imx; i++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      if (s[4][i]==9)  s[4][i]=-1;         for (cpt=1; cpt<=cptcoveff;cpt++) 
      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(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   /* Calculation of the number of parameter from char model*/       /* Pij */
   Tvar=ivector(1,15);       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>
   Tprod=ivector(1,15);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   Tvaraff=ivector(1,15);       /* Quasi-incidences */
   Tvard=imatrix(1,15,1,2);       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>
   Tage=ivector(1,15);        <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
             /* Stable prevalence in each health state */
   if (strlen(model) >1){         for(cpt=1; cpt<nlstate;cpt++){
     j=0, j1=0, k1=1, k2=1;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
     j=nbocc(model,'+');  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     j1=nbocc(model,'*');         }
     cptcovn=j+1;       for(cpt=1; cpt<=nlstate;cpt++) {
     cptcovprod=j1;          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);
     strcpy(modelsav,model);       }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       fprintf(fichtm,"\n<br>- Total life expectancy by age and
       printf("Error. Non available option model=%s ",model);  health expectancies in states (1) and (2): e%s%d.png<br>
       goto end;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     }     } /* end i1 */
       }/* End k1 */
     for(i=(j+1); i>=1;i--){   fprintf(fichtm,"</ul>");
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       /*scanf("%d",i);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
       if (strchr(strb,'*')) {   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
         cutv(strd,strc,strb,'*');   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
         if (strcmp(strc,"age")==0) {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
           cptcovprod--;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
           cutv(strb,stre,strd,'V');   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
           Tvar[i]=atoi(stre);   - 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);
           cptcovage++;  
             Tage[cptcovage]=i;   if(popforecast==1) fprintf(fichtm,"\n
             /*printf("stre=%s ", stre);*/   - 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
         else if (strcmp(strd,"age")==0) {          <br>",fileres,fileres,fileres,fileres);
           cptcovprod--;   else 
           cutv(strb,stre,strc,'V');     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);
           Tvar[i]=atoi(stre);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           cptcovage++;  
           Tage[cptcovage]=i;   m=cptcoveff;
         }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         else {  
           cutv(strb,stre,strc,'V');   jj1=0;
           Tvar[i]=ncovcol+k1;   for(k1=1; k1<=m;k1++){
           cutv(strb,strc,strd,'V');     for(i1=1; i1<=ncodemax[k1];i1++){
           Tprod[k1]=i;       jj1++;
           Tvard[k1][1]=atoi(strc);       if (cptcovn > 0) {
           Tvard[k1][2]=atoi(stre);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           Tvar[cptcovn+k2]=Tvard[k1][1];         for (cpt=1; cpt<=cptcoveff;cpt++) 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           for (k=1; k<=lastobs;k++)         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       }
           k1++;       for(cpt=1; cpt<=nlstate;cpt++) {
           k2=k2+2;         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
         }  interval) in state (%d): v%s%d%d.png <br>
       }  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
       else {       }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/     } /* end i1 */
        /*  scanf("%d",i);*/   }/* End k1 */
       cutv(strd,strc,strb,'V');   fprintf(fichtm,"</ul>");
       Tvar[i]=atoi(strc);  fclose(fichtm);
       }  }
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  /******************* Gnuplot file **************/
         scanf("%d",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;
      int ng;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   printf("cptcovprod=%d ", cptcovprod);      printf("Problem with file %s",optionfilegnuplot);
   scanf("%d ",i);*/      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     fclose(fic);    }
   
     /*  if(mle==1){*/    /*#ifdef windows */
     if (weightopt != 1) { /* Maximisation without weights*/      fprintf(ficgp,"cd \"%s\" \n",pathc);
       for(i=1;i<=n;i++) weight[i]=1.0;      /*#endif */
     }  m=pow(2,cptcoveff);
     /*-calculation of age at interview from date of interview and age at death -*/    
     agev=matrix(1,maxwav,1,imx);   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
     for (i=1; i<=imx; i++) {     for (k1=1; k1<= m ; k1 ++) {
       for(m=2; (m<= maxwav); m++) {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
          anint[m][i]=9999;  
          s[m][i]=-1;       for (i=1; i<= nlstate ; i ++) {
        }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       }
     }       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
     for (i=1; i<=imx; i++)  {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(m=1; (m<= maxwav); m++){       } 
         if(s[m][i] >0){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
           if (s[m][i] >= nlstate+1) {       for (i=1; i<= nlstate ; i ++) {
             if(agedc[i]>0)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
               if(moisdc[i]!=99 && andc[i]!=9999)         else fprintf(ficgp," \%%*lf (\%%*lf)");
                 agev[m][i]=agedc[i];       }  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
            else {     }
               if (andc[i]!=9999){    }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /*2 eme*/
               agev[m][i]=-1;    
               }    for (k1=1; k1<= m ; k1 ++) { 
             }      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
           }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           else if(s[m][i] !=9){ /* Should no more exist */      
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      for (i=1; i<= nlstate+1 ; i ++) {
             if(mint[m][i]==99 || anint[m][i]==9999)        k=2*i;
               agev[m][i]=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
             else if(agev[m][i] <agemin){        for (j=1; j<= nlstate+1 ; j ++) {
               agemin=agev[m][i];          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
             }        }   
             else if(agev[m][i] >agemax){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
               agemax=agev[m][i];        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        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 ++) {
             /*agev[m][i]=anint[m][i]-annais[i];*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             /*   agev[m][i] = age[i]+2*m;*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
           }        }   
           else { /* =9 */        fprintf(ficgp,"\" t\"\" w l 0,");
             agev[m][i]=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
             s[m][i]=-1;        for (j=1; j<= nlstate+1 ; j ++) {
           }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         else /*= 0 Unknown */        }   
           agev[m][i]=1;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       }        else fprintf(ficgp,"\" t\"\" w l 0,");
          }
     }    }
     for (i=1; i<=imx; i++)  {    
       for(m=1; (m<= maxwav); m++){    /*3eme*/
         if (s[m][i] > (nlstate+ndeath)) {    
           printf("Error: Wrong value in nlstate or ndeath\n");      for (k1=1; k1<= m ; k1 ++) { 
           goto end;      for (cpt=1; cpt<= nlstate ; cpt ++) {
         }        k=2+nlstate*(2*cpt-2);
       }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     }        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     free_vector(severity,1,maxwav);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     free_imatrix(outcome,1,maxwav+1,1,n);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     free_vector(moisnais,1,n);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     free_vector(annais,1,n);          
     /* free_matrix(mint,1,maxwav,1,n);        */
        free_matrix(anint,1,maxwav,1,n);*/        for (i=1; i< nlstate ; i ++) {
     free_vector(moisdc,1,n);          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);
     free_vector(andc,1,n);          
         } 
          }
     wav=ivector(1,imx);    }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* CV preval stat */
        for (k1=1; k1<= m ; k1 ++) { 
     /* Concatenates waves */      for (cpt=1; cpt<nlstate ; cpt ++) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
       Tcode=ivector(1,100);        
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        for (i=1; i< nlstate ; i ++)
       ncodemax[1]=1;          fprintf(ficgp,"+$%d",k+i+1);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
              
    codtab=imatrix(1,100,1,10);        l=3+(nlstate+ndeath)*cpt;
    h=0;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
    m=pow(2,cptcoveff);        for (i=1; i< nlstate ; i ++) {
            l=3+(nlstate+ndeath)*cpt;
    for(k=1;k<=cptcoveff; k++){          fprintf(ficgp,"+$%d",l+i+1);
      for(i=1; i <=(m/pow(2,k));i++){        }
        for(j=1; j <= ncodemax[k]; j++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      } 
            h++;    }  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    /* proba elementaires */
          }    for(i=1,jk=1; i <=nlstate; i++){
        }      for(k=1; k <=(nlstate+ndeath); k++){
      }        if (k != i) {
    }          for(j=1; j <=ncovmodel; j++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       codtab[1][2]=1;codtab[2][2]=2; */            jk++; 
    /* for(i=1; i <=m ;i++){            fprintf(ficgp,"\n");
       for(k=1; k <=cptcovn; k++){          }
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        }
       }      }
       printf("\n");     }
       }  
       scanf("%d",i);*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
           for(jk=1; jk <=m; jk++) {
    /* Calculates basic frequencies. Computes observed prevalence at single age         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
        and prints on file fileres'p'. */         if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             else
               fprintf(ficgp,"\nset title \"Probability\"\n");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         i=1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for(k2=1; k2<=nlstate; k2++) {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           k3=i;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */           for(k=1; k<=(nlstate+ndeath); k++) {
                   if (k != k2){
     /* For Powell, parameters are in a vector p[] starting at p[1]               if(ng==2)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     if(mle==1){               ij=1;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);               for(j=3; j <=ncovmodel; j++) {
     }                 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]]]);
     /*--------- results files --------------*/                   ij++;
     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);                 }
                   else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
    jk=1;               }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");               fprintf(ficgp,")/(1");
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");               
    for(i=1,jk=1; i <=nlstate; i++){               for(k1=1; k1 <=nlstate; k1++){   
      for(k=1; k <=(nlstate+ndeath); k++){                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
        if (k != i)                 ij=1;
          {                 for(j=3; j <=ncovmodel; j++){
            printf("%d%d ",i,k);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
            fprintf(ficres,"%1d%1d ",i,k);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
            for(j=1; j <=ncovmodel; j++){                     ij++;
              printf("%f ",p[jk]);                   }
              fprintf(ficres,"%f ",p[jk]);                   else
              jk++;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
            }                 }
            printf("\n");                 fprintf(ficgp,")");
            fprintf(ficres,"\n");               }
          }               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
      }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
    }               i=i+ncovmodel;
  if(mle==1){             }
     /* Computing hessian and covariance matrix */           } /* end k */
     ftolhess=ftol; /* Usually correct */         } /* end k2 */
     hesscov(matcov, p, npar, delti, ftolhess, func);       } /* end jk */
  }     } /* end ng */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");     fclose(ficgp); 
     printf("# Scales (for hessian or gradient estimation)\n");  }  /* end gnuplot */
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {  /*************** Moving average **************/
           fprintf(ficres,"%1d%1d",i,j);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){    int i, cpt, cptcod;
             printf(" %.5e",delti[jk]);    int modcovmax =1;
             fprintf(ficres," %.5e",delti[jk]);    int mobilavrange, mob;
             jk++;    double age;
           }  
           printf("\n");    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           fprintf(ficres,"\n");                             a covariate has 2 modalities */
         }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       }  
      }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
          if(mobilav==1) mobilavrange=5; /* default */
     k=1;      else mobilavrange=mobilav;
     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");      for (age=bage; age<=fage; age++)
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        for (i=1; i<=nlstate;i++)
     for(i=1;i<=npar;i++){          for (cptcod=1;cptcod<=modcovmax;cptcod++)
       /*  if (k>nlstate) k=1;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       i1=(i-1)/(ncovmodel*nlstate)+1;      /* We keep the original values on the extreme ages bage, fage and for 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
       printf("%s%d%d",alph[k],i1,tab[i]);*/         we use a 5 terms etc. until the borders are no more concerned. 
       fprintf(ficres,"%3d",i);      */ 
       printf("%3d",i);      for (mob=3;mob <=mobilavrange;mob=mob+2){
       for(j=1; j<=i;j++){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
         fprintf(ficres," %.5e",matcov[i][j]);          for (i=1; i<=nlstate;i++){
         printf(" %.5e",matcov[i][j]);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
       fprintf(ficres,"\n");                for (cpt=1;cpt<=(mob-1)/2;cpt++){
       printf("\n");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       k++;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     }                }
                  mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     while((c=getc(ficpar))=='#' && c!= EOF){            }
       ungetc(c,ficpar);          }
       fgets(line, MAXLINE, ficpar);        }/* end age */
       puts(line);      }/* end mob */
       fputs(line,ficparo);    }else return -1;
     }    return 0;
     ungetc(c,ficpar);  }/* End movingaverage */
     estepm=0;  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  
     if (estepm==0 || estepm < stepm) estepm=stepm;  /************** Forecasting ******************/
     if (fage <= 2) {  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
       bage = ageminpar;    /* proj1, year, month, day of starting projection 
       fage = agemaxpar;       agemin, agemax range of age
     }       dateprev1 dateprev2 range of dates during which prevalence is computed
           anproj2 year of en of projection (same day and month as proj1).
     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);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    int *popage;
      double agec; /* generic age */
     while((c=getc(ficpar))=='#' && c!= EOF){    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     ungetc(c,ficpar);    double *popeffectif,*popcount;
     fgets(line, MAXLINE, ficpar);    double ***p3mat;
     puts(line);    double ***mobaverage;
     fputs(line,ficparo);    char fileresf[FILENAMELENGTH];
   }  
   ungetc(c,ficpar);    agelim=AGESUP;
      prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);   
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcpy(fileresf,"f"); 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    strcat(fileresf,fileres);
          if((ficresf=fopen(fileresf,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with forecast resultfile: %s\n", fileresf);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    printf("Computing forecasting: result on file '%s' \n", fileresf);
     fputs(line,ficparo);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
   ungetc(c,ficpar);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
     if (mobilav!=0) {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficparo,"pop_based=%d\n",popbased);        }
   fprintf(ficres,"pop_based=%d\n",popbased);      }
    
   while((c=getc(ficpar))=='#' && c!= EOF){    stepsize=(int) (stepm+YEARM-1)/YEARM;
     ungetc(c,ficpar);    if (stepm<=12) stepsize=1;
     fgets(line, MAXLINE, ficpar);    
     puts(line);    hstepm=1;
     fputs(line,ficparo);    hstepm=hstepm/stepm; 
   }    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   ungetc(c,ficpar);                                 fractional in yp1 */
     anprojmean=yp;
   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);    yp2=modf((yp1*12),&yp);
 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);    mprojmean=yp;
 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);    yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
 while((c=getc(ficpar))=='#' && c!= EOF){    if(mprojmean==0) jprojmean=1;
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     puts(line);    
     fputs(line,ficparo);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   }    for(cptcov=1, k=0;cptcov<=cptcoveff;cptcov++){
   ungetc(c,ficpar);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        fprintf(ficresf,"\n#******");
   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(j=1;j<=cptcoveff;j++) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
 /*------------ gnuplot -------------*/        for(j=1; j<=nlstate+ndeath;j++){ 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);          for(i=1; i<=nlstate;i++)              
              fprintf(ficresf," p%d%d",i,j);
 /*------------ free_vector  -------------*/          fprintf(ficresf," p.%d",j);
  chdir(path);        }
          for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { 
  free_ivector(wav,1,imx);          fprintf(ficresf,"\n");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
  free_vector(agedc,1,n);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            nhstepm = nhstepm/hstepm; 
  fclose(ficparo);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fclose(ficres);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
 /*--------- index.htm --------*/          
             for (h=0; h<=nhstepm; h++){
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);              if (h==(int) (YEARM*yearp)) {
                 fprintf(ficresf,"\n");
                  for(j=1;j<=cptcoveff;j++) 
   /*--------------- Prevalence limit --------------*/                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                  fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   strcpy(filerespl,"pl");              } 
   strcat(filerespl,fileres);              for(j=1; j<=nlstate+ndeath;j++) {
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                ppij=0.;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                for(i=1; i<=nlstate;i++) {
   }                  if (mobilav==1) 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   fprintf(ficrespl,"#Prevalence limit\n");                  else {
   fprintf(ficrespl,"#Age ");                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                  }
   fprintf(ficrespl,"\n");                  if (h==(int)(YEARM*yearp))
                      fprintf(ficresf," %.3f", p3mat[i][j][h]);
   prlim=matrix(1,nlstate,1,nlstate);                }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if (h==(int)(YEARM*yearp)){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  fprintf(ficresf," %.3f", ppij);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            }
   k=0;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   agebase=ageminpar;          }
   agelim=agemaxpar;        }
   ftolpl=1.e-10;      }
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}         
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fclose(ficresf);
         k=k+1;  }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");  /************** Forecasting *****not tested NB*************/
         for(j=1;j<=cptcoveff;j++)  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(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         fprintf(ficrespl,"******\n");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
            int *popage;
         for (age=agebase; age<=agelim; age++){    double calagedatem, agelim, kk1, kk2;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double *popeffectif,*popcount;
           fprintf(ficrespl,"%.0f",age );    double ***p3mat,***tabpop,***tabpopprev;
           for(i=1; i<=nlstate;i++)    double ***mobaverage;
           fprintf(ficrespl," %.5f", prlim[i][i]);    char filerespop[FILENAMELENGTH];
           fprintf(ficrespl,"\n");  
         }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    agelim=AGESUP;
   fclose(ficrespl);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
   /*------------- h Pij x at various ages ------------*/    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
      
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    strcpy(filerespop,"pop"); 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    strcat(filerespop,fileres);
   }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   printf("Computing pij: result on file '%s' \n", filerespij);      printf("Problem with forecast resultfile: %s\n", filerespop);
        fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    }
   /*if (stepm<=24) stepsize=2;*/    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
      if (mobilav!=0) {
   k=0;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(cptcov=1;cptcov<=i1;cptcov++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       k=k+1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         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");    stepsize=(int) (stepm+YEARM-1)/YEARM;
            if (stepm<=12) stepsize=1;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    agelim=AGESUP;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=1;
           oldm=oldms;savm=savms;    hstepm=hstepm/stepm; 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           fprintf(ficrespij,"# Age");    if (popforecast==1) {
           for(i=1; i<=nlstate;i++)      if((ficpop=fopen(popfile,"r"))==NULL) {
             for(j=1; j<=nlstate+ndeath;j++)        printf("Problem with population file : %s\n",popfile);exit(0);
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
           fprintf(ficrespij,"\n");      } 
           for (h=0; h<=nhstepm; h++){      popage=ivector(0,AGESUP);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      popeffectif=vector(0,AGESUP);
             for(i=1; i<=nlstate;i++)      popcount=vector(0,AGESUP);
               for(j=1; j<=nlstate+ndeath;j++)      
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      i=1;   
             fprintf(ficrespij,"\n");      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
           }     
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      imx=i;
           fprintf(ficrespij,"\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
         }    }
     }  
   }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        k=k+1;
         fprintf(ficrespop,"\n#******");
   fclose(ficrespij);        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
   /*---------- Forecasting ------------------*/        fprintf(ficrespop,"******\n");
   if((stepm == 1) && (strcmp(model,".")==0)){        fprintf(ficrespop,"# Age");
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        if (popforecast==1)  fprintf(ficrespop," [Population]");
     free_matrix(mint,1,maxwav,1,n);        
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        for (cpt=0; cpt<=0;cpt++) { 
     free_vector(weight,1,n);}          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   else{          
     erreur=108;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     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);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
              
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*---------- Health expectancies and variances ------------*/            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   strcpy(filerest,"t");          
   strcat(filerest,fileres);            for (h=0; h<=nhstepm; h++){
   if((ficrest=fopen(filerest,"w"))==NULL) {              if (h==(int) (calagedatem+YEARM*cpt)) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   }              } 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
   strcpy(filerese,"e");                  if (mobilav==1) 
   strcat(filerese,fileres);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   if((ficreseij=fopen(filerese,"w"))==NULL) {                  else {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   }                  }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                }
                 if (h==(int)(calagedatem+12*cpt)){
  strcpy(fileresv,"v");                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   strcat(fileresv,fileres);                    /*fprintf(ficrespop," %.3f", kk1);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                }
   }              }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              for(i=1; i<=nlstate;i++){
                 kk1=0.;
   k=0;                  for(j=1; j<=nlstate;j++){
   for(cptcov=1;cptcov<=i1;cptcov++){                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  }
       k=k+1;                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
       fprintf(ficrest,"\n#****** ");              }
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
       fprintf(ficrest,"******\n");                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
       fprintf(ficreseij,"\n#****** ");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       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++)        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       fprintf(ficresvij,"******\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            nhstepm = nhstepm/hstepm; 
       oldm=oldms;savm=savms;            
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            oldm=oldms;savm=savms;
       oldm=oldms;savm=savms;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);            for (h=0; h<=nhstepm; h++){
                  if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                } 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              for(j=1; j<=nlstate+ndeath;j++) {
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                kk1=0.;kk2=0;
       fprintf(ficrest,"\n");                for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
       epj=vector(1,nlstate+1);                }
       for(age=bage; age <=fage ;age++){                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              }
         if (popbased==1) {            }
           for(i=1; i<=nlstate;i++)            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             prlim[i][i]=probs[(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++) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
           }    if (popforecast==1) {
           epj[nlstate+1] +=epj[j];      free_ivector(popage,0,AGESUP);
         }      free_vector(popeffectif,0,AGESUP);
         for(i=1, vepp=0.;i <=nlstate;i++)      free_vector(popcount,0,AGESUP);
           for(j=1;j <=nlstate;j++)    }
             vepp += vareij[i][j][(int)age];    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1;j <=nlstate;j++){    fclose(ficrespop);
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));  }
         }  
         fprintf(ficrest,"\n");  /***********************************************/
       }  /**************** Main Program *****************/
     }  /***********************************************/
   }  
   int main(int argc, char *argv[])
   fclose(ficreseij);  {
   fclose(ficresvij);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   fclose(ficrest);    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   fclose(ficpar);    double agedeb, agefin,hf;
   free_vector(epj,1,nlstate+1);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
    
   /*------- Variance limit prevalence------*/      double fret;
     double **xi,tmp,delta;
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);    double dum; /* Dummy variable */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    double ***p3mat;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double ***mobaverage;
     exit(0);    int *indx;
   }    char line[MAXLINE], linepar[MAXLINE];
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
   k=0;    int sdeb, sfin; /* Status at beginning and end */
   for(cptcov=1;cptcov<=i1;cptcov++){    int c,  h , cpt,l;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int ju,jl, mi;
       k=k+1;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
       fprintf(ficresvpl,"\n#****** ");    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
       for(j=1;j<=cptcoveff;j++)    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int mobilav=0,popforecast=0;
       fprintf(ficresvpl,"******\n");    int hstepm, nhstepm;
          double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    double bage, fage, age, agelim, agebase;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double ftolpl=FTOL;
     }    double **prlim;
  }    double *severity;
     double ***param; /* Matrix of parameters */
   fclose(ficresvpl);    double  *p;
     double **matcov; /* Matrix of covariance */
   /*---------- End : free ----------------*/    double ***delti3; /* Scale */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double *delti; /* Scale */
      double ***eij, ***vareij;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double **varpl; /* Variances of prevalence limits by age */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double *epj, vepp;
      double kk1, kk2;
      double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      char z[1]="c", occ;
   free_matrix(matcov,1,npar,1,npar);  #include <sys/time.h>
   free_vector(delti,1,npar);  #include <time.h>
   free_matrix(agev,1,maxwav,1,imx);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);   
     /* long total_usecs;
   if(erreur >0)       struct timeval start_time, end_time;
     printf("End of Imach with error or warning %d\n",erreur);    
   else   printf("End of Imach\n");       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    getcwd(pathcd, size);
    
   /* 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("\n%s",version);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    if(argc <=1){
   /*------ End -----------*/      printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
  end:    else{
 #ifdef windows      strcpy(pathtot,argv[1]);
   /* chdir(pathcd);*/    }
 #endif    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
  /*system("wgnuplot graph.plt");*/    /*cygwin_split_path(pathtot,path,optionfile);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
  /*system("cd ../gp37mgw");*/    /* cutv(path,optionfile,pathtot,'\\');*/
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
  strcat(plotcmd," ");    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
  strcat(plotcmd,optionfilegnuplot);    chdir(path);
  system(plotcmd);    replace(pathc,path);
   
 #ifdef windows    /*-------- arguments in the command line --------*/
   while (z[0] != 'q') {  
     /* chdir(path); */    /* Log file */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    strcat(filelog, optionfilefiname);
     scanf("%s",z);    strcat(filelog,".log");    /* */
     if (z[0] == 'c') system("./imach");    if((ficlog=fopen(filelog,"w"))==NULL)    {
     else if (z[0] == 'e') system(optionfilehtm);      printf("Problem with logfile %s\n",filelog);
     else if (z[0] == 'g') system(plotcmd);      goto end;
     else if (z[0] == 'q') exit(0);    }
   }    fprintf(ficlog,"Log filename:%s\n",filelog);
 #endif    fprintf(ficlog,"\n%s",version);
 }    fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       if(stepm ==1){
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         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);
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_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 */
   }
   
   

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  Added in v.1.71


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