Diff for /imach/src/imach.c between versions 1.44 and 1.69

version 1.44, 2002/05/24 13:01:48 version 1.69, 2003/02/04 20:55:29
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #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 0.91, November 2002, 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);          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 */
   indx=ivector(1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (i=1;i<=npar;i++)          /*if(lli ==000.0)*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   ludcmp(a,npar,indx,&pd);          ipmx +=1;
           sw += weight[i];
   for (j=1;j<=npar;j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++) x[i]=0;        } /* end of wave */
     x[j]=1;      } /* end of individual */
     lubksb(a,npar,indx,x);    }  else if(mle==2){
     for (i=1;i<=npar;i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       matcov[i][j]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   printf("\n#Hessian matrix#\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++) {            }
       printf("%.3e ",hess[i][j]);          for(d=0; d<=dh[mi][i]; d++){
     }            newm=savm;
     printf("\n");            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];
   /* Recompute Inverse */            }
   for (i=1;i<=npar;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   ludcmp(a,npar,indx,&pd);            savm=oldm;
             oldm=newm;
   /*  printf("\n#Hessian matrix recomputed#\n");          } /* end mult */
         
   for (j=1;j<=npar;j++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (i=1;i<=npar;i++) x[i]=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
     x[j]=1;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     lubksb(a,npar,indx,x);           * (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
       y[i][j]=x[i];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       printf("%.3e ",y[i][j]);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
     printf("\n");           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   }           * -stepm/2 to stepm/2 .
   */           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   free_matrix(a,1,npar,1,npar);           */
   free_matrix(y,1,npar,1,npar);          s1=s[mw[mi][i]][i];
   free_vector(x,1,npar);          s2=s[mw[mi+1][i]][i];
   free_ivector(indx,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(hess,1,npar,1,npar);          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
 }          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]));*/
 /*************** hessian matrix ****************/          /*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 */
 double hessii( double x[], double delta, int theta, double delti[])          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int l=1, lmax=20;          ipmx +=1;
   double k1,k2;          sw += weight[i];
   double p2[NPARMAX+1];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double res;        } /* end of wave */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } /* end of individual */
   double fx;    }  else if(mle==3){  /* exponential inter-extrapolation */
   int k=0,kmax=10;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double l1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   fx=func(x);          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++) p2[i]=x[i];            for (j=1;j<=nlstate+ndeath;j++){
   for(l=0 ; l <=lmax; l++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     l1=pow(10,l);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     delts=delt;            }
     for(k=1 ; k <kmax; k=k+1){          for(d=0; d<dh[mi][i]; d++){
       delt = delta*(l1*k);            newm=savm;
       p2[theta]=x[theta] +delt;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       k1=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
       p2[theta]=x[theta]-delt;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       k2=func(p2)-fx;            }
       /*res= (k1-2.0*fx+k2)/delt/delt; */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
 #ifdef DEBUG            oldm=newm;
       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);          } /* end mult */
 #endif        
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /* But now since version 0.9 we anticipate for bias and large stepm.
         k=kmax;           * 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 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */           * the nearest (and in case of equal distance, to the lowest) interval but now
         k=kmax; l=lmax*10.;           * 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
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * probability in order to take into account the bias as a fraction of the way
         delts=delt;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
   delti[theta]=delts;           */
   return res;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 double hessij( double x[], double delti[], int thetai,int thetaj)           * is higher than the multiple of stepm and negative otherwise.
 {           */
   int i;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   int l=1, l1, lmax=20;          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 */
   double k1,k2,k3,k4,res,fx;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double p2[NPARMAX+1];          /*if(lli ==000.0)*/
   int k;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
   fx=func(x);          sw += weight[i];
   for (k=1; k<=2; k++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++) p2[i]=x[i];        } /* end of wave */
     p2[thetai]=x[thetai]+delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }else{  /* ml=4 no inter-extrapolation */
     k1=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k2=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]-delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k3=func(p2)-fx;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
     p2[thetai]=x[thetai]-delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k4=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            }
 #ifdef DEBUG          
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   return res;            oldm=newm;
 }          } /* end mult */
         
 /************** Inverse of matrix **************/          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 void ludcmp(double **a, int n, int *indx, double *d)          ipmx +=1;
 {          sw += weight[i];
   int i,imax,j,k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double big,dum,sum,temp;        } /* end of wave */
   double *vv;      } /* end of individual */
      } /* End of if */
   vv=vector(1,n);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   *d=1.0;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (i=1;i<=n;i++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     big=0.0;    return -l;
     for (j=1;j<=n;j++)  }
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /*********** Maximum Likelihood Estimation ***************/
   }  
   for (j=1;j<=n;j++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    int i,j, iter;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    double **xi,*delti;
       a[i][j]=sum;    double fret;
     }    xi=matrix(1,npar,1,npar);
     big=0.0;    for (i=1;i<=npar;i++)
     for (i=j;i<=n;i++) {      for (j=1;j<=npar;j++)
       sum=a[i][j];        xi[i][j]=(i==j ? 1.0 : 0.0);
       for (k=1;k<j;k++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         sum -= a[i][k]*a[k][j];    powell(p,xi,npar,ftol,&iter,&fret,func);
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         big=dum;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         imax=i;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
     }  }
     if (j != imax) {  
       for (k=1;k<=n;k++) {  /**** Computes Hessian and covariance matrix ***/
         dum=a[imax][k];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    double  **a,**y,*x,pd;
       }    double **hess;
       *d = -(*d);    int i, j,jk;
       vv[imax]=vv[j];    int *indx;
     }  
     indx[j]=imax;    double hessii(double p[], double delta, int theta, double delti[]);
     if (a[j][j] == 0.0) a[j][j]=TINY;    double hessij(double p[], double delti[], int i, int j);
     if (j != n) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
       dum=1.0/(a[j][j]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    hess=matrix(1,npar,1,npar);
   }  
   free_vector(vv,1,n);  /* Doesn't work */    printf("\nCalculation of the hessian matrix. Wait...\n");
 ;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 }    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
 void lubksb(double **a, int n, int *indx, double b[])      fprintf(ficlog,"%d",i);fflush(ficlog);
 {      hess[i][i]=hessii(p,ftolhess,i,delti);
   int i,ii=0,ip,j;      /*printf(" %f ",p[i]);*/
   double sum;      /*printf(" %lf ",hess[i][i]);*/
      }
   for (i=1;i<=n;i++) {    
     ip=indx[i];    for (i=1;i<=npar;i++) {
     sum=b[ip];      for (j=1;j<=npar;j++)  {
     b[ip]=b[i];        if (j>i) { 
     if (ii)          printf(".%d%d",i,j);fflush(stdout);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     else if (sum) ii=i;          hess[i][j]=hessij(p,delti,i,j);
     b[i]=sum;          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
   for (i=n;i>=1;i--) {        }
     sum=b[i];      }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    }
     b[i]=sum/a[i][i];    printf("\n");
   }    fprintf(ficlog,"\n");
 }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 /************ Frequencies ********************/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 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 */    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    x=vector(1,npar);
   double ***freq; /* Frequencies */    indx=ivector(1,npar);
   double *pp;    for (i=1;i<=npar;i++)
   double pos, k2, dateintsum=0,k2cpt=0;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   FILE *ficresp;    ludcmp(a,npar,indx,&pd);
   char fileresp[FILENAMELENGTH];  
      for (j=1;j<=npar;j++) {
   pp=vector(1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      x[j]=1;
   strcpy(fileresp,"p");      lubksb(a,npar,indx,x);
   strcat(fileresp,fileres);      for (i=1;i<=npar;i++){ 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        matcov[i][j]=x[i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);      }
     exit(0);    }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    printf("\n#Hessian matrix#\n");
   j1=0;    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   j=cptcoveff;      for (j=1;j<=npar;j++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        printf("%.3e ",hess[i][j]);
          fprintf(ficlog,"%.3e ",hess[i][j]);
   for(k1=1; k1<=j;k1++){      }
     for(i1=1; i1<=ncodemax[k1];i1++){      printf("\n");
       j1++;      fprintf(ficlog,"\n");
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    }
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      /* Recompute Inverse */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for (i=1;i<=npar;i++)
           for(m=agemin; m <= agemax+3; m++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             freq[i][jk][m]=0;    ludcmp(a,npar,indx,&pd);
        
       dateintsum=0;    /*  printf("\n#Hessian matrix recomputed#\n");
       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;        y[i][j]=x[i];
         }        printf("%.3e ",y[i][j]);
         if (bool==1) {        fprintf(ficlog,"%.3e ",y[i][j]);
           for(m=firstpass; m<=lastpass; m++){      }
             k2=anint[m][i]+(mint[m][i]/12.);      printf("\n");
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      fprintf(ficlog,"\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    */
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    free_matrix(a,1,npar,1,npar);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    free_matrix(y,1,npar,1,npar);
               }    free_vector(x,1,npar);
                  free_ivector(indx,1,npar);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    free_matrix(hess,1,npar,1,npar);
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  
               }  }
             }  
           }  /*************** hessian matrix ****************/
         }  double hessii( double x[], double delta, int theta, double delti[])
       }  {
            int i;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int l=1, lmax=20;
     double k1,k2;
       if  (cptcovn>0) {    double p2[NPARMAX+1];
         fprintf(ficresp, "\n#********** Variable ");    double res;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         fprintf(ficresp, "**********\n#");    double fx;
       }    int k=0,kmax=10;
       for(i=1; i<=nlstate;i++)    double l1;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");    fx=func(x);
          for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for(l=0 ; l <=lmax; l++){
         if(i==(int)agemax+3)      l1=pow(10,l);
           printf("Total");      delts=delt;
         else      for(k=1 ; k <kmax; k=k+1){
           printf("Age %d", i);        delt = delta*(l1*k);
         for(jk=1; jk <=nlstate ; jk++){        p2[theta]=x[theta] +delt;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        k1=func(p2)-fx;
             pp[jk] += freq[jk][m][i];        p2[theta]=x[theta]-delt;
         }        k2=func(p2)-fx;
         for(jk=1; jk <=nlstate ; jk++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
           for(m=-1, pos=0; m <=0 ; m++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             pos += freq[jk][m][i];        
           if(pp[jk]>=1.e-10)  #ifdef DEBUG
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        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);
           else        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  #endif
         }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(jk=1; jk <=nlstate ; jk++){          k=kmax;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        }
             pp[jk] += freq[jk][m][i];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         }
         for(jk=1,pos=0; jk <=nlstate ; jk++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           pos += pp[jk];          delts=delt;
         for(jk=1; jk <=nlstate ; jk++){        }
           if(pos>=1.e-5)      }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    }
           else    delti[theta]=delts;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    return res; 
           if( i <= (int) agemax){    
             if(pos>=1.e-5){  }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;  double hessij( double x[], double delti[], int thetai,int thetaj)
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  {
             }    int i;
             else    int l=1, l1, lmax=20;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double k1,k2,k3,k4,res,fx;
           }    double p2[NPARMAX+1];
         }    int k;
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)    fx=func(x);
           for(m=-1; m <=nlstate+ndeath; m++)    for (k=1; k<=2; k++) {
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for (i=1;i<=npar;i++) p2[i]=x[i];
         if(i <= (int) agemax)      p2[thetai]=x[thetai]+delti[thetai]/k;
           fprintf(ficresp,"\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         printf("\n");      k1=func(p2)-fx;
       }    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   dateintmean=dateintsum/k2cpt;      k2=func(p2)-fx;
      
   fclose(ficresp);      p2[thetai]=x[thetai]-delti[thetai]/k;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   free_vector(pp,1,nlstate);      k3=func(p2)-fx;
      
   /* End of Freq */      p2[thetai]=x[thetai]-delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
 /************ Prevalence ********************/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 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)  #ifdef DEBUG
 {  /* Some frequencies */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #endif
   double ***freq; /* Frequencies */    }
   double *pp;    return res;
   double pos, k2;  }
   
   pp=vector(1,nlstate);  /************** Inverse of matrix **************/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  void ludcmp(double **a, int n, int *indx, double *d) 
    { 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int i,imax,j,k; 
   j1=0;    double big,dum,sum,temp; 
      double *vv; 
   j=cptcoveff;   
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    vv=vector(1,n); 
      *d=1.0; 
   for(k1=1; k1<=j;k1++){    for (i=1;i<=n;i++) { 
     for(i1=1; i1<=ncodemax[k1];i1++){      big=0.0; 
       j1++;      for (j=1;j<=n;j++) 
              if ((temp=fabs(a[i][j])) > big) big=temp; 
       for (i=-1; i<=nlstate+ndeath; i++)        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        vv[i]=1.0/big; 
           for(m=agemin; m <= agemax+3; m++)    } 
             freq[i][jk][m]=0;    for (j=1;j<=n;j++) { 
            for (i=1;i<j;i++) { 
       for (i=1; i<=imx; i++) {        sum=a[i][j]; 
         bool=1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         if  (cptcovn>0) {        a[i][j]=sum; 
           for (z1=1; z1<=cptcoveff; z1++)      } 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      big=0.0; 
               bool=0;      for (i=j;i<=n;i++) { 
         }        sum=a[i][j]; 
         if (bool==1) {        for (k=1;k<j;k++) 
           for(m=firstpass; m<=lastpass; m++){          sum -= a[i][k]*a[k][j]; 
             k2=anint[m][i]+(mint[m][i]/12.);        a[i][j]=sum; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;          big=dum; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          imax=i; 
               if (m<lastpass) {        } 
                 if (calagedate>0)      } 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      if (j != imax) { 
                 else        for (k=1;k<=n;k++) { 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          dum=a[imax][k]; 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          a[imax][k]=a[j][k]; 
               }          a[j][k]=dum; 
             }        } 
           }        *d = -(*d); 
         }        vv[imax]=vv[j]; 
       }      } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      indx[j]=imax; 
         for(jk=1; jk <=nlstate ; jk++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      if (j != n) { 
             pp[jk] += freq[jk][m][i];        dum=1.0/(a[j][j]); 
         }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         for(jk=1; jk <=nlstate ; jk++){      } 
           for(m=-1, pos=0; m <=0 ; m++)    } 
             pos += freq[jk][m][i];    free_vector(vv,1,n);  /* Doesn't work */
         }  ;
          } 
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  void lubksb(double **a, int n, int *indx, double b[]) 
             pp[jk] += freq[jk][m][i];  { 
         }    int i,ii=0,ip,j; 
            double sum; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];   
            for (i=1;i<=n;i++) { 
         for(jk=1; jk <=nlstate ; jk++){          ip=indx[i]; 
           if( i <= (int) agemax){      sum=b[ip]; 
             if(pos>=1.e-5){      b[ip]=b[i]; 
               probs[i][jk][j1]= pp[jk]/pos;      if (ii) 
             }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           }      else if (sum) ii=i; 
         }      b[i]=sum; 
            } 
       }    for (i=n;i>=1;i--) { 
     }      sum=b[i]; 
   }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  } 
   free_vector(pp,1,nlstate);  
    /************ Frequencies ********************/
 }  /* End of Freq */  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   {  /* Some frequencies */
 /************* Waves Concatenation ***************/    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    int first;
 {    double ***freq; /* Frequencies */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    double *pp;
      Death is a valid wave (if date is known).    double pos, k2, dateintsum=0,k2cpt=0;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    FILE *ficresp;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    char fileresp[FILENAMELENGTH];
      and mw[mi+1][i]. dh depends on stepm.    
      */    pp=vector(1,nlstate);
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   int i, mi, m;    strcpy(fileresp,"p");
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    strcat(fileresp,fileres);
      double sum=0., jmean=0.;*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   int j, k=0,jk, ju, jl;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   double sum=0.;      exit(0);
   jmin=1e+5;    }
   jmax=-1;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   jmean=0.;    j1=0;
   for(i=1; i<=imx; i++){    
     mi=0;    j=cptcoveff;
     m=firstpass;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     while(s[m][i] <= nlstate){  
       if(s[m][i]>=1)    first=1;
         mw[++mi][i]=m;  
       if(m >=lastpass)    for(k1=1; k1<=j;k1++){
         break;      for(i1=1; i1<=ncodemax[k1];i1++){
       else        j1++;
         m++;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }/* end while */          scanf("%d", i);*/
     if (s[m][i] > nlstate){        for (i=-1; i<=nlstate+ndeath; i++)  
       mi++;     /* Death is another wave */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       /* if(mi==0)  never been interviewed correctly before death */            for(m=agemin; m <= agemax+3; m++)
          /* Only death is a correct wave */              freq[i][jk][m]=0;
       mw[mi][i]=m;        
     }        dateintsum=0;
         k2cpt=0;
     wav[i]=mi;        for (i=1; i<=imx; i++) {
     if(mi==0)          bool=1;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          if  (cptcovn>0) {
   }            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   for(i=1; i<=imx; i++){                bool=0;
     for(mi=1; mi<wav[i];mi++){          }
       if (stepm <=0)          if (bool==1){
         dh[mi][i]=1;            for(m=firstpass; m<=lastpass; m++){
       else{              k2=anint[m][i]+(mint[m][i]/12.);
         if (s[mw[mi+1][i]][i] > nlstate) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           if (agedc[i] < 2*AGESUP) {                if(agev[m][i]==0) agev[m][i]=agemax+1;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                if(agev[m][i]==1) agev[m][i]=agemax+2;
           if(j==0) j=1;  /* Survives at least one month after exam */                if (m<lastpass) {
           k=k+1;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           if (j >= jmax) jmax=j;                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
           if (j <= jmin) jmin=j;                }
           sum=sum+j;                
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           }                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
         else{                }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              }
           k=k+1;            }
           if (j >= jmax) jmax=j;          }
           else if (j <= jmin)jmin=j;        }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */         
           sum=sum+j;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         }  
         jk= j/stepm;        if  (cptcovn>0) {
         jl= j -jk*stepm;          fprintf(ficresp, "\n#********** Variable "); 
         ju= j -(jk+1)*stepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if(jl <= -ju)          fprintf(ficresp, "**********\n#");
           dh[mi][i]=jk;        }
         else        for(i=1; i<=nlstate;i++) 
           dh[mi][i]=jk+1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         if(dh[mi][i]==0)        fprintf(ficresp, "\n");
           dh[mi][i]=1; /* At least one step */        
       }        for(i=(int)agemin; i <= (int)agemax+3; i++){
     }          if(i==(int)agemax+3){
   }            fprintf(ficlog,"Total");
   jmean=sum/k;          }else{
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            if(first==1){
  }              first=0;
 /*********** Tricode ****************************/              printf("See log file for details...\n");
 void tricode(int *Tvar, int **nbcode, int imx)            }
 {            fprintf(ficlog,"Age %d", i);
   int Ndum[20],ij=1, k, j, i;          }
   int cptcode=0;          for(jk=1; jk <=nlstate ; jk++){
   cptcoveff=0;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   for (k=0; k<19; k++) Ndum[k]=0;          }
   for (k=1; k<=7; k++) ncodemax[k]=0;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              pos += freq[jk][m][i];
     for (i=1; i<=imx; i++) {            if(pp[jk]>=1.e-10){
       ij=(int)(covar[Tvar[j]][i]);              if(first==1){
       Ndum[ij]++;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              }
       if (ij > cptcode) cptcode=ij;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }            }else{
               if(first==1)
     for (i=0; i<=cptcode; i++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       if(Ndum[i]!=0) ncodemax[j]++;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
     ij=1;          }
   
           for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=ncodemax[j]; i++) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for (k=0; k<=19; k++) {              pp[jk] += freq[jk][m][i];
         if (Ndum[k] != 0) {          }
           nbcode[Tvar[j]][ij]=k;  
                    for(jk=1,pos=0; jk <=nlstate ; jk++)
           ij++;            pos += pp[jk];
         }          for(jk=1; jk <=nlstate ; jk++){
         if (ij > ncodemax[j]) break;            if(pos>=1.e-5){
       }                if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
  for (k=0; k<19; k++) Ndum[k]=0;              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  for (i=1; i<=ncovmodel-2; i++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       ij=Tvar[i];            }
       Ndum[ij]++;            if( i <= (int) agemax){
     }              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
  ij=1;                probs[i][jk][j1]= pp[jk]/pos;
  for (i=1; i<=10; i++) {                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){              }
      Tvaraff[ij]=i;              else
      ij++;                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
    }            }
  }          }
            
     cptcoveff=ij-1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
 }            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
 /*********** Health Expectancies ****************/              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 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 )                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
 {          if(i <= (int) agemax)
   /* Health expectancies */            fprintf(ficresp,"\n");
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          if(first==1)
   double age, agelim, hf;            printf("Others in log...\n");
   double ***p3mat,***varhe;          fprintf(ficlog,"\n");
   double **dnewm,**doldm;        }
   double *xp;      }
   double **gp, **gm;    }
   double ***gradg, ***trgradg;    dateintmean=dateintsum/k2cpt; 
   int theta;   
     fclose(ficresp);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   xp=vector(1,npar);    free_vector(pp,1,nlstate);
   dnewm=matrix(1,nlstate*2,1,npar);    
   doldm=matrix(1,nlstate*2,1,nlstate*2);    /* End of Freq */
    }
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");  /************ Prevalence ********************/
   for(i=1; i<=nlstate;i++)  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 calagedatem)
     for(j=1; j<=nlstate;j++)  {  
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   fprintf(ficreseij,"\n");       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   if(estepm < stepm){    */
     printf ("Problem %d lower than %d\n",estepm, stepm);   
   }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   else  hstepm=estepm;      double ***freq; /* Frequencies */
   /* We compute the life expectancy from trapezoids spaced every estepm months    double *pp;
    * This is mainly to measure the difference between two models: for example    double pos; 
    * if stepm=24 months pijx are given only every 2 years and by summing them    double  y2; /* in fractional years */
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according    pp=vector(1,nlstate);
    * 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    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
    * to compare the new estimate of Life expectancy with the same linear    j1=0;
    * hypothesis. A more precise result, taking into account a more precise    
    * curvature will be obtained if estepm is as small as stepm. */    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /* 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(k1=1; k1<=j;k1++){
      nhstepm is the number of hstepm from age to agelim      for(i1=1; i1<=ncodemax[k1];i1++){
      nstepm is the number of stepm from age to agelin.        j1++;
      Look at hpijx to understand the reason of that which relies in memory size        
      and note for a fixed period like estepm months */        for (i=-1; i<=nlstate+ndeath; i++)  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for (jk=-1; jk<=nlstate+ndeath; jk++)  
      survival function given by stepm (the optimization length). Unfortunately it            for(m=agemin; m <= agemax+3; m++)
      means that if the survival funtion is printed only each two years of age and if              freq[i][jk][m]=0;
      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 (i=1; i<=imx; i++) { /* Each individual */
   */          bool=1;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   agelim=AGESUP;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                bool=0;
     /* nhstepm age range expressed in number of stepm */          } 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          if (bool==1) { 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     /* if (stepm >= YEARM) hstepm=1;*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if(agev[m][i]==0) agev[m][i]=agemax+1;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);                if(agev[m][i]==1) agev[m][i]=agemax+2;
     gp=matrix(0,nhstepm,1,nlstate*2);                if (m<lastpass) {
     gm=matrix(0,nhstepm,1,nlstate*2);                  if (calagedatem>0) /* We compute prevalence at exact age, agev in fractional years */
                     freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedatem %12)/12.)] += weight[i];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                  else
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                    freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
                  }
               }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            } /* end selection of waves */
           }
     /* Computing Variances of health expectancies */        }
         for(i=(int)agemin; i <= (int)agemax+3; i++){ 
      for(theta=1; theta <=npar; theta++){          for(jk=1; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              pp[jk] += freq[jk][m][i]; 
       }          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pos=0; m <=0 ; m++)
       cptj=0;              pos += freq[jk][m][i];
       for(j=1; j<= nlstate; j++){          }
         for(i=1; i<=nlstate; i++){          
           cptj=cptj+1;          for(jk=1; jk <=nlstate ; jk++){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;              pp[jk] += freq[jk][m][i];
           }          }
         }          
       }          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
                
                for(jk=1; jk <=nlstate ; jk++){    
       for(i=1; i<=npar; i++)            if( i <= (int) agemax){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              if(pos>=1.e-5){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  probs[i][jk][j1]= pp[jk]/pos;
                    }
       cptj=0;            }
       for(j=1; j<= nlstate; j++){          }/* end jk */
         for(i=1;i<=nlstate;i++){        }/* end i */
           cptj=cptj+1;      } /* end i1 */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    } /* end k1 */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    
         }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
       }    free_vector(pp,1,nlstate);
          
      }  /* End of Freq */
   
       for(j=1; j<= nlstate*2; j++)  /************* Waves Concatenation ***************/
         for(h=0; h<=nhstepm-1; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
         }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      }       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
 /* End theta */       dh[m][i] or 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.
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);       */
   
      for(h=0; h<=nhstepm-1; h++)    int i, mi, m;
       for(j=1; j<=nlstate*2;j++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         for(theta=1; theta <=npar; theta++)       double sum=0., jmean=0.;*/
         trgradg[h][j][theta]=gradg[h][theta][j];    int first;
     int j, k=0,jk, ju, jl;
     double sum=0.;
      for(i=1;i<=nlstate*2;i++)    first=0;
       for(j=1;j<=nlstate*2;j++)    jmin=1e+5;
         varhe[i][j][(int)age] =0.;    jmax=-1;
     jmean=0.;
      printf("%d|",(int)age);fflush(stdout);    for(i=1; i<=imx; i++){
     for(h=0;h<=nhstepm-1;h++){      mi=0;
       for(k=0;k<=nhstepm-1;k++){      m=firstpass;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      while(s[m][i] <= nlstate){
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        if(s[m][i]>=1)
         for(i=1;i<=nlstate*2;i++)          mw[++mi][i]=m;
           for(j=1;j<=nlstate*2;j++)        if(m >=lastpass)
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          break;
       }        else
     }          m++;
       }/* end while */
            if (s[m][i] > nlstate){
     /* Computing expectancies */        mi++;     /* Death is another wave */
     for(i=1; i<=nlstate;i++)        /* if(mi==0)  never been interviewed correctly before death */
       for(j=1; j<=nlstate;j++)           /* Only death is a correct wave */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        mw[mi][i]=m;
           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]);*/      wav[i]=mi;
       if(mi==0){
         }        if(first==0){
           printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
     fprintf(ficreseij,"%3.0f",age );          first=1;
     cptj=0;        }
     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);
         cptj++;        }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      } /* end mi==0 */
       }    }
     fprintf(ficreseij,"\n");  
        for(i=1; i<=imx; i++){
     free_matrix(gm,0,nhstepm,1,nlstate*2);      for(mi=1; mi<wav[i];mi++){
     free_matrix(gp,0,nhstepm,1,nlstate*2);        if (stepm <=0)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          dh[mi][i]=1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        else{
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (s[mw[mi+1][i]][i] > nlstate) {
   }            if (agedc[i] < 2*AGESUP) {
   free_vector(xp,1,npar);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   free_matrix(dnewm,1,nlstate*2,1,npar);            if(j==0) j=1;  /* Survives at least one month after exam */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);            k=k+1;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);            if (j >= jmax) jmax=j;
 }            if (j <= jmin) jmin=j;
             sum=sum+j;
 /************ Variance ******************/            /*if (j<0) printf("j=%d num=%d \n",j,i); */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 {            }
   /* Variance of health expectancies */          }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          else{
   double **newm;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   double **dnewm,**doldm;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   int i, j, nhstepm, hstepm, h, nstepm ;            k=k+1;
   int k, cptcode;            if (j >= jmax) jmax=j;
   double *xp;            else if (j <= jmin)jmin=j;
   double **gp, **gm;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   double ***gradg, ***trgradg;            sum=sum+j;
   double ***p3mat;          }
   double age,agelim, hf;          jk= j/stepm;
   int theta;          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   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");          if(mle <=1){ 
   fprintf(ficresvij,"# Age");            if(jl==0){
   for(i=1; i<=nlstate;i++)              dh[mi][i]=jk;
     for(j=1; j<=nlstate;j++)              bh[mi][i]=0;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            }else{ /* We want a negative bias in order to only have interpolation ie
   fprintf(ficresvij,"\n");                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   xp=vector(1,npar);              bh[mi][i]=ju;
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          }else{
              if(jl <= -ju){
   if(estepm < stepm){              dh[mi][i]=jk;
     printf ("Problem %d lower than %d\n",estepm, stepm);              bh[mi][i]=jl;       /* bias is positive if real duration
   }                                   * is higher than the multiple of stepm and negative otherwise.
   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.            else{
      nhstepm is the number of hstepm from age to agelim              dh[mi][i]=jk+1;
      nstepm is the number of stepm from age to agelin.              bh[mi][i]=ju;
      Look at hpijx to understand the reason of that which relies in memory size            }
      and note for a fixed period like k years */            if(dh[mi][i]==0){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              dh[mi][i]=1; /* At least one step */
      survival function given by stepm (the optimization length). Unfortunately it              bh[mi][i]=ju; /* At least one step */
      means that if the survival funtion is printed only each two years of age and if              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);
      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.          }
   */        } /* end if mle */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      } /* end wave */
   agelim = AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    jmean=sum/k;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  /*********** Tricode ****************************/
     gm=matrix(0,nhstepm,1,nlstate);  void tricode(int *Tvar, int **nbcode, int imx)
   {
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */    int Ndum[20],ij=1, k, j, i, maxncov=19;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int cptcode=0;
       }    cptcoveff=0; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       }                                 modality*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for(j=1; j<= nlstate; j++){        Ndum[ij]++; /*store the modality */
         for(h=0; h<=nhstepm; h++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                                         Tvar[j]. If V=sex and male is 0 and 
         }                                         female is 1, then  cptcode=1.*/
       }      }
      
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=0; i<=cptcode; i++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        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 */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
        ij=1; 
       if (popbased==1) {      for (i=1; i<=ncodemax[j]; i++) {
         for(i=1; i<=nlstate;i++)        for (k=0; k<= maxncov; k++) {
           prlim[i][i]=probs[(int)age][i][ij];          if (Ndum[k] != 0) {
       }            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; */
       for(j=1; j<= nlstate; j++){            
         for(h=0; h<=nhstepm; h++){            ij++;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          if (ij > ncodemax[j]) break; 
         }        }  
       }      } 
     }  
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }   for (i=1; i<=ncovmodel-2; i++) { 
     } /* End theta */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);     Ndum[ij]++;
    }
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)   ij=1;
         for(theta=1; theta <=npar; theta++)   for (i=1; i<= maxncov; i++) {
           trgradg[h][j][theta]=gradg[h][theta][j];     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       ij++;
     for(i=1;i<=nlstate;i++)     }
       for(j=1;j<=nlstate;j++)   }
         vareij[i][j][(int)age] =0.;   
    cptcoveff=ij-1; /*Number of simple covariates*/
     for(h=0;h<=nhstepm;h++){  }
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  /*********** Health Expectancies ****************/
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  {
       }    /* Health expectancies */
     }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
     fprintf(ficresvij,"%.0f ",age );    double ***p3mat,***varhe;
     for(i=1; i<=nlstate;i++)    double **dnewm,**doldm;
       for(j=1; j<=nlstate;j++){    double *xp;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    double **gp, **gm;
       }    double ***gradg, ***trgradg;
     fprintf(ficresvij,"\n");    int theta;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    xp=vector(1,npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    dnewm=matrix(1,nlstate*2,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldm=matrix(1,nlstate*2,1,nlstate*2);
   } /* End age */    
      fprintf(ficreseij,"# Health expectancies\n");
   free_vector(xp,1,npar);    fprintf(ficreseij,"# Age");
   free_matrix(doldm,1,nlstate,1,npar);    for(i=1; i<=nlstate;i++)
   free_matrix(dnewm,1,nlstate,1,nlstate);      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
 }    fprintf(ficreseij,"\n");
   
 /************ Variance of prevlim ******************/    if(estepm < stepm){
 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 ("Problem %d lower than %d\n",estepm, stepm);
 {    }
   /* Variance of prevalence limit */    else  hstepm=estepm;   
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
   double **newm;     * This is mainly to measure the difference between two models: for example
   double **dnewm,**doldm;     * if stepm=24 months pijx are given only every 2 years and by summing them
   int i, j, nhstepm, hstepm;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   int k, cptcode;     * progression in between and thus overestimating or underestimating according
   double *xp;     * to the curvature of the survival function. If, for the same date, we 
   double *gp, *gm;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   double **gradg, **trgradg;     * to compare the new estimate of Life expectancy with the same linear 
   double age,agelim;     * hypothesis. A more precise result, taking into account a more precise
   int theta;     * curvature will be obtained if estepm is as small as stepm. */
      
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    /* For example we decided to compute the life expectancy with the smallest unit */
   fprintf(ficresvpl,"# Age");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   for(i=1; i<=nlstate;i++)       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficresvpl," %1d-%1d",i,i);       nstepm is the number of stepm from age to agelin. 
   fprintf(ficresvpl,"\n");       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   xp=vector(1,npar);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   dnewm=matrix(1,nlstate,1,npar);       survival function given by stepm (the optimization length). Unfortunately it
   doldm=matrix(1,nlstate,1,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 
   hstepm=1*YEARM; /* Every year of age */       results. So we changed our mind and took the option of the best precision.
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    */
   agelim = AGESUP;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    agelim=AGESUP;
     if (stepm >= YEARM) hstepm=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /* nhstepm age range expressed in number of stepm */
     gradg=matrix(1,npar,1,nlstate);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     gp=vector(1,nlstate);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     gm=vector(1,nlstate);      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(theta=1; theta <=npar; theta++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(i=1; i<=npar; i++){ /* Computes gradient */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      gp=matrix(0,nhstepm,1,nlstate*2);
       }      gm=matrix(0,nhstepm,1,nlstate*2);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         gp[i] = prlim[i][i];         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       for(i=1; i<=npar; i++) /* Computes gradient */   
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];      /* Computing Variances of health expectancies */
   
       for(i=1;i<=nlstate;i++)       for(theta=1; theta <=npar; theta++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for(i=1; i<=npar; i++){ 
     } /* End theta */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
     trgradg =matrix(1,nlstate,1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     
     for(j=1; j<=nlstate;j++)        cptj=0;
       for(theta=1; theta <=npar; theta++)        for(j=1; j<= nlstate; j++){
         trgradg[j][theta]=gradg[theta][j];          for(i=1; i<=nlstate; i++){
             cptj=cptj+1;
     for(i=1;i<=nlstate;i++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       varpl[i][(int)age] =0.;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          }
     for(i=1;i<=nlstate;i++)        }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       
        
     fprintf(ficresvpl,"%.0f ",age );        for(i=1; i<=npar; i++) 
     for(i=1; i<=nlstate;i++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficresvpl,"\n");        
     free_vector(gp,1,nlstate);        cptj=0;
     free_vector(gm,1,nlstate);        for(j=1; j<= nlstate; j++){
     free_matrix(gradg,1,npar,1,nlstate);          for(i=1;i<=nlstate;i++){
     free_matrix(trgradg,1,nlstate,1,npar);            cptj=cptj+1;
   } /* End age */            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);        }
         for(j=1; j<= nlstate*2; j++)
 }          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 /************ Variance of one-step probabilities  ******************/          }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)       } 
 {     
   int i, j, i1, k1, j1, z1;  /* End theta */
   int k=0, cptcode;  
   double **dnewm,**doldm;       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   double *xp;  
   double *gp, *gm;       for(h=0; h<=nhstepm-1; h++)
   double **gradg, **trgradg;        for(j=1; j<=nlstate*2;j++)
   double age,agelim, cov[NCOVMAX];          for(theta=1; theta <=npar; theta++)
   int theta;            trgradg[h][j][theta]=gradg[h][theta][j];
   char fileresprob[FILENAMELENGTH];       
   
   strcpy(fileresprob,"prob");       for(i=1;i<=nlstate*2;i++)
   strcat(fileresprob,fileres);        for(j=1;j<=nlstate*2;j++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          varhe[i][j][(int)age] =0.;
     printf("Problem with resultfile: %s\n", fileresprob);  
   }       printf("%d|",(int)age);fflush(stdout);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");        for(k=0;k<=nhstepm-1;k++){
   fprintf(ficresprob,"# Age");          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   for(i=1; i<=nlstate;i++)          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     for(j=1; j<=(nlstate+ndeath);j++)          for(i=1;i<=nlstate*2;i++)
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            for(j=1;j<=nlstate*2;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   fprintf(ficresprob,"\n");      }
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   xp=vector(1,npar);        for(j=1; j<=nlstate;j++)
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
              
   cov[1]=1;  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          }
   j1=0;  
   for(k1=1; k1<=1;k1++){      fprintf(ficreseij,"%3.0f",age );
     for(i1=1; i1<=ncodemax[k1];i1++){      cptj=0;
     j1++;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
     if  (cptcovn>0) {          cptj++;
       fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
       fprintf(ficresprob, "**********\n#");      fprintf(ficreseij,"\n");
     }     
          free_matrix(gm,0,nhstepm,1,nlstate*2);
       for (age=bage; age<=fage; age ++){      free_matrix(gp,0,nhstepm,1,nlstate*2);
         cov[2]=age;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
         for (k=1; k<=cptcovn;k++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              }
         }    printf("\n");
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    fprintf(ficlog,"\n");
         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]]];    free_vector(xp,1,npar);
            free_matrix(dnewm,1,nlstate*2,1,npar);
         gradg=matrix(1,npar,1,9);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
         trgradg=matrix(1,9,1,npar);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
      /************ Variance ******************/
         for(theta=1; theta <=npar; theta++){  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
           for(i=1; i<=npar; i++)  {
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* Variance of health expectancies */
              /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    /* double **newm;*/
              double **dnewm,**doldm;
           k=0;    double **dnewmp,**doldmp;
           for(i=1; i<= (nlstate+ndeath); i++){    int i, j, nhstepm, hstepm, h, nstepm ;
             for(j=1; j<=(nlstate+ndeath);j++){    int k, cptcode;
               k=k+1;    double *xp;
               gp[k]=pmmij[i][j];    double **gp, **gm;  /* for var eij */
             }    double ***gradg, ***trgradg; /*for var eij */
           }    double **gradgp, **trgradgp; /* for var p point j */
              double *gpp, *gmp; /* for var p point j */
           for(i=1; i<=npar; i++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    double ***p3mat;
        double age,agelim, hf;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double ***mobaverage;
           k=0;    int theta;
           for(i=1; i<=(nlstate+ndeath); i++){    char digit[4];
             for(j=1; j<=(nlstate+ndeath);j++){    char digitp[25];
               k=k+1;  
               gm[k]=pmmij[i][j];    char fileresprobmorprev[FILENAMELENGTH];
             }  
           }    if(popbased==1){
            if(mobilav!=0)
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        strcpy(digitp,"-populbased-mobilav-");
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        else strcpy(digitp,"-populbased-nomobil-");
         }    }
     else 
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      strcpy(digitp,"-stablbased-");
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];    if (mobilav!=0) {
              mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                printf(" Error in movingaverage mobilav=%d\n",mobilav);
         pmij(pmmij,cov,ncovmodel,x,nlstate);      }
            }
         k=0;  
         for(i=1; i<=(nlstate+ndeath); i++){    strcpy(fileresprobmorprev,"prmorprev"); 
           for(j=1; j<=(nlstate+ndeath);j++){    sprintf(digit,"%-d",ij);
             k=k+1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
             gm[k]=pmmij[i][j];    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         }    strcat(fileresprobmorprev,fileres);
          if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
      /*printf("\n%d ",(int)age);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    }
      }*/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficresprob,"\n%d ",(int)age);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));      fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
       }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficresprobmorprev,"\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      exit(0);
   free_vector(xp,1,npar);    }
   fclose(ficresprob);    else{
        fprintf(ficgp,"\n# Routine varevsij");
 }    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
 /******************* Printing html file ***********/      printf("Problem with html file: %s\n", optionfilehtm);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
                   int lastpass, int stepm, int weightopt, char model[],\      exit(0);
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    }
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    else{
                   char version[], int popforecast, int estepm ,/* \ */      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");
                   double jprev1, double mprev1,double anprev1, \      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   double jprev2, double mprev2,double anprev2){    }
   int jj1, k1, i1, cpt;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
     fprintf(ficresvij,"# Age");
   strcpy(optionfilehtm,optionfile);    for(i=1; i<=nlstate;i++)
   strcat(optionfilehtm,".htm");      for(j=1; j<=nlstate;j++)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     printf("Problem with %s \n",optionfilehtm), exit(0);    fprintf(ficresvij,"\n");
   }  
     xp=vector(1,npar);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    dnewm=matrix(1,nlstate,1,npar);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    doldm=matrix(1,nlstate,1,nlstate);
 \n    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 Total number of observations=%d <br>\n    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  
 <hr  size=\"2\" color=\"#EC5E5E\">    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  <ul><li>Parameter files<br>\n    gpp=vector(nlstate+1,nlstate+ndeath);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    gmp=vector(nlstate+1,nlstate+ndeath);
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    if(estepm < stepm){
  - 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      printf ("Problem %d lower than %d\n",estepm, stepm);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    }
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    else  hstepm=estepm;   
  - Life expectancies by age and initial health status (estepm=%2d months):    /* For example we decided to compute the life expectancy with the smallest unit */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n       Look at hpijx to understand the reason of that which relies in memory size
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n       and note for a fixed period like k years */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n       survival function given by stepm (the optimization length). Unfortunately it
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n       means that if the survival funtion is printed every two years of age and if
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);       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.
  if(popforecast==1) fprintf(fichtm,"\n    */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    agelim = AGESUP;
         <br>",fileres,fileres,fileres,fileres);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  else      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    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);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 fprintf(fichtm," <li>Graphs</li><p>");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
  m=cptcoveff;      gp=matrix(0,nhstepm,1,nlstate);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      gm=matrix(0,nhstepm,1,nlstate);
   
  jj1=0;  
  for(k1=1; k1<=m;k1++){      for(theta=1; theta <=npar; theta++){
    for(i1=1; i1<=ncodemax[k1];i1++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
        jj1++;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        if (cptcovn > 0) {        }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          for (cpt=1; cpt<=cptcoveff;cpt++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        if (popbased==1) {
        }          if(mobilav ==0){
        /* Pij */            for(i=1; i<=nlstate;i++)
        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>              prlim[i][i]=probs[(int)age][i][ij];
 <img src=\"pe%s%d1.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);              }else{ /* mobilav */ 
        /* Quasi-incidences */            for(i=1; i<=nlstate;i++)
        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>              prlim[i][i]=mobaverage[(int)age][i][ij];
 <img src=\"pe%s%d2.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);              }
        /* Stable prevalence in each health state */        }
        for(cpt=1; cpt<nlstate;cpt++){    
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        for(j=1; j<= nlstate; j++){
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(h=0; h<=nhstepm; h++){
        }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     for(cpt=1; cpt<=nlstate;cpt++) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
        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);          /* This for computing probability of death (h=1 means
      }           computed over hstepm matrices product = hstepm*stepm months) 
      for(cpt=1; cpt<=nlstate;cpt++) {           as a weighted average of prlim.
         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);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 health expectancies in states (1) and (2): e%s%d.png<br>        }    
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        /* end probability of death */
 fprintf(fichtm,"\n</body>");  
    }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
    }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 fclose(fichtm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
 /******************* Gnuplot file **************/        if (popbased==1) {
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              prlim[i][i]=probs[(int)age][i][ij];
   int ng;          }else{ /* mobilav */ 
   strcpy(optionfilegnuplot,optionfilefiname);            for(i=1; i<=nlstate;i++)
   strcat(optionfilegnuplot,".gp.txt");              prlim[i][i]=mobaverage[(int)age][i][ij];
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          }
     printf("Problem with file %s",optionfilegnuplot);        }
   }  
         for(j=1; j<= nlstate; j++){
 #ifdef windows          for(h=0; h<=nhstepm; h++){
     fprintf(ficgp,"cd \"%s\" \n",pathc);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 #endif              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 m=pow(2,cptcoveff);          }
          }
  /* 1eme*/        /* This for computing probability of death (h=1 means
   for (cpt=1; cpt<= nlstate ; cpt ++) {           computed over hstepm matrices product = hstepm*stepm months) 
    for (k1=1; k1<= m ; k1 ++) {           as a weighted average of prlim.
         */
 #ifdef windows        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
      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);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 #endif        }    
 #ifdef unix        /* end probability of death */
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        for(j=1; j<= nlstate; j++) /* vareij */
 #endif          for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     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 (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } /* End theta */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {      for(h=0; h<=nhstepm; h++) /* veij */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(theta=1; theta <=npar; theta++)
 }              trgradg[h][j][theta]=gradg[h][theta][j];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for(theta=1; theta <=npar; theta++)
 #endif          trgradgp[j][theta]=gradgp[theta][j];
    }    
   }  
   /*2 eme*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {        for(j=1;j<=nlstate;j++)
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          vareij[i][j][(int)age] =0.;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);  
          for(h=0;h<=nhstepm;h++){
     for (i=1; i<= nlstate+1 ; i ++) {        for(k=0;k<=nhstepm;k++){
       k=2*i;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       for (j=1; j<= nlstate+1 ; j ++) {          for(i=1;i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(j=1;j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 }          }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* pptj */
       for (j=1; j<= nlstate+1 ; j ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }       for(j=nlstate+1;j<=nlstate+ndeath;j++)
       fprintf(ficgp,"\" t\"\" w l 0,");       for(i=nlstate+1;i<=nlstate+ndeath;i++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          varppt[j][i]=doldmp[j][i];
       for (j=1; j<= nlstate+1 ; j ++) {      /* end ppptj */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /*  x centered again */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 }        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");   
       else fprintf(ficgp,"\" t\"\" w l 0,");      if (popbased==1) {
     }        if(mobilav ==0){
   }          for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
   /*3eme*/        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
     for (cpt=1; cpt<= nlstate ; cpt ++) {        }
       k=2+nlstate*(2*cpt-2);      }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      /* This for computing probability of death (h=1 means
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");         as a weighted average of prlim.
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      */
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
 */      /* end probability of death */
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     }        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
   /* CV preval stat */      } 
     for (k1=1; k1<= m ; k1 ++) {      fprintf(ficresprobmorprev,"\n");
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;      fprintf(ficresvij,"%.0f ",age );
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      for(i=1; i<=nlstate;i++)
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       for (i=1; i< nlstate ; i ++)        }
         fprintf(ficgp,"+$%d",k+i+1);      fprintf(ficresvij,"\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      free_matrix(gp,0,nhstepm,1,nlstate);
            free_matrix(gm,0,nhstepm,1,nlstate);
       l=3+(nlstate+ndeath)*cpt;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       for (i=1; i< nlstate ; i ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         l=3+(nlstate+ndeath)*cpt;    } /* End age */
         fprintf(ficgp,"+$%d",l+i+1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       }    free_vector(gmp,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      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 */
   /* proba elementaires */    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    for(i=1,jk=1; i <=nlstate; i++){  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     for(k=1; k <=(nlstate+ndeath); k++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       if (k != i) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         for(j=1; j <=ncovmodel; j++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
            fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
           jk++;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
           fprintf(ficgp,"\n");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
         }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       }  */
     }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
    }  
     free_vector(xp,1,npar);
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    free_matrix(doldm,1,nlstate,1,nlstate);
      for(jk=1; jk <=m; jk++) {    free_matrix(dnewm,1,nlstate,1,npar);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        if (ng==2)    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        else    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          fprintf(ficgp,"\nset title \"Probability\"\n");    fclose(ficresprobmorprev);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    fclose(ficgp);
        i=1;    fclose(fichtm);
        for(k2=1; k2<=nlstate; k2++) {  }
          k3=i;  
          for(k=1; k<=(nlstate+ndeath); k++) {  /************ Variance of prevlim ******************/
            if (k != k2){  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)
              if(ng==2)  {
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);    /* Variance of prevalence limit */
              else    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    double **newm;
              ij=1;    double **dnewm,**doldm;
              for(j=3; j <=ncovmodel; j++) {    int i, j, nhstepm, hstepm;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int k, cptcode;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double *xp;
                  ij++;    double *gp, *gm;
                }    double **gradg, **trgradg;
                else    double age,agelim;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int theta;
              }     
              fprintf(ficgp,")/(1");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
                  fprintf(ficresvpl,"# Age");
              for(k1=1; k1 <=nlstate; k1++){      for(i=1; i<=nlstate;i++)
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        fprintf(ficresvpl," %1d-%1d",i,i);
                ij=1;    fprintf(ficresvpl,"\n");
                for(j=3; j <=ncovmodel; j++){  
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    xp=vector(1,npar);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    dnewm=matrix(1,nlstate,1,npar);
                    ij++;    doldm=matrix(1,nlstate,1,nlstate);
                  }    
                  else    hstepm=1*YEARM; /* Every year of age */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                }    agelim = AGESUP;
                fprintf(ficgp,")");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      if (stepm >= YEARM) hstepm=1;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
              i=i+ncovmodel;      gradg=matrix(1,npar,1,nlstate);
            }      gp=vector(1,nlstate);
          }      gm=vector(1,nlstate);
        }  
      }      for(theta=1; theta <=npar; theta++){
    }        for(i=1; i<=npar; i++){ /* Computes gradient */
    fclose(ficgp);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 }  /* end gnuplot */        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
 /*************** Moving average **************/          gp[i] = prlim[i][i];
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      
         for(i=1; i<=npar; i++) /* Computes gradient */
   int i, cpt, cptcod;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for (i=1; i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          gm[i] = prlim[i][i];
           mobaverage[(int)agedeb][i][cptcod]=0.;  
            for(i=1;i<=nlstate;i++)
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       for (i=1; i<=nlstate;i++){      } /* End theta */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){      trgradg =matrix(1,nlstate,1,npar);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }      for(j=1; j<=nlstate;j++)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        for(theta=1; theta <=npar; theta++)
         }          trgradg[j][theta]=gradg[theta][j];
       }  
     }      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] =0.;
 }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
 /************** Forecasting ******************/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 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){  
        fprintf(ficresvpl,"%.0f ",age );
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      for(i=1; i<=nlstate;i++)
   int *popage;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      fprintf(ficresvpl,"\n");
   double *popeffectif,*popcount;      free_vector(gp,1,nlstate);
   double ***p3mat;      free_vector(gm,1,nlstate);
   char fileresf[FILENAMELENGTH];      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
  agelim=AGESUP;    } /* End age */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
     free_vector(xp,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
    
   strcpy(fileresf,"f");  }
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {  /************ Variance of one-step probabilities  ******************/
     printf("Problem with forecast resultfile: %s\n", fileresf);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   }  {
   printf("Computing forecasting: result on file '%s' \n", fileresf);    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int k=0,l, cptcode;
     int first=1, first1;
   if (mobilav==1) {    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **dnewm,**doldm;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double *xp;
   }    double *gp, *gm;
     double **gradg, **trgradg;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double **mu;
   if (stepm<=12) stepsize=1;    double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   agelim=AGESUP;    int theta;
      char fileresprob[FILENAMELENGTH];
   hstepm=1;    char fileresprobcov[FILENAMELENGTH];
   hstepm=hstepm/stepm;    char fileresprobcor[FILENAMELENGTH];
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    double ***varpij;
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;    strcpy(fileresprob,"prob"); 
   yp1=modf((yp2*30.5),&yp);    strcat(fileresprob,fileres);
   jprojmean=yp;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if(jprojmean==0) jprojmean=1;      printf("Problem with resultfile: %s\n", fileresprob);
   if(mprojmean==0) jprojmean=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    strcpy(fileresprobcov,"probcov"); 
      strcat(fileresprobcov,fileres);
   for(cptcov=1;cptcov<=i2;cptcov++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf("Problem with resultfile: %s\n", fileresprobcov);
       k=k+1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficresf,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    strcpy(fileresprobcor,"probcor"); 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(fileresprobcor,fileres);
       }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       fprintf(ficresf,"******\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficresf,"# StartingAge FinalAge");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    }
          printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
          fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficresf,"\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           nhstepm = nhstepm/hstepm;    fprintf(ficresprob,"# Age");
              fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobcov,"# Age");
           oldm=oldms;savm=savms;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprobcov,"# Age");
          
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      for(j=1; j<=(nlstate+ndeath);j++){
             }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
             for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               kk1=0.;kk2=0;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
               for(i=1; i<=nlstate;i++) {                    }  
                 if (mobilav==1)   /* fprintf(ficresprob,"\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficresprobcov,"\n");
                 else {    fprintf(ficresprobcor,"\n");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   */
                 }   xp=vector(1,npar);
                    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               if (h==(int)(calagedate+12*cpt)){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                 fprintf(ficresf," %.3f", kk1);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                            first=1;
               }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
             }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
           }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      exit(0);
         }    }
       }    else{
     }      fprintf(ficgp,"\n# Routine varprob");
   }    }
            if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   fclose(ficresf);      exit(0);
 }    }
 /************** Forecasting ******************/    else{
 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(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      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 *popeffectif,*popcount;      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 ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];    }
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cov[1]=1;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    tj=cptcoveff;
   agelim=AGESUP;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    j1=0;
      for(t=1; t<=tj;t++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(i1=1; i1<=ncodemax[t];i1++){ 
          j1++;
          if  (cptcovn>0) {
   strcpy(filerespop,"pop");          fprintf(ficresprob, "\n#********** Variable "); 
   strcat(filerespop,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          fprintf(ficresprob, "**********\n#\n");
     printf("Problem with forecast resultfile: %s\n", filerespop);          fprintf(ficresprobcov, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   printf("Computing forecasting: result on file '%s' \n", filerespop);          fprintf(ficresprobcov, "**********\n#\n");
           
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (mobilav==1) {          fprintf(ficgp, "**********\n#\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
     movingaverage(agedeb, fage, ageminpar, mobaverage);          
   }          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]]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   if (stepm<=12) stepsize=1;          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   agelim=AGESUP;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcor, "**********\n#");    
   hstepm=1;        }
   hstepm=hstepm/stepm;        
          for (age=bage; age<=fage; age ++){ 
   if (popforecast==1) {          cov[2]=age;
     if((ficpop=fopen(popfile,"r"))==NULL) {          for (k=1; k<=cptcovn;k++) {
       printf("Problem with population file : %s\n",popfile);exit(0);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     }          }
     popage=ivector(0,AGESUP);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     popeffectif=vector(0,AGESUP);          for (k=1; k<=cptcovprod;k++)
     popcount=vector(0,AGESUP);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              
     i=1;            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
              gp=vector(1,(nlstate)*(nlstate+ndeath));
     imx=i;          gm=vector(1,(nlstate)*(nlstate+ndeath));
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      
   }          for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
   for(cptcov=1;cptcov<=i2;cptcov++){              xp[i] = x[i] + (i==theta ?delti[theta]:0);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            
       k=k+1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficrespop,"\n#******");            
       for(j=1;j<=cptcoveff;j++) {            k=0;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1; i<= (nlstate); i++){
       }              for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficrespop,"******\n");                k=k+1;
       fprintf(ficrespop,"# Age");                gp[k]=pmmij[i][j];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);              }
       if (popforecast==1)  fprintf(ficrespop," [Population]");            }
                  
       for (cpt=0; cpt<=0;cpt++) {            for(i=1; i<=npar; i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                xp[i] = x[i] - (i==theta ?delti[theta]:0);
              
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            k=0;
           nhstepm = nhstepm/hstepm;            for(i=1; i<=(nlstate); i++){
                        for(j=1; j<=(nlstate+ndeath);j++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                k=k+1;
           oldm=oldms;savm=savms;                gm[k]=pmmij[i][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                }
                    }
           for (h=0; h<=nhstepm; h++){       
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
               for(i=1; i<=nlstate;i++) {                          for(theta=1; theta <=npar; theta++)
                 if (mobilav==1)              trgradg[j][theta]=gradg[theta][j];
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          
                 else {          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                 }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
               }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
               if (h==(int)(calagedate+12*cpt)){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          pmij(pmmij,cov,ncovmodel,x,nlstate);
               }          
             }          k=0;
             for(i=1; i<=nlstate;i++){          for(i=1; i<=(nlstate); i++){
               kk1=0.;            for(j=1; j<=(nlstate+ndeath);j++){
                 for(j=1; j<=nlstate;j++){              k=k+1;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              mu[k][(int) age]=pmmij[i][j];
                 }            }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          }
             }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              varpij[i][j][(int)age] = doldm[i][j];
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }          /*printf("\n%d ",(int)age);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            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]));
       }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
   /******/  
           fprintf(ficresprob,"\n%d ",(int)age);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          fprintf(ficresprobcov,"\n%d ",(int)age);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficresprobcor,"\n%d ",(int)age);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           nhstepm = nhstepm/hstepm;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                    for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           oldm=oldms;savm=savms;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
           for (h=0; h<=nhstepm; h++){          i=0;
             if (h==(int) (calagedate+YEARM*cpt)) {          for (k=1; k<=(nlstate);k++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            for (l=1; l<=(nlstate+ndeath);l++){ 
             }              i=i++;
             for(j=1; j<=nlstate+ndeath;j++) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               kk1=0.;kk2=0;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for(i=1; i<=nlstate;i++) {                            for (j=1; j<=i;j++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                    fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
               }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              }
             }            }
           }          }/* end of loop for state */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* end of loop for age */
         }  
       }        /* Confidence intervalle of pij  */
    }        /*
   }          fprintf(ficgp,"\nset noparametric;unset label");
            fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   if (popforecast==1) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     free_ivector(popage,0,AGESUP);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     free_vector(popeffectif,0,AGESUP);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     free_vector(popcount,0,AGESUP);        */
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        first1=1;
   fclose(ficrespop);        for (k2=1; k2<=(nlstate);k2++){
 }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
 /***********************************************/            j=(k2-1)*(nlstate+ndeath)+l2;
 /**************** Main Program *****************/            for (k1=1; k1<=(nlstate);k1++){
 /***********************************************/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
 int main(int argc, char *argv[])                i=(k1-1)*(nlstate+ndeath)+l1;
 {                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                  if ((int)age %5==0){
   double agedeb, agefin,hf;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   double fret;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   double **xi,tmp,delta;                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
   double dum; /* Dummy variable */                    /* Computing eigen value of matrix of covariance */
   double ***p3mat;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   int *indx;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   char line[MAXLINE], linepar[MAXLINE];                    /* Eigen vectors */
   char title[MAXLINE];                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                    /*v21=sqrt(1.-v11*v11); *//* error */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                    v21=(lc1-v1)/cv12*v11;
                      v12=-v21;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];                    v22=v11;
                     tnalp=v21/v11;
   char filerest[FILENAMELENGTH];                    if(first1==1){
   char fileregp[FILENAMELENGTH];                      first1=0;
   char popfile[FILENAMELENGTH];                      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);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                    }
   int firstobs=1, lastobs=10;                    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);
   int sdeb, sfin; /* Status at beginning and end */                    /*printf(fignu*/
   int c,  h , cpt,l;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   int ju,jl, mi;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                    if(first==1){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                      first=0;
   int mobilav=0,popforecast=0;                      fprintf(ficgp,"\nset parametric;unset label");
   int hstepm, nhstepm;                      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);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   double bage, fage, age, agelim, agebase;                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   double ftolpl=FTOL;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   double **prlim;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   double *severity;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double ***param; /* Matrix of parameters */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double  *p;                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   double **matcov; /* Matrix of covariance */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double ***delti3; /* Scale */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double *delti; /* Scale */                    }else{
   double ***eij, ***vareij;                      first=0;
   double **varpl; /* Variances of prevalence limits by age */                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   double *epj, vepp;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double kk1, kk2;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   char version[80]="Imach version 0.8e, May 2002, INED-EUROREVES ";                    }/* if first */
   char *alph[]={"a","a","b","c","d","e"}, str[4];                  } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   char z[1]="c", occ;                first=1;
 #include <sys/time.h>              } /*l12 */
 #include <time.h>            } /* k12 */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          } /*l1 */
          }/* k1 */
   /* long total_usecs;      } /* loop covariates */
   struct timeval start_time, end_time;    }
      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   getcwd(pathcd, size);    free_vector(xp,1,npar);
     fclose(ficresprob);
   printf("\n%s",version);    fclose(ficresprobcov);
   if(argc <=1){    fclose(ficresprobcor);
     printf("\nEnter the parameter file name: ");    fclose(ficgp);
     scanf("%s",pathtot);    fclose(fichtm);
   }  }
   else{  
     strcpy(pathtot,argv[1]);  
   }  /******************* Printing html file ***********/
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   /*cygwin_split_path(pathtot,path,optionfile);                    int lastpass, int stepm, int weightopt, char model[],\
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   /* cutv(path,optionfile,pathtot,'\\');*/                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                    double jprev2, double mprev2,double anprev2){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    int jj1, k1, i1, cpt;
   chdir(path);    /*char optionfilehtm[FILENAMELENGTH];*/
   replace(pathc,path);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
 /*-------- arguments in the command line --------*/      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   strcat(fileres,".txt");    /* Other files have txt extension */   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   /*---------arguments file --------*/   - 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): 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     printf("Problem with optionfile %s\n",optionfile);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     goto end;  
   }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   strcpy(filereso,"o");   m=cptcoveff;
   strcat(filereso,fileres);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;   jj1=0;
   }   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   /* Reads comments: lines beginning with '#' */       jj1++;
   while((c=getc(ficpar))=='#' && c!= EOF){       if (cptcovn > 0) {
     ungetc(c,ficpar);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fgets(line, MAXLINE, ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     puts(line);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fputs(line,ficparo);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
   ungetc(c,ficpar);       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
   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);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   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);       /* Quasi-incidences */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);       fprintf(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>
 while((c=getc(ficpar))=='#' && c!= EOF){  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     ungetc(c,ficpar);         /* Stable prevalence in each health state */
     fgets(line, MAXLINE, ficpar);         for(cpt=1; cpt<nlstate;cpt++){
     puts(line);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
     fputs(line,ficparo);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   }         }
   ungetc(c,ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
            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);
   covar=matrix(0,NCOVMAX,1,n);       }
   cptcovn=0;       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   ncovmodel=2+cptcovn;     } /* end i1 */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */   }/* End k1 */
     fprintf(fichtm,"</ul>");
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     ungetc(c,ficpar);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     fgets(line, MAXLINE, ficpar);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
     puts(line);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     fputs(line,ficparo);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
   ungetc(c,ficpar);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)   if(popforecast==1) fprintf(fichtm,"\n
     for(j=1; j <=nlstate+ndeath-1; j++){   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
       fscanf(ficpar,"%1d%1d",&i1,&j1);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
       fprintf(ficparo,"%1d%1d",i1,j1);          <br>",fileres,fileres,fileres,fileres);
       printf("%1d%1d",i,j);   else 
       for(k=1; k<=ncovmodel;k++){     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);
         fscanf(ficpar," %lf",&param[i][j][k]);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);   m=cptcoveff;
       }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fscanf(ficpar,"\n");  
       printf("\n");   jj1=0;
       fprintf(ficparo,"\n");   for(k1=1; k1<=m;k1++){
     }     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   p=param[1][1];         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /* Reads comments: lines beginning with '#' */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   while((c=getc(ficpar))=='#' && c!= EOF){       }
     ungetc(c,ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
     fgets(line, MAXLINE, ficpar);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     puts(line);  interval) in state (%d): v%s%d%d.png <br>
     fputs(line,ficparo);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   }       }
   ungetc(c,ficpar);     } /* end i1 */
    }/* End k1 */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);   fprintf(fichtm,"</ul>");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  fclose(fichtm);
   for(i=1; i <=nlstate; i++){  }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  /******************* Gnuplot file **************/
       printf("%1d%1d",i,j);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    int ng;
         printf(" %le",delti3[i][j][k]);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         fprintf(ficparo," %le",delti3[i][j][k]);      printf("Problem with file %s",optionfilegnuplot);
       }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
       fscanf(ficpar,"\n");    }
       printf("\n");  
       fprintf(ficparo,"\n");    /*#ifdef windows */
     }      fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   delti=delti3[1][1];  m=pow(2,cptcoveff);
      
   /* Reads comments: lines beginning with '#' */   /* 1eme*/
   while((c=getc(ficpar))=='#' && c!= EOF){    for (cpt=1; cpt<= nlstate ; cpt ++) {
     ungetc(c,ficpar);     for (k1=1; k1<= m ; k1 ++) {
     fgets(line, MAXLINE, ficpar);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     puts(line);       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);
     fputs(line,ficparo);  
   }       for (i=1; i<= nlstate ; i ++) {
   ungetc(c,ficpar);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
   matcov=matrix(1,npar,1,npar);       }
   for(i=1; i <=npar; i++){       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);
     fscanf(ficpar,"%s",&str);       for (i=1; i<= nlstate ; i ++) {
     printf("%s",str);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     fprintf(ficparo,"%s",str);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(j=1; j <=i; j++){       } 
       fscanf(ficpar," %le",&matcov[i][j]);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
       printf(" %.5le",matcov[i][j]);       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficparo," %.5le",matcov[i][j]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
     fscanf(ficpar,"\n");       }  
     printf("\n");       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     fprintf(ficparo,"\n");     }
   }    }
   for(i=1; i <=npar; i++)    /*2 eme*/
     for(j=i+1;j<=npar;j++)    
       matcov[i][j]=matcov[j][i];    for (k1=1; k1<= m ; k1 ++) { 
          fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   printf("\n");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
     /*-------- Rewriting paramater file ----------*/        k=2*i;
      strcpy(rfileres,"r");    /* "Rparameterfile */        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        for (j=1; j<= nlstate+1 ; j ++) {
      strcat(rfileres,".");    /* */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          else fprintf(ficgp," \%%*lf (\%%*lf)");
     if((ficres =fopen(rfileres,"w"))==NULL) {        }   
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     fprintf(ficres,"#%s\n",version);        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 ++) {
     /*-------- data file ----------*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     if((fic=fopen(datafile,"r"))==NULL)    {          else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("Problem with datafile: %s\n", datafile);goto end;        }   
     }        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     n= lastobs;        for (j=1; j<= nlstate+1 ; j ++) {
     severity = vector(1,maxwav);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     outcome=imatrix(1,maxwav+1,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     num=ivector(1,n);        }   
     moisnais=vector(1,n);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     annais=vector(1,n);        else fprintf(ficgp,"\" t\"\" w l 0,");
     moisdc=vector(1,n);      }
     andc=vector(1,n);    }
     agedc=vector(1,n);    
     cod=ivector(1,n);    /*3eme*/
     weight=vector(1,n);    
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for (k1=1; k1<= m ; k1 ++) { 
     mint=matrix(1,maxwav,1,n);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     anint=matrix(1,maxwav,1,n);        k=2+nlstate*(2*cpt-2);
     s=imatrix(1,maxwav+1,1,n);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     tab=ivector(1,NCOVMAX);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     ncodemax=ivector(1,8);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     i=1;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     while (fgets(line, MAXLINE, fic) != NULL)    {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       if ((i >= firstobs) && (i <=lastobs)) {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                  
         for (j=maxwav;j>=1;j--){        */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        for (i=1; i< nlstate ; i ++) {
           strcpy(line,stra);          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);
           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);    /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for (cpt=1; cpt<nlstate ; cpt ++) {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         for (j=ncovcol;j>=1;j--){        
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=1; i< nlstate ; i ++)
         }          fprintf(ficgp,"+$%d",k+i+1);
         num[i]=atol(stra);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
                
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        l=3+(nlstate+ndeath)*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])); ij=ij+1;}*/        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
         i=i+1;          l=3+(nlstate+ndeath)*cpt;
       }          fprintf(ficgp,"+$%d",l+i+1);
     }        }
     /* printf("ii=%d", ij);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
        scanf("%d",i);*/      } 
   imx=i-1; /* Number of individuals */    }  
     
   /* for (i=1; i<=imx; i++){    /* proba elementaires */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    for(i=1,jk=1; i <=nlstate; i++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      for(k=1; k <=(nlstate+ndeath); k++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        if (k != i) {
     }*/          for(j=1; j <=ncovmodel; j++){
    /*  for (i=1; i<=imx; i++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
      if (s[4][i]==9)  s[4][i]=-1;            jk++; 
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/            fprintf(ficgp,"\n");
            }
          }
   /* Calculation of the number of parameter from char model*/      }
   Tvar=ivector(1,15);     }
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   Tvard=imatrix(1,15,1,2);       for(jk=1; jk <=m; jk++) {
   Tage=ivector(1,15);               fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
             if (ng==2)
   if (strlen(model) >1){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     j=0, j1=0, k1=1, k2=1;         else
     j=nbocc(model,'+');           fprintf(ficgp,"\nset title \"Probability\"\n");
     j1=nbocc(model,'*');         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     cptcovn=j+1;         i=1;
     cptcovprod=j1;         for(k2=1; k2<=nlstate; k2++) {
               k3=i;
     strcpy(modelsav,model);           for(k=1; k<=(nlstate+ndeath); k++) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){             if (k != k2){
       printf("Error. Non available option model=%s ",model);               if(ng==2)
       goto end;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     }               else
                     fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     for(i=(j+1); i>=1;i--){               ij=1;
       cutv(stra,strb,modelsav,'+');               for(j=3; j <=ncovmodel; j++) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       /*scanf("%d",i);*/                   ij++;
       if (strchr(strb,'*')) {                 }
         cutv(strd,strc,strb,'*');                 else
         if (strcmp(strc,"age")==0) {                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           cptcovprod--;               }
           cutv(strb,stre,strd,'V');               fprintf(ficgp,")/(1");
           Tvar[i]=atoi(stre);               
           cptcovage++;               for(k1=1; k1 <=nlstate; k1++){   
             Tage[cptcovage]=i;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
             /*printf("stre=%s ", stre);*/                 ij=1;
         }                 for(j=3; j <=ncovmodel; j++){
         else if (strcmp(strd,"age")==0) {                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           cptcovprod--;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           cutv(strb,stre,strc,'V');                     ij++;
           Tvar[i]=atoi(stre);                   }
           cptcovage++;                   else
           Tage[cptcovage]=i;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         }                 }
         else {                 fprintf(ficgp,")");
           cutv(strb,stre,strc,'V');               }
           Tvar[i]=ncovcol+k1;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           cutv(strb,strc,strd,'V');               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           Tprod[k1]=i;               i=i+ncovmodel;
           Tvard[k1][1]=atoi(strc);             }
           Tvard[k1][2]=atoi(stre);           } /* end k */
           Tvar[cptcovn+k2]=Tvard[k1][1];         } /* end k2 */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];       } /* end jk */
           for (k=1; k<=lastobs;k++)     } /* end ng */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     fclose(ficgp); 
           k1++;  }  /* end gnuplot */
           k2=k2+2;  
         }  
       }  /*************** Moving average **************/
       else {  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/    int i, cpt, cptcod;
       cutv(strd,strc,strb,'V');    int modcovmax =1;
       Tvar[i]=atoi(strc);    int mobilavrange, mob;
       }    double age;
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
         scanf("%d",i);*/                             a covariate has 2 modalities */
     }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
 }  
      if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      if(mobilav==1) mobilavrange=5; /* default */
   printf("cptcovprod=%d ", cptcovprod);      else mobilavrange=mobilav;
   scanf("%d ",i);*/      for (age=bage; age<=fage; age++)
     fclose(fic);        for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
     /*  if(mle==1){*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     if (weightopt != 1) { /* Maximisation without weights*/      /* We keep the original values on the extreme ages bage, fage and for 
       for(i=1;i<=n;i++) weight[i]=1.0;         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     }         we use a 5 terms etc. until the borders are no more concerned. 
     /*-calculation of age at interview from date of interview and age at death -*/      */ 
     agev=matrix(1,maxwav,1,imx);      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     for (i=1; i<=imx; i++) {          for (i=1; i<=nlstate;i++){
       for(m=2; (m<= maxwav); m++) {            for (cptcod=1;cptcod<=modcovmax;cptcod++){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
          anint[m][i]=9999;                for (cpt=1;cpt<=(mob-1)/2;cpt++){
          s[m][i]=-1;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
        }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;                }
       }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     }            }
           }
     for (i=1; i<=imx; i++)  {        }/* end age */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      }/* end mob */
       for(m=1; (m<= maxwav); m++){    }else return -1;
         if(s[m][i] >0){    return 0;
           if (s[m][i] >= nlstate+1) {  }/* End movingaverage */
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];  /************** Forecasting ******************/
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
            else {    /* proj1, year, month, day of starting projection 
               if (andc[i]!=9999){       agemin, agemax range of age
               printf("Warning negative age at death: %d line:%d\n",num[i],i);       dateprev1 dateprev2 range of dates during which prevalence is computed
               agev[m][i]=-1;       
               }    */
             }    int yearp, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
           }    int *popage;
           else if(s[m][i] !=9){ /* Should no more exist */    double calagedatem, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    double *popeffectif,*popcount;
             if(mint[m][i]==99 || anint[m][i]==9999)    double ***p3mat;
               agev[m][i]=1;    double ***mobaverage;
             else if(agev[m][i] <agemin){    char fileresf[FILENAMELENGTH];
               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);*/    agelim=AGESUP;
             }    calagedatem=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; /* offset
             else if(agev[m][i] >agemax){        from the mean date of interviews between dateprev1 and dateprev2
               agemax=agev[m][i];        (in fractional years converted to fractional months) */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    /* Computing age-specific starting prevalence between exact 
             }       dateprev1 and dateprev2 (in float years) and
             /*agev[m][i]=anint[m][i]-annais[i];*/   shifting ages from calagedatem.
             /*   agev[m][i] = age[i]+2*m;*/    */
           }    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
           else { /* =9 */   
             agev[m][i]=1;    strcpy(fileresf,"f"); 
             s[m][i]=-1;    strcat(fileresf,fileres);
           }    if((ficresf=fopen(fileresf,"w"))==NULL) {
         }      printf("Problem with forecast resultfile: %s\n", fileresf);
         else /*= 0 Unknown */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           agev[m][i]=1;    }
       }    printf("Computing forecasting: result on file '%s' \n", fileresf);
        fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     }  
     for (i=1; i<=imx; i++)  {    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    if (mobilav!=0) {
           printf("Error: Wrong value in nlstate or ndeath\n");        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           goto end;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     }      }
     }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     free_vector(severity,1,maxwav);    if (stepm<=12) stepsize=1;
     free_imatrix(outcome,1,maxwav+1,1,n);    
     free_vector(moisnais,1,n);    agelim=AGESUP;
     free_vector(annais,1,n);    
     /* free_matrix(mint,1,maxwav,1,n);    hstepm=1;
        free_matrix(anint,1,maxwav,1,n);*/    hstepm=hstepm/stepm; 
     free_vector(moisdc,1,n);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     free_vector(andc,1,n);                                 fractional in yp1 */
     anprojmean=yp;
        yp2=modf((yp1*12),&yp);
     wav=ivector(1,imx);    mprojmean=yp;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    yp1=modf((yp2*30.5),&yp);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    jprojmean=yp;
        if(jprojmean==0) jprojmean=1;
     /* Concatenates waves */    if(mprojmean==0) jprojmean=1;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f ",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
       Tcode=ivector(1,100);    for(cptcov=1, k=0;cptcov<=i2;cptcov++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       ncodemax[1]=1;        k=k+1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        fprintf(ficresf,"\n#******");
              for(j=1;j<=cptcoveff;j++) {
    codtab=imatrix(1,100,1,10);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    h=0;        }
    m=pow(2,cptcoveff);        fprintf(ficresf,"******\n");
          fprintf(ficresf,"# StartingAge FinalAge");
    for(k=1;k<=cptcoveff; k++){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
      for(i=1; i <=(m/pow(2,k));i++){        for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { 
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficresf,"\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
            h++;  
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
          }            nhstepm = nhstepm/hstepm; 
        }            
      }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }            oldm=oldms;savm=savms;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       codtab[1][2]=1;codtab[2][2]=2; */          
    /* for(i=1; i <=m ;i++){            for (h=0; h<=nhstepm; h++){
       for(k=1; k <=cptcovn; k++){              if (h==(int) (calagedatem+YEARM*yearp)) {
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                fprintf(ficresf,"\n");
       }                for(j=1;j<=cptcoveff;j++) 
       printf("\n");                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agedeb+h*hstepm/YEARM*stepm);
       scanf("%d",i);*/              } 
                  for(j=1; j<=nlstate+ndeath;j++) {
    /* Calculates basic frequencies. Computes observed prevalence at single age                kk1=0.;kk2=0;
        and prints on file fileres'p'. */                for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                        kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                      else {
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     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 */                if (h==(int)(calagedatem+12*yearp)){
                        fprintf(ficresf," %.3f", kk1);
     /* 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){            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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);         
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
    jk=1;    fclose(ficresf);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  }
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /************** Forecasting ******************/
    for(i=1,jk=1; i <=nlstate; i++){  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
      for(k=1; k <=(nlstate+ndeath); k++){    
        if (k != i)    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
          {    int *popage;
            printf("%d%d ",i,k);    double calagedatem, agelim, kk1, kk2;
            fprintf(ficres,"%1d%1d ",i,k);    double *popeffectif,*popcount;
            for(j=1; j <=ncovmodel; j++){    double ***p3mat,***tabpop,***tabpopprev;
              printf("%f ",p[jk]);    double ***mobaverage;
              fprintf(ficres,"%f ",p[jk]);    char filerespop[FILENAMELENGTH];
              jk++;  
            }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            printf("\n");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            fprintf(ficres,"\n");    agelim=AGESUP;
          }    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
      }    
    }    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
  if(mle==1){    
     /* Computing hessian and covariance matrix */    
     ftolhess=ftol; /* Usually correct */    strcpy(filerespop,"pop"); 
     hesscov(matcov, p, npar, delti, ftolhess, func);    strcat(filerespop,fileres);
  }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      printf("Problem with forecast resultfile: %s\n", filerespop);
     printf("# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
      for(i=1,jk=1; i <=nlstate; i++){    }
       for(j=1; j <=nlstate+ndeath; j++){    printf("Computing forecasting: result on file '%s' \n", filerespop);
         if (j!=i) {    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);    if (mobilav!=0) {
             fprintf(ficres," %.5e",delti[jk]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             jk++;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf("\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficres,"\n");      }
         }    }
       }  
      }    stepsize=(int) (stepm+YEARM-1)/YEARM;
        if (stepm<=12) stepsize=1;
     k=1;    
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    agelim=AGESUP;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
     for(i=1;i<=npar;i++){    hstepm=1;
       /*  if (k>nlstate) k=1;    hstepm=hstepm/stepm; 
       i1=(i-1)/(ncovmodel*nlstate)+1;    
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    if (popforecast==1) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/      if((ficpop=fopen(popfile,"r"))==NULL) {
       fprintf(ficres,"%3d",i);        printf("Problem with population file : %s\n",popfile);exit(0);
       printf("%3d",i);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       for(j=1; j<=i;j++){      } 
         fprintf(ficres," %.5e",matcov[i][j]);      popage=ivector(0,AGESUP);
         printf(" %.5e",matcov[i][j]);      popeffectif=vector(0,AGESUP);
       }      popcount=vector(0,AGESUP);
       fprintf(ficres,"\n");      
       printf("\n");      i=1;   
       k++;      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     }     
          imx=i;
     while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
       ungetc(c,ficpar);    }
       fgets(line, MAXLINE, ficpar);  
       puts(line);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       fputs(line,ficparo);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     }        k=k+1;
     ungetc(c,ficpar);        fprintf(ficrespop,"\n#******");
     estepm=0;        for(j=1;j<=cptcoveff;j++) {
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     if (estepm==0 || estepm < stepm) estepm=stepm;        }
     if (fage <= 2) {        fprintf(ficrespop,"******\n");
       bage = ageminpar;        fprintf(ficrespop,"# Age");
       fage = agemaxpar;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     }        if (popforecast==1)  fprintf(ficrespop," [Population]");
            
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        for (cpt=0; cpt<=0;cpt++) { 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          
            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     while((c=getc(ficpar))=='#' && c!= EOF){            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     ungetc(c,ficpar);            nhstepm = nhstepm/hstepm; 
     fgets(line, MAXLINE, ficpar);            
     puts(line);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);            oldm=oldms;savm=savms;
   }            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   ungetc(c,ficpar);          
              for (h=0; h<=nhstepm; h++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              if (h==(int) (calagedatem+YEARM*cpt)) {
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              } 
                    for(j=1; j<=nlstate+ndeath;j++) {
   while((c=getc(ficpar))=='#' && c!= EOF){                kk1=0.;kk2=0;
     ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {              
     fgets(line, MAXLINE, ficpar);                  if (mobilav==1) 
     puts(line);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     fputs(line,ficparo);                  else {
   }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   ungetc(c,ficpar);                  }
                  }
                 if (h==(int)(calagedatem+12*cpt)){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                    /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);                }
   fprintf(ficparo,"pop_based=%d\n",popbased);                }
   fprintf(ficres,"pop_based=%d\n",popbased);                for(i=1; i<=nlstate;i++){
                  kk1=0.;
   while((c=getc(ficpar))=='#' && c!= EOF){                  for(j=1; j<=nlstate;j++){
     ungetc(c,ficpar);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     fgets(line, MAXLINE, ficpar);                  }
     puts(line);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
     fputs(line,ficparo);              }
   }  
   ungetc(c,ficpar);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 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);          }
         }
    
 while((c=getc(ficpar))=='#' && c!= EOF){    /******/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     puts(line);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fputs(line,ficparo);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   ungetc(c,ficpar);            nhstepm = nhstepm/hstepm; 
             
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            oldm=oldms;savm=savms;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 /*------------ gnuplot -------------*/              } 
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);              for(j=1; j<=nlstate+ndeath;j++) {
                  kk1=0.;kk2=0;
 /*------------ free_vector  -------------*/                for(i=1; i<=nlstate;i++) {              
  chdir(path);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                  }
  free_ivector(wav,1,imx);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              }
  free_ivector(num,1,n);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  free_vector(agedc,1,n);          }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        }
  fclose(ficparo);     } 
  fclose(ficres);    }
    
 /*--------- index.htm --------*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
        free_vector(popeffectif,0,AGESUP);
   /*--------------- Prevalence limit --------------*/      free_vector(popcount,0,AGESUP);
      }
   strcpy(filerespl,"pl");    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(filerespl,fileres);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fclose(ficrespop);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  }
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /***********************************************/
   fprintf(ficrespl,"#Prevalence limit\n");  /**************** Main Program *****************/
   fprintf(ficrespl,"#Age ");  /***********************************************/
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  int main(int argc, char *argv[])
    {
   prlim=matrix(1,nlstate,1,nlstate);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double agedeb, agefin,hf;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double fret;
   k=0;    double **xi,tmp,delta;
   agebase=ageminpar;  
   agelim=agemaxpar;    double dum; /* Dummy variable */
   ftolpl=1.e-10;    double ***p3mat;
   i1=cptcoveff;    double ***mobaverage;
   if (cptcovn < 1){i1=1;}    int *indx;
     char line[MAXLINE], linepar[MAXLINE];
   for(cptcov=1;cptcov<=i1;cptcov++){    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int firstobs=1, lastobs=10;
         k=k+1;    int sdeb, sfin; /* Status at beginning and end */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    int c,  h , cpt,l;
         fprintf(ficrespl,"\n#******");    int ju,jl, mi;
         for(j=1;j<=cptcoveff;j++)    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
         fprintf(ficrespl,"******\n");    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
            int mobilav=0,popforecast=0;
         for (age=agebase; age<=agelim; age++){    int hstepm, nhstepm;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedatem;
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    double bage, fage, age, agelim, agebase;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double ftolpl=FTOL;
           fprintf(ficrespl,"\n");    double **prlim;
         }    double *severity;
       }    double ***param; /* Matrix of parameters */
     }    double  *p;
   fclose(ficrespl);    double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
   /*------------- h Pij x at various ages ------------*/    double *delti; /* Scale */
      double ***eij, ***vareij;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double **varpl; /* Variances of prevalence limits by age */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double *epj, vepp;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    double kk1, kk2;
   }    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   printf("Computing pij: result on file '%s' \n", filerespij);  
      char *alph[]={"a","a","b","c","d","e"}, str[4];
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/  
     char z[1]="c", occ;
   agelim=AGESUP;  #include <sys/time.h>
   hstepm=stepsize*YEARM; /* Every year of age */  #include <time.h>
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     
   k=0;    /* long total_usecs;
   for(cptcov=1;cptcov<=i1;cptcov++){       struct timeval start_time, end_time;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         fprintf(ficrespij,"\n#****** ");    getcwd(pathcd, size);
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    printf("\n%s",version);
         fprintf(ficrespij,"******\n");    if(argc <=1){
              printf("\nEnter the parameter file name: ");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      scanf("%s",pathtot);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    else{
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      strcpy(pathtot,argv[1]);
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
           fprintf(ficrespij,"# Age");    /*cygwin_split_path(pathtot,path,optionfile);
           for(i=1; i<=nlstate;i++)      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
             for(j=1; j<=nlstate+ndeath;j++)    /* cutv(path,optionfile,pathtot,'\\');*/
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
            for (h=0; h<=nhstepm; h++){    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    chdir(path);
             for(i=1; i<=nlstate;i++)    replace(pathc,path);
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    /*-------- arguments in the command line --------*/
             fprintf(ficrespij,"\n");  
              }    /* Log file */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(filelog, optionfilefiname);
           fprintf(ficrespij,"\n");    strcat(filelog,".log");    /* */
         }    if((ficlog=fopen(filelog,"w"))==NULL)    {
     }      printf("Problem with logfile %s\n",filelog);
   }      goto end;
     }
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
   fclose(ficrespij);    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);
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    /* */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    strcpy(fileres,"r");
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    strcat(fileres, optionfilefiname);
   }    strcat(fileres,".txt");    /* Other files have txt extension */
   else{  
     erreur=108;    /*---------arguments file --------*/
     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);  
   }    if((ficpar=fopen(optionfile,"r"))==NULL)    {
        printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   /*---------- Health expectancies and variances ------------*/      goto end;
     }
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    strcpy(filereso,"o");
   if((ficrest=fopen(filerest,"w"))==NULL) {    strcat(filereso,fileres);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if((ficparo=fopen(filereso,"w"))==NULL) {
   }      printf("Problem with Output resultfile: %s\n", filereso);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   strcpy(filerese,"e");  
   strcat(filerese,fileres);    /* Reads comments: lines beginning with '#' */
   if((ficreseij=fopen(filerese,"w"))==NULL) {    while((c=getc(ficpar))=='#' && c!= EOF){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      ungetc(c,ficpar);
   }      fgets(line, MAXLINE, ficpar);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      puts(line);
       fputs(line,ficparo);
  strcpy(fileresv,"v");    }
   strcat(fileresv,fileres);    ungetc(c,ficpar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    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);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    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);
   calagedate=-1;    while((c=getc(ficpar))=='#' && c!= EOF){
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   k=0;      puts(line);
   for(cptcov=1;cptcov<=i1;cptcov++){      fputs(line,ficparo);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    ungetc(c,ficpar);
       fprintf(ficrest,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)     
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    covar=matrix(0,NCOVMAX,1,n); 
       fprintf(ficrest,"******\n");    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
       fprintf(ficreseij,"******\n");    
     /* Read guess parameters */
       fprintf(ficresvij,"\n#****** ");    /* Reads comments: lines beginning with '#' */
       for(j=1;j<=cptcoveff;j++)    while((c=getc(ficpar))=='#' && c!= EOF){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      ungetc(c,ficpar);
       fprintf(ficresvij,"******\n");      fgets(line, MAXLINE, ficpar);
       puts(line);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fputs(line,ficparo);
       oldm=oldms;savm=savms;    }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      ungetc(c,ficpar);
      
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       oldm=oldms;savm=savms;    for(i=1; i <=nlstate; i++)
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      for(j=1; j <=nlstate+ndeath-1; j++){
            fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
          if(mle==1)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          printf("%1d%1d",i,j);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        fprintf(ficlog,"%1d%1d",i,j);
       fprintf(ficrest,"\n");        for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
       epj=vector(1,nlstate+1);          if(mle==1){
       for(age=bage; age <=fage ;age++){            printf(" %lf",param[i][j][k]);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            fprintf(ficlog," %lf",param[i][j][k]);
         if (popbased==1) {          }
           for(i=1; i<=nlstate;i++)          else
             prlim[i][i]=probs[(int)age][i][k];            fprintf(ficlog," %lf",param[i][j][k]);
         }          fprintf(ficparo," %lf",param[i][j][k]);
                }
         fprintf(ficrest," %4.0f",age);        fscanf(ficpar,"\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        if(mle==1)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          printf("\n");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        fprintf(ficlog,"\n");
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        fprintf(ficparo,"\n");
           }      }
           epj[nlstate+1] +=epj[j];    
         }    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
         for(i=1, vepp=0.;i <=nlstate;i++)    p=param[1][1];
           for(j=1;j <=nlstate;j++)    
             vepp += vareij[i][j][(int)age];    /* Reads comments: lines beginning with '#' */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    while((c=getc(ficpar))=='#' && c!= EOF){
         for(j=1;j <=nlstate;j++){      ungetc(c,ficpar);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      fgets(line, MAXLINE, ficpar);
         }      puts(line);
         fprintf(ficrest,"\n");      fputs(line,ficparo);
       }    }
     }    ungetc(c,ficpar);
   }  
 free_matrix(mint,1,maxwav,1,n);    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     free_vector(weight,1,n);    for(i=1; i <=nlstate; i++){
   fclose(ficreseij);      for(j=1; j <=nlstate+ndeath-1; j++){
   fclose(ficresvij);        fscanf(ficpar,"%1d%1d",&i1,&j1);
   fclose(ficrest);        printf("%1d%1d",i,j);
   fclose(ficpar);        fprintf(ficparo,"%1d%1d",i1,j1);
   free_vector(epj,1,nlstate+1);        for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar,"%le",&delti3[i][j][k]);
   /*------- Variance limit prevalence------*/            printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
   strcpy(fileresvpl,"vpl");        }
   strcat(fileresvpl,fileres);        fscanf(ficpar,"\n");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        printf("\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficparo,"\n");
     exit(0);      }
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    delti=delti3[1][1];
     
   k=0;    /* Reads comments: lines beginning with '#' */
   for(cptcov=1;cptcov<=i1;cptcov++){    while((c=getc(ficpar))=='#' && c!= EOF){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      ungetc(c,ficpar);
       k=k+1;      fgets(line, MAXLINE, ficpar);
       fprintf(ficresvpl,"\n#****** ");      puts(line);
       for(j=1;j<=cptcoveff;j++)      fputs(line,ficparo);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficresvpl,"******\n");    ungetc(c,ficpar);
          
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    matcov=matrix(1,npar,1,npar);
       oldm=oldms;savm=savms;    for(i=1; i <=npar; i++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fscanf(ficpar,"%s",&str);
     }      if(mle==1)
  }        printf("%s",str);
       fprintf(ficlog,"%s",str);
   fclose(ficresvpl);      fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
   /*---------- End : free ----------------*/        fscanf(ficpar," %le",&matcov[i][j]);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        if(mle==1){
            printf(" %.5le",matcov[i][j]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          fprintf(ficlog," %.5le",matcov[i][j]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
          else
            fprintf(ficlog," %.5le",matcov[i][j]);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficparo," %.5le",matcov[i][j]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      fscanf(ficpar,"\n");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      if(mle==1)
          printf("\n");
   free_matrix(matcov,1,npar,1,npar);      fprintf(ficlog,"\n");
   free_vector(delti,1,npar);      fprintf(ficparo,"\n");
   free_matrix(agev,1,maxwav,1,imx);    }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
   if(erreur >0)        matcov[i][j]=matcov[j][i];
     printf("End of Imach with error or warning %d\n",erreur);     
   else   printf("End of Imach\n");    if(mle==1)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      printf("\n");
      fprintf(ficlog,"\n");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/    /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
  end:    strcat(rfileres,".");    /* */
 #ifdef windows    strcat(rfileres,optionfilext);    /* Other files have txt extension */
   /* chdir(pathcd);*/    if((ficres =fopen(rfileres,"w"))==NULL) {
 #endif      printf("Problem writing new parameter file: %s\n", fileres);goto end;
  /*system("wgnuplot graph.plt");*/      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    }
  /*system("cd ../gp37mgw");*/    fprintf(ficres,"#%s\n",version);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      
  strcpy(plotcmd,GNUPLOTPROGRAM);    /*-------- data file ----------*/
  strcat(plotcmd," ");    if((fic=fopen(datafile,"r"))==NULL)    {
  strcat(plotcmd,optionfilegnuplot);      printf("Problem with datafile: %s\n", datafile);goto end;
  system(plotcmd);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
 #ifdef windows  
   while (z[0] != 'q') {    n= lastobs;
     /* chdir(path); */    severity = vector(1,maxwav);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    outcome=imatrix(1,maxwav+1,1,n);
     scanf("%s",z);    num=ivector(1,n);
     if (z[0] == 'c') system("./imach");    moisnais=vector(1,n);
     else if (z[0] == 'e') system(optionfilehtm);    annais=vector(1,n);
     else if (z[0] == 'g') system(plotcmd);    moisdc=vector(1,n);
     else if (z[0] == 'q') exit(0);    andc=vector(1,n);
   }    agedc=vector(1,n);
 #endif    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]));}*/
     
    
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }<
           else if(s[m][i] !=9){ /* 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=1; (m<= maxwav); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     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+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"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 mobilaverage=%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 mobilaverage=%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 mobilaverage=%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*/
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       if(stepm ==1){
         prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilavproj, agedeb, fage, popforecast, popfile, anproj2,p, i1);
         if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
       } 
       else{
         erreur=108;
         printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
         fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       }
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     calagedatem=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.44  
changed lines
  Added in v.1.69


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