Diff for /imach/src/imach.c between versions 1.15 and 1.69

version 1.15, 2002/02/20 17:08:52 version 1.69, 2003/02/04 20:55:29
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status    
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    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
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
   Also this programme outputs the covariance matrix of the parameters but also    conditional to the observed state i at age x. The delay 'h' can be
   of the life expectancies. It also computes the prevalence limits.    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is modelled as a multinomial logistic.  The hPx
            Institut national d'études démographiques, Paris.    matrix is simply the matrix product of nh*stepm elementary matrices
   This software have been partly granted by Euro-REVES, a concerted action    and the contribution of each individual to the likelihood is simply
   from the European Union.    hPijx.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Also this programme outputs the covariance matrix of the parameters but also
   can be accessed at http://euroreves.ined.fr/imach .    of the life expectancies. It also computes the stable prevalence. 
   **********************************************************************/    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <math.h>             Institut national d'études démographiques, Paris.
 #include <stdio.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdlib.h>    from the European Union.
 #include <unistd.h>    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXLINE 256    can be accessed at http://euroreves.ined.fr/imach .
 #define FILENAMELENGTH 80    **********************************************************************/
 /*#define DEBUG*/   
 #define windows  #include <math.h>
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #include <stdio.h>
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #include <stdlib.h>
   #include <unistd.h>
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 #define NINTERVMAX 8  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define FILENAMELENGTH 80
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  /*#define DEBUG*/
 #define NCOVMAX 8 /* Maximum number of covariates */  #define windows
 #define MAXN 20000  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define YEARM 12. /* Number of months per year */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define AGESUP 130  
 #define AGEBASE 40  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int nvar;  #define NINTERVMAX 8
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int npar=NPARMAX;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int nlstate=2; /* Number of live states */  #define NCOVMAX 8 /* Maximum number of covariates */
 int ndeath=1; /* Number of dead states */  #define MAXN 20000
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #define YEARM 12. /* Number of months per year */
 int popbased=0;  #define AGESUP 130
   #define AGEBASE 40
 int *wav; /* Number of waves for this individuual 0 is possible */  #ifdef windows
 int maxwav; /* Maxim number of waves */  #define DIRSEPARATOR '\\'
 int jmin, jmax; /* min, max spacing between 2 waves */  #define ODIRSEPARATOR '/'
 int mle, weightopt;  #else
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define DIRSEPARATOR '/'
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define ODIRSEPARATOR '\\'
 double jmean; /* Mean space between 2 waves */  #endif
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  int erreur; /* Error number */
 FILE *ficgp, *fichtm,*ficresprob;  int nvar;
 FILE *ficreseij;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   char filerese[FILENAMELENGTH];  int npar=NPARMAX;
  FILE  *ficresvij;  int nlstate=2; /* Number of live states */
   char fileresv[FILENAMELENGTH];  int ndeath=1; /* Number of dead states */
  FILE  *ficresvpl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   char fileresvpl[FILENAMELENGTH];  int popbased=0;
   
 #define NR_END 1  int *wav; /* Number of waves for this individuual 0 is possible */
 #define FREE_ARG char*  int maxwav; /* Maxim number of waves */
 #define FTOL 1.0e-10  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 #define NRANSI  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define ITMAX 200  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #define TOL 2.0e-4             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 #define CGOLD 0.3819660  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define ZEPS 1.0e-10  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 #define GOLD 1.618034  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define GLIMIT 100.0  FILE *ficresprobmorprev;
 #define TINY 1.0e-20  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 static double maxarg1,maxarg2;  char filerese[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvij;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char fileresvpl[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 static double sqrarg;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 int imx;  char filerest[FILENAMELENGTH];
 int stepm;  char fileregp[FILENAMELENGTH];
 /* Stepm, step in month: minimum step interpolation*/  char popfile[FILENAMELENGTH];
   
 int m,nb;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define NR_END 1
 double **pmmij, ***probs, ***mobaverage;  #define FREE_ARG char*
   #define FTOL 1.0e-10
 double *weight;  
 int **s; /* Status */  #define NRANSI 
 double *agedc, **covar, idx;  #define ITMAX 200 
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #define TOL 2.0e-4 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /**************** split *************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 static  int split( char *path, char *dirc, char *name )  
 {  #define GOLD 1.618034 
    char *s;                             /* pointer */  #define GLIMIT 100.0 
    int  l1, l2;                         /* length counters */  #define TINY 1.0e-20 
   
    l1 = strlen( path );                 /* length of path */  static double maxarg1,maxarg2;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    s = strrchr( path, '\\' );           /* find last / */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    if ( s == NULL ) {                   /* no directory, so use current */    
 #if     defined(__bsd__)                /* get current working directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       extern char       *getwd( );  #define rint(a) floor(a+0.5)
   
       if ( getwd( dirc ) == NULL ) {  static double sqrarg;
 #else  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       extern char       *getcwd( );  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int imx; 
 #endif  int stepm;
          return( GLOCK_ERROR_GETCWD );  /* Stepm, step in month: minimum step interpolation*/
       }  
       strcpy( name, path );             /* we've got it */  int estepm;
    } else {                             /* strip direcotry from path */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  int m,nb;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       strcpy( name, s );                /* save file name */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double **pmmij, ***probs;
       dirc[l1-l2] = 0;                  /* add zero */  double dateintmean=0;
    }  
    l1 = strlen( dirc );                 /* length of directory */  double *weight;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int **s; /* Status */
    return( 0 );                         /* we're done */  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /******************************************/  double ftolhess; /* Tolerance for computing hessian */
   
 void replace(char *s, char*t)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int i;  {
   int lg=20;    char  *ss;                            /* pointer */
   i=0;    int   l1, l2;                         /* length counters */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    l1 = strlen(path );                   /* length of path */
     (s[i] = t[i]);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (t[i]== '\\') s[i]='/';    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so use current */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 int nbocc(char *s, char occ)  #if     defined(__bsd__)                /* get current working directory */
 {      extern char *getwd( );
   int i,j=0;  
   int lg=20;      if ( getwd( dirc ) == NULL ) {
   i=0;  #else
   lg=strlen(s);      extern char *getcwd( );
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   }  #endif
   return j;        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 void cutv(char *u,char *v, char*t, char occ)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   int i,lg,j,p=0;      l2 = strlen( ss );                  /* length of filename */
   i=0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<=strlen(t)-1; j++) {      strcpy( name, ss );         /* save file name */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
     }
   lg=strlen(t);    l1 = strlen( dirc );                  /* length of directory */
   for(j=0; j<p; j++) {  #ifdef windows
     (u[j] = t[j]);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      u[p]='\0';    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
    for(j=0; j<= lg; j++) {    ss = strrchr( name, '.' );            /* find last / */
     if (j>=(p+1))(v[j-p-1] = t[j]);    ss++;
   }    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /********************** nrerror ********************/    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 void nrerror(char error_text[])    return( 0 );                          /* we're done */
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /******************************************/
 }  
 /*********************** vector *******************/  void replace(char *s, char*t)
 double *vector(int nl, int nh)  {
 {    int i;
   double *v;    int lg=20;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ivector *******************************/    int lg=20;
 int *ivector(long nl,long nh)    i=0;
 {    lg=strlen(s);
   int *v;    for(i=0; i<= lg; i++) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    if  (s[i] == occ ) j++;
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;    return j;
 }  }
   
 /******************free ivector **************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_ivector(int *v, long nl, long nh)  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(v+nl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************* imatrix *******************************/    i=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<=strlen(t)-1; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* allocate pointers to rows */      (u[j] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");       u[p]='\0';
   m += NR_END;  
   m -= nrl;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
      }
   /* allocate rows and set pointers to them */  }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   /* return pointer to array of pointers to rows */    exit(EXIT_FAILURE);
   return m;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    double *v;
       int **m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       long nch,ncl,nrh,nrl;    if (!v) nrerror("allocation failure in vector");
      /* free an int matrix allocated by imatrix() */    return v-nl+NR_END;
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* matrix *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /************************ivector *******************************/
   double **m;  int *ivector(long nl,long nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m -= nrl;    return v-nl+NR_END;
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_ivector(int *v, long nl, long nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /*************************free matrix ************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int **m; 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /******************* ma3x *******************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m += NR_END; 
 {    m -= nrl; 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    
     /* allocate rows and set pointers to them */ 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m += NR_END;    m[nrl] += NR_END; 
   m -= nrl;    m[nrl] -= ncl; 
     
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* return pointer to array of pointers to rows */ 
   m[nrl] -= ncl;    return m; 
   } 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /****************** free_imatrix *************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_imatrix(m,nrl,nrh,ncl,nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        int **m;
   m[nrl][ncl] += NR_END;        long nch,ncl,nrh,nrl; 
   m[nrl][ncl] -= nll;       /* free an int matrix allocated by imatrix() */ 
   for (j=ncl+1; j<=nch; j++)  { 
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   for (i=nrl+1; i<=nrh; i++) {  } 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /******************* matrix *******************************/
       m[i][j]=m[i][j-1]+nlay;  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
   return m;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /*************************free ma3x ************************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m -= nrl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /***************** f1dim *************************/    m[nrl] -= ncl;
 extern int ncom;  
 extern double *pcom,*xicom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double (*nrfunc)(double []);    return m;
    }
 double f1dim(double x)  
 {  /*************************free matrix ************************/
   int j;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double f;  {
   double *xt;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   xt=vector(1,ncom);  }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /******************* ma3x *******************************/
   free_vector(xt,1,ncom);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   return f;  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int iter;    m += NR_END;
   double a,b,d,etemp;    m -= nrl;
   double fu,fv,fw,fx;  
   double ftemp;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double e=0.0;    m[nrl] += NR_END;
      m[nrl] -= ncl;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (iter=1;iter<=ITMAX;iter++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     xm=0.5*(a+b);    m[nrl][ncl] += NR_END;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl][ncl] -= nll;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (j=ncl+1; j<=nch; j++) 
     printf(".");fflush(stdout);      m[nrl][j]=m[nrl][j-1]+nlay;
 #ifdef DEBUG    
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    for (i=nrl+1; i<=nrh; i++) {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #endif      for (j=ncl+1; j<=nch; j++) 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){        m[i][j]=m[i][j-1]+nlay;
       *xmin=x;    }
       return fx;    return m;
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /*************************free ma3x ************************/
       r=(x-w)*(fx-fv);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       q=2.0*(q-r);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if (q > 0.0) p = -p;    free((FREE_ARG)(m+nrl-NR_END));
       q=fabs(q);  }
       etemp=e;  
       e=d;  /***************** f1dim *************************/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  extern int ncom; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern double *pcom,*xicom;
       else {  extern double (*nrfunc)(double []); 
         d=p/q;   
         u=x+d;  double f1dim(double x) 
         if (u-a < tol2 || b-u < tol2)  { 
           d=SIGN(tol1,xm-x);    int j; 
       }    double f;
     } else {    double *xt; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));   
     }    xt=vector(1,ncom); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     fu=(*f)(u);    f=(*nrfunc)(xt); 
     if (fu <= fx) {    free_vector(xt,1,ncom); 
       if (u >= x) a=x; else b=x;    return f; 
       SHFT(v,w,x,u)  } 
         SHFT(fv,fw,fx,fu)  
         } else {  /*****************brent *************************/
           if (u < x) a=u; else b=u;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           if (fu <= fw || w == x) {  { 
             v=w;    int iter; 
             w=u;    double a,b,d,etemp;
             fv=fw;    double fu,fv,fw,fx;
             fw=fu;    double ftemp;
           } else if (fu <= fv || v == x || v == w) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             v=u;    double e=0.0; 
             fv=fu;   
           }    a=(ax < cx ? ax : cx); 
         }    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
   nrerror("Too many iterations in brent");    fw=fv=fx=(*f)(x); 
   *xmin=x;    for (iter=1;iter<=ITMAX;iter++) { 
   return fx;      xm=0.5*(a+b); 
 }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 /****************** mnbrak ***********************/      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #ifdef DEBUG
             double (*func)(double))      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      fprintf(ficlog,"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);
   double ulim,u,r,q, dum;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double fu;  #endif
        if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   *fa=(*func)(*ax);        *xmin=x; 
   *fb=(*func)(*bx);        return fx; 
   if (*fb > *fa) {      } 
     SHFT(dum,*ax,*bx,dum)      ftemp=fu;
       SHFT(dum,*fb,*fa,dum)      if (fabs(e) > tol1) { 
       }        r=(x-w)*(fx-fv); 
   *cx=(*bx)+GOLD*(*bx-*ax);        q=(x-v)*(fx-fw); 
   *fc=(*func)(*cx);        p=(x-v)*q-(x-w)*r; 
   while (*fb > *fc) {        q=2.0*(q-r); 
     r=(*bx-*ax)*(*fb-*fc);        if (q > 0.0) p = -p; 
     q=(*bx-*cx)*(*fb-*fa);        q=fabs(q); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        etemp=e; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        e=d; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     if ((*bx-u)*(u-*cx) > 0.0) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       fu=(*func)(u);        else { 
     } else if ((*cx-u)*(u-ulim) > 0.0) {          d=p/q; 
       fu=(*func)(u);          u=x+d; 
       if (fu < *fc) {          if (u-a < tol2 || b-u < tol2) 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))            d=SIGN(tol1,xm-x); 
           SHFT(*fb,*fc,fu,(*func)(u))        } 
           }      } else { 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       u=ulim;      } 
       fu=(*func)(u);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     } else {      fu=(*f)(u); 
       u=(*cx)+GOLD*(*cx-*bx);      if (fu <= fx) { 
       fu=(*func)(u);        if (u >= x) a=x; else b=x; 
     }        SHFT(v,w,x,u) 
     SHFT(*ax,*bx,*cx,u)          SHFT(fv,fw,fx,fu) 
       SHFT(*fa,*fb,*fc,fu)          } else { 
       }            if (u < x) a=u; else b=u; 
 }            if (fu <= fw || w == x) { 
               v=w; 
 /*************** linmin ************************/              w=u; 
               fv=fw; 
 int ncom;              fw=fu; 
 double *pcom,*xicom;            } else if (fu <= fv || v == x || v == w) { 
 double (*nrfunc)(double []);              v=u; 
                fv=fu; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))            } 
 {          } 
   double brent(double ax, double bx, double cx,    } 
                double (*f)(double), double tol, double *xmin);    nrerror("Too many iterations in brent"); 
   double f1dim(double x);    *xmin=x; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    return fx; 
               double *fc, double (*func)(double));  } 
   int j;  
   double xx,xmin,bx,ax;  /****************** mnbrak ***********************/
   double fx,fb,fa;  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   ncom=n;              double (*func)(double)) 
   pcom=vector(1,n);  { 
   xicom=vector(1,n);    double ulim,u,r,q, dum;
   nrfunc=func;    double fu; 
   for (j=1;j<=n;j++) {   
     pcom[j]=p[j];    *fa=(*func)(*ax); 
     xicom[j]=xi[j];    *fb=(*func)(*bx); 
   }    if (*fb > *fa) { 
   ax=0.0;      SHFT(dum,*ax,*bx,dum) 
   xx=1.0;        SHFT(dum,*fb,*fa,dum) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *cx=(*bx)+GOLD*(*bx-*ax); 
 #ifdef DEBUG    *fc=(*func)(*cx); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    while (*fb > *fc) { 
 #endif      r=(*bx-*ax)*(*fb-*fc); 
   for (j=1;j<=n;j++) {      q=(*bx-*cx)*(*fb-*fa); 
     xi[j] *= xmin;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     p[j] += xi[j];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   free_vector(xicom,1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
   free_vector(pcom,1,n);        fu=(*func)(u); 
 }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
 /*************** powell ************************/        if (fu < *fc) { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             double (*func)(double []))            SHFT(*fb,*fc,fu,(*func)(u)) 
 {            } 
   void linmin(double p[], double xi[], int n, double *fret,      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
               double (*func)(double []));        u=ulim; 
   int i,ibig,j;        fu=(*func)(u); 
   double del,t,*pt,*ptt,*xit;      } else { 
   double fp,fptt;        u=(*cx)+GOLD*(*cx-*bx); 
   double *xits;        fu=(*func)(u); 
   pt=vector(1,n);      } 
   ptt=vector(1,n);      SHFT(*ax,*bx,*cx,u) 
   xit=vector(1,n);        SHFT(*fa,*fb,*fc,fu) 
   xits=vector(1,n);        } 
   *fret=(*func)(p);  } 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /*************** linmin ************************/
     fp=(*fret);  
     ibig=0;  int ncom; 
     del=0.0;  double *pcom,*xicom;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double (*nrfunc)(double []); 
     for (i=1;i<=n;i++)   
       printf(" %d %.12f",i, p[i]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("\n");  { 
     for (i=1;i<=n;i++) {    double brent(double ax, double bx, double cx, 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];                 double (*f)(double), double tol, double *xmin); 
       fptt=(*fret);    double f1dim(double x); 
 #ifdef DEBUG    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("fret=%lf \n",*fret);                double *fc, double (*func)(double)); 
 #endif    int j; 
       printf("%d",i);fflush(stdout);    double xx,xmin,bx,ax; 
       linmin(p,xit,n,fret,func);    double fx,fb,fa;
       if (fabs(fptt-(*fret)) > del) {   
         del=fabs(fptt-(*fret));    ncom=n; 
         ibig=i;    pcom=vector(1,n); 
       }    xicom=vector(1,n); 
 #ifdef DEBUG    nrfunc=func; 
       printf("%d %.12e",i,(*fret));    for (j=1;j<=n;j++) { 
       for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      xicom[j]=xi[j]; 
         printf(" x(%d)=%.12e",j,xit[j]);    } 
       }    ax=0.0; 
       for(j=1;j<=n;j++)    xx=1.0; 
         printf(" p=%.12e",p[j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       printf("\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 #endif  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #ifdef DEBUG  #endif
       int k[2],l;    for (j=1;j<=n;j++) { 
       k[0]=1;      xi[j] *= xmin; 
       k[1]=-1;      p[j] += xi[j]; 
       printf("Max: %.12e",(*func)(p));    } 
       for (j=1;j<=n;j++)    free_vector(xicom,1,n); 
         printf(" %.12e",p[j]);    free_vector(pcom,1,n); 
       printf("\n");  } 
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /*************** powell ************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);              double (*func)(double [])) 
         }  { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
 #endif    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
     double fp,fptt;
       free_vector(xit,1,n);    double *xits;
       free_vector(xits,1,n);    pt=vector(1,n); 
       free_vector(ptt,1,n);    ptt=vector(1,n); 
       free_vector(pt,1,n);    xit=vector(1,n); 
       return;    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (j=1;j<=n;j++) {    for (*iter=1;;++(*iter)) { 
       ptt[j]=2.0*p[j]-pt[j];      fp=(*fret); 
       xit[j]=p[j]-pt[j];      ibig=0; 
       pt[j]=p[j];      del=0.0; 
     }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     fptt=(*func)(ptt);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     if (fptt < fp) {      for (i=1;i<=n;i++) 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf(" %d %.12f",i, p[i]);
       if (t < 0.0) {      fprintf(ficlog," %d %.12f",i, p[i]);
         linmin(p,xit,n,fret,func);      printf("\n");
         for (j=1;j<=n;j++) {      fprintf(ficlog,"\n");
           xi[j][ibig]=xi[j][n];      for (i=1;i<=n;i++) { 
           xi[j][n]=xit[j];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        printf("fret=%lf \n",*fret);
         for(j=1;j<=n;j++)        fprintf(ficlog,"fret=%lf \n",*fret);
           printf(" %.12e",xit[j]);  #endif
         printf("\n");        printf("%d",i);fflush(stdout);
 #endif        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
 }          ibig=i; 
         } 
 /**** Prevalence limit ****************/  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
      matrix by transitions matrix until convergence is reached */          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   int i, ii,j,k;        }
   double min, max, maxmin, maxmax,sumnew=0.;        for(j=1;j<=n;j++) {
   double **matprod2();          printf(" p=%.12e",p[j]);
   double **out, cov[NCOVMAX], **pmij();          fprintf(ficlog," p=%.12e",p[j]);
   double **newm;        }
   double agefin, delaymax=50 ; /* Max number of years to converge */        printf("\n");
         fprintf(ficlog,"\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)  #endif
     for (j=1;j<=nlstate+ndeath;j++){      } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
         int k[2],l;
    cov[1]=1.;        k[0]=1;
          k[1]=-1;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf("Max: %.12e",(*func)(p));
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fprintf(ficlog,"Max: %.12e",(*func)(p));
     newm=savm;        for (j=1;j<=n;j++) {
     /* Covariates have to be included here again */          printf(" %.12e",p[j]);
      cov[2]=agefin;          fprintf(ficlog," %.12e",p[j]);
          }
       for (k=1; k<=cptcovn;k++) {        printf("\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fprintf(ficlog,"\n");
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        for(l=0;l<=1;l++) {
       }          for (j=1;j<=n;j++) {
       for (k=1; k<=cptcovage;k++)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (k=1; k<=cptcovprod;k++)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        }
   #endif
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   
     savm=oldm;        free_vector(xit,1,n); 
     oldm=newm;        free_vector(xits,1,n); 
     maxmax=0.;        free_vector(ptt,1,n); 
     for(j=1;j<=nlstate;j++){        free_vector(pt,1,n); 
       min=1.;        return; 
       max=0.;      } 
       for(i=1; i<=nlstate; i++) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         sumnew=0;      for (j=1;j<=n;j++) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        ptt[j]=2.0*p[j]-pt[j]; 
         prlim[i][j]= newm[i][j]/(1-sumnew);        xit[j]=p[j]-pt[j]; 
         max=FMAX(max,prlim[i][j]);        pt[j]=p[j]; 
         min=FMIN(min,prlim[i][j]);      } 
       }      fptt=(*func)(ptt); 
       maxmin=max-min;      if (fptt < fp) { 
       maxmax=FMAX(maxmax,maxmin);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
     if(maxmax < ftolpl){          linmin(p,xit,n,fret,func); 
       return prlim;          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
 }          }
   #ifdef DEBUG
 /*************** transition probabilities ***************/          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);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          for(j=1;j<=n;j++){
 {            printf(" %.12e",xit[j]);
   double s1, s2;            fprintf(ficlog," %.12e",xit[j]);
   /*double t34;*/          }
   int i,j,j1, nc, ii, jj;          printf("\n");
           fprintf(ficlog,"\n");
     for(i=1; i<= nlstate; i++){  #endif
     for(j=1; j<i;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } 
         /*s2 += param[i][j][nc]*cov[nc];*/    } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  } 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /**** Prevalence limit (stable prevalence)  ****************/
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     }  {
     for(j=i+1; j<=nlstate+ndeath;j++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       matrix by transitions matrix until convergence is reached */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
       ps[i][j]=(s2);    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
   }    double **newm;
     /*ps[3][2]=1;*/    double agefin, delaymax=50 ; /* Max number of years to converge */
   
   for(i=1; i<= nlstate; i++){    for (ii=1;ii<=nlstate+ndeath;ii++)
      s1=0;      for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<i; j++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       s1+=exp(ps[i][j]);      }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);     cov[1]=1.;
     ps[i][i]=1./(s1+1.);   
     for(j=1; j<i; j++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(j=i+1; j<=nlstate+ndeath; j++)      newm=savm;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      /* Covariates have to be included here again */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */       cov[2]=agefin;
   } /* end i */    
         for (k=1; k<=cptcovn;k++) {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(jj=1; jj<= nlstate+ndeath; jj++){          /*      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[ii][jj]=0;        }
       ps[ii][ii]=1;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
   }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      printf("%lf ",ps[ii][jj]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
    }  
     printf("\n ");      savm=oldm;
     }      oldm=newm;
     printf("\n ");printf("%lf ",cov[2]);*/      maxmax=0.;
 /*      for(j=1;j<=nlstate;j++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        min=1.;
   goto end;*/        max=0.;
     return ps;        for(i=1; i<=nlstate; i++) {
 }          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 /**************** Product of 2 matrices ******************/          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          min=FMIN(min,prlim[i][j]);
 {        }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        maxmin=max-min;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        maxmax=FMAX(maxmax,maxmin);
   /* in, b, out are matrice of pointers which should have been initialized      }
      before: only the contents of out is modified. The function returns      if(maxmax < ftolpl){
      a pointer to pointers identical to out */        return prlim;
   long i, j, k;      }
   for(i=nrl; i<= nrh; i++)    }
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /*************** transition probabilities ***************/ 
   
   return out;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 }  {
     double s1, s2;
     /*double t34;*/
 /************* Higher Matrix Product ***************/    int i,j,j1, nc, ii, jj;
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for(i=1; i<= nlstate; i++){
 {      for(j=1; j<i;j++){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      duration (i.e. until          /*s2 += param[i][j][nc]*cov[nc];*/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      (typically every 2 years instead of every month which is too big).        }
      Model is determined by parameters x and covariates have to be        ps[i][j]=s2;
      included manually here.        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
      */      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i, j, d, h, k;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double **out, cov[NCOVMAX];          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double **newm;        }
         ps[i][j]=s2;
   /* Hstepm could be zero and should return the unit matrix */      }
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){      /*ps[3][2]=1;*/
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);    for(i=1; i<= nlstate; i++){
     }       s1=0;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for(j=1; j<i; j++)
   for(h=1; h <=nhstepm; h++){        s1+=exp(ps[i][j]);
     for(d=1; d <=hstepm; d++){      for(j=i+1; j<=nlstate+ndeath; j++)
       newm=savm;        s1+=exp(ps[i][j]);
       /* Covariates have to be included here again */      ps[i][i]=1./(s1+1.);
       cov[1]=1.;      for(j=1; j<i; j++)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      for(j=i+1; j<=nlstate+ndeath; j++)
       for (k=1; k<=cptcovage;k++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for (k=1; k<=cptcovprod;k++)    } /* end i */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        ps[ii][jj]=0;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        ps[ii][ii]=1;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    }
       savm=oldm;  
       oldm=newm;  
     }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     for(i=1; i<=nlstate+ndeath; i++)      for(jj=1; jj<= nlstate+ndeath; jj++){
       for(j=1;j<=nlstate+ndeath;j++) {       printf("%lf ",ps[ii][jj]);
         po[i][j][h]=newm[i][j];     }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      printf("\n ");
          */      }
       }      printf("\n ");printf("%lf ",cov[2]);*/
   } /* end h */  /*
   return po;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 }    goto end;*/
       return ps;
   }
 /*************** log-likelihood *************/  
 double func( double *x)  /**************** Product of 2 matrices ******************/
 {  
   int i, ii, j, k, mi, d, kk;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double sw; /* Sum of weights */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double lli; /* Individual log likelihood */    /* in, b, out are matrice of pointers which should have been initialized 
   long ipmx;       before: only the contents of out is modified. The function returns
   /*extern weight */       a pointer to pointers identical to out */
   /* We are differentiating ll according to initial status */    long i, j, k;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for(i=nrl; i<= nrh; i++)
   /*for(i=1;i<imx;i++)      for(k=ncolol; k<=ncoloh; k++)
     printf(" %d\n",s[4][i]);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   */          out[i][k] +=in[i][j]*b[j][k];
   cov[1]=1.;  
     return out;
   for(k=1; k<=nlstate; k++) ll[k]=0.;  }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){  /************* Higher Matrix Product ***************/
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for(d=0; d<dh[mi][i]; d++){  {
         newm=savm;    /* Computes the transition matrix starting at age 'age' over 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       'nhstepm*hstepm*stepm' months (i.e. until
         for (kk=1; kk<=cptcovage;kk++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       nhstepm*hstepm matrices. 
         }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               (typically every 2 years instead of every month which is too big 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       for the memory).
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       Model is determined by parameters x and covariates have to be 
         savm=oldm;       included manually here. 
         oldm=newm;  
               */
          
       } /* end mult */    int i, j, d, h, k;
          double **out, cov[NCOVMAX];
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double **newm;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;    /* Hstepm could be zero and should return the unit matrix */
       sw += weight[i];    for (i=1;i<=nlstate+ndeath;i++)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for (j=1;j<=nlstate+ndeath;j++){
     } /* end of wave */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   } /* end of individual */        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for(h=1; h <=nhstepm; h++){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for(d=1; d <=hstepm; d++){
   return -l;        newm=savm;
 }        /* Covariates have to be included here again */
         cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 /*********** Maximum Likelihood Estimation ***************/        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 {        for (k=1; k<=cptcovprod;k++)
   int i,j, iter;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double **xi,*delti;  
   double fret;  
   xi=matrix(1,npar,1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for (i=1;i<=npar;i++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for (j=1;j<=npar;j++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       xi[i][j]=(i==j ? 1.0 : 0.0);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("Powell\n");        savm=oldm;
   powell(p,xi,npar,ftol,&iter,&fret,func);        oldm=newm;
       }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      for(i=1; i<=nlstate+ndeath; i++)
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
 }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
 /**** Computes Hessian and covariance matrix ***/        }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    } /* end h */
 {    return po;
   double  **a,**y,*x,pd;  }
   double **hess;  
   int i, j,jk;  
   int *indx;  /*************** log-likelihood *************/
   double func( double *x)
   double hessii(double p[], double delta, int theta, double delti[]);  {
   double hessij(double p[], double delti[], int i, int j);    int i, ii, j, k, mi, d, kk;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double **out;
     double sw; /* Sum of weights */
   hess=matrix(1,npar,1,npar);    double lli; /* Individual log likelihood */
     int s1, s2;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double bbh, survp;
   for (i=1;i<=npar;i++){    long ipmx;
     printf("%d",i);fflush(stdout);    /*extern weight */
     hess[i][i]=hessii(p,ftolhess,i,delti);    /* We are differentiating ll according to initial status */
     /*printf(" %f ",p[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*printf(" %lf ",hess[i][i]);*/    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
      */
   for (i=1;i<=npar;i++) {    cov[1]=1.;
     for (j=1;j<=npar;j++)  {  
       if (j>i) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);    if(mle==1){
         hess[j][i]=hess[i][j];          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /*printf(" %lf ",hess[i][j]);*/        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");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            }
            for(d=0; d<dh[mi][i]; d++){
   a=matrix(1,npar,1,npar);            newm=savm;
   y=matrix(1,npar,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   x=vector(1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   indx=ivector(1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (i=1;i<=npar;i++)            }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   ludcmp(a,npar,indx,&pd);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for (j=1;j<=npar;j++) {            oldm=newm;
     for (i=1;i<=npar;i++) x[i]=0;          } /* end mult */
     x[j]=1;        
     lubksb(a,npar,indx,x);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (i=1;i<=npar;i++){          /* But now since version 0.9 we anticipate for bias and large stepm.
       matcov[i][j]=x[i];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   printf("\n#Hessian matrix#\n");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for (i=1;i<=npar;i++) {           * probability in order to take into account the bias as a fraction of the way
     for (j=1;j<=npar;j++) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       printf("%.3e ",hess[i][j]);           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
     printf("\n");           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
           s1=s[mw[mi][i]][i];
   /* Recompute Inverse */          s2=s[mw[mi+1][i]][i];
   for (i=1;i<=npar;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          /* bias is positive if real duration
   ludcmp(a,npar,indx,&pd);           * is higher than the multiple of stepm and negative otherwise.
            */
   /*  printf("\n#Hessian matrix recomputed#\n");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
   for (j=1;j<=npar;j++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for (i=1;i<=npar;i++) x[i]=0;          /*if(lli ==000.0)*/
     x[j]=1;          /*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); */
     lubksb(a,npar,indx,x);          ipmx +=1;
     for (i=1;i<=npar;i++){          sw += weight[i];
       y[i][j]=x[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       printf("%.3e ",y[i][j]);        } /* end of wave */
     }      } /* end of individual */
     printf("\n");    }  else if(mle==2){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(a,1,npar,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(y,1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   free_vector(x,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ivector(indx,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(hess,1,npar,1,npar);            }
           for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /*************** hessian matrix ****************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 double hessii( double x[], double delta, int theta, double delti[])            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int l=1, lmax=20;            savm=oldm;
   double k1,k2;            oldm=newm;
   double p2[NPARMAX+1];          } /* end mult */
   double res;        
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double fx;          /* But now since version 0.9 we anticipate for bias and large stepm.
   int k=0,kmax=10;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double l1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
   fx=func(x);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   for (i=1;i<=npar;i++) p2[i]=x[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for(l=0 ; l <=lmax; l++){           * probability in order to take into account the bias as a fraction of the way
     l1=pow(10,l);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     delts=delt;           * -stepm/2 to stepm/2 .
     for(k=1 ; k <kmax; k=k+1){           * For stepm=1 the results are the same as for previous versions of Imach.
       delt = delta*(l1*k);           * For stepm > 1 the results are less biased than in previous versions. 
       p2[theta]=x[theta] +delt;           */
       k1=func(p2)-fx;          s1=s[mw[mi][i]][i];
       p2[theta]=x[theta]-delt;          s2=s[mw[mi+1][i]][i];
       k2=func(p2)-fx;          bbh=(double)bh[mi][i]/(double)stepm; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */          /* bias is positive if real duration
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           * is higher than the multiple of stepm and negative otherwise.
                 */
 #ifdef DEBUG          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 #endif          /*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 */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*if(lli ==000.0)*/
         k=kmax;          /*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;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          sw += weight[i];
         k=kmax; l=lmax*10.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      } /* end of individual */
         delts=delt;    }  else if(mle==3){  /* exponential inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   delti[theta]=delts;          for (ii=1;ii<=nlstate+ndeath;ii++)
   return res;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 double hessij( double x[], double delti[], int thetai,int thetaj)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   int i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int l=1, l1, lmax=20;            for (kk=1; kk<=cptcovage;kk++) {
   double k1,k2,k3,k4,res,fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double p2[NPARMAX+1];            }
   int k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fx=func(x);            savm=oldm;
   for (k=1; k<=2; k++) {            oldm=newm;
     for (i=1;i<=npar;i++) p2[i]=x[i];          } /* end mult */
     p2[thetai]=x[thetai]+delti[thetai]/k;        
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     k1=func(p2)-fx;          /* 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 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     k2=func(p2)-fx;           * 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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * probability in order to take into account the bias as a fraction of the way
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     k3=func(p2)-fx;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           */
     k4=func(p2)-fx;          s1=s[mw[mi][i]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          s2=s[mw[mi+1][i]][i];
 #ifdef DEBUG          bbh=(double)bh[mi][i]/(double)stepm; 
     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);          /* bias is positive if real duration
 #endif           * is higher than the multiple of stepm and negative otherwise.
   }           */
   return res;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
 }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 /************** Inverse of matrix **************/          /*if(lli ==000.0)*/
 void ludcmp(double **a, int n, int *indx, double *d)          /*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;
   int i,imax,j,k;          sw += weight[i];
   double big,dum,sum,temp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *vv;        } /* end of wave */
        } /* end of individual */
   vv=vector(1,n);    }else{  /* ml=4 no inter-extrapolation */
   *d=1.0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     big=0.0;        for(mi=1; mi<= wav[i]-1; mi++){
     for (j=1;j<=n;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       if ((temp=fabs(a[i][j])) > big) big=temp;            for (j=1;j<=nlstate+ndeath;j++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     vv[i]=1.0/big;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   for (j=1;j<=n;j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1;i<j;i++) {            newm=savm;
       sum=a[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            for (kk=1; kk<=cptcovage;kk++) {
       a[i][j]=sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     big=0.0;          
     for (i=j;i<=n;i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       sum=a[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<j;k++)            savm=oldm;
         sum -= a[i][k]*a[k][j];            oldm=newm;
       a[i][j]=sum;          } /* end mult */
       if ( (dum=vv[i]*fabs(sum)) >= big) {        
         big=dum;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         imax=i;          ipmx +=1;
       }          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (j != imax) {        } /* end of wave */
       for (k=1;k<=n;k++) {      } /* end of individual */
         dum=a[imax][k];    } /* End of if */
         a[imax][k]=a[j][k];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         a[j][k]=dum;    /* 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 */
       *d = -(*d);    return -l;
       vv[imax]=vv[j];  }
     }  
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*********** Maximum Likelihood Estimation ***************/
     if (j != n) {  
       dum=1.0/(a[j][j]);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  {
     }    int i,j, iter;
   }    double **xi,*delti;
   free_vector(vv,1,n);  /* Doesn't work */    double fret;
 ;    xi=matrix(1,npar,1,npar);
 }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 void lubksb(double **a, int n, int *indx, double b[])        xi[i][j]=(i==j ? 1.0 : 0.0);
 {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int i,ii=0,ip,j;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double sum;  
       printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (i=1;i<=n;i++) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     ip=indx[i];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     sum=b[ip];  
     b[ip]=b[i];  }
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /**** Computes Hessian and covariance matrix ***/
     else if (sum) ii=i;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     b[i]=sum;  {
   }    double  **a,**y,*x,pd;
   for (i=n;i>=1;i--) {    double **hess;
     sum=b[i];    int i, j,jk;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int *indx;
     b[i]=sum/a[i][i];  
   }    double hessii(double p[], double delta, int theta, double delti[]);
 }    double hessij(double p[], double delti[], int i, int j);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
 /************ Frequencies ********************/    void ludcmp(double **a, int npar, int *indx, double *d) ;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)  
 {  /* Some frequencies */    hess=matrix(1,npar,1,npar);
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    printf("\nCalculation of the hessian matrix. Wait...\n");
   double ***freq; /* Frequencies */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double *pp;    for (i=1;i<=npar;i++){
   double pos;      printf("%d",i);fflush(stdout);
   FILE *ficresp;      fprintf(ficlog,"%d",i);fflush(ficlog);
   char fileresp[FILENAMELENGTH];      hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
   pp=vector(1,nlstate);      /*printf(" %lf ",hess[i][i]);*/
  probs= ma3x(1,130 ,1,8, 1,8);    }
   strcpy(fileresp,"p");    
   strcat(fileresp,fileres);    for (i=1;i<=npar;i++) {
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for (j=1;j<=npar;j++)  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);        if (j>i) { 
     exit(0);          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          hess[i][j]=hessij(p,delti,i,j);
   j1=0;          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
     }
   for(k1=1; k1<=j;k1++){    printf("\n");
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficlog,"\n");
        j1++;  
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
          scanf("%d", i);*/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         for (i=-1; i<=nlstate+ndeath; i++)      
          for (jk=-1; jk<=nlstate+ndeath; jk++)      a=matrix(1,npar,1,npar);
            for(m=agemin; m <= agemax+3; m++)    y=matrix(1,npar,1,npar);
              freq[i][jk][m]=0;    x=vector(1,npar);
            indx=ivector(1,npar);
        for (i=1; i<=imx; i++) {    for (i=1;i<=npar;i++)
          bool=1;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
          if  (cptcovn>0) {    ludcmp(a,npar,indx,&pd);
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (j=1;j<=npar;j++) {
                bool=0;      for (i=1;i<=npar;i++) x[i]=0;
          }      x[j]=1;
           if (bool==1) {      lubksb(a,npar,indx,x);
            for(m=fprev1; m<=lprev1; m++){      for (i=1;i<=npar;i++){ 
              if(agev[m][i]==0) agev[m][i]=agemax+1;        matcov[i][j]=x[i];
              if(agev[m][i]==1) agev[m][i]=agemax+2;      }
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    }
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
            }    printf("\n#Hessian matrix#\n");
          }    fprintf(ficlog,"\n#Hessian matrix#\n");
        }    for (i=1;i<=npar;i++) { 
         if  (cptcovn>0) {      for (j=1;j<=npar;j++) { 
          fprintf(ficresp, "\n#********** Variable ");        printf("%.3e ",hess[i][j]);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        fprintf(ficlog,"%.3e ",hess[i][j]);
        fprintf(ficresp, "**********\n#");      }
         }      printf("\n");
        for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    }
        fprintf(ficresp, "\n");  
            /* Recompute Inverse */
   for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=npar;i++)
     if(i==(int)agemax+3)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       printf("Total");    ludcmp(a,npar,indx,&pd);
     else  
       printf("Age %d", i);    /*  printf("\n#Hessian matrix recomputed#\n");
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    for (j=1;j<=npar;j++) {
         pp[jk] += freq[jk][m][i];      for (i=1;i<=npar;i++) x[i]=0;
     }      x[j]=1;
     for(jk=1; jk <=nlstate ; jk++){      lubksb(a,npar,indx,x);
       for(m=-1, pos=0; m <=0 ; m++)      for (i=1;i<=npar;i++){ 
         pos += freq[jk][m][i];        y[i][j]=x[i];
       if(pp[jk]>=1.e-10)        printf("%.3e ",y[i][j]);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        fprintf(ficlog,"%.3e ",y[i][j]);
       else      }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      printf("\n");
     }      fprintf(ficlog,"\n");
     }
      for(jk=1; jk <=nlstate ; jk++){    */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];    free_matrix(a,1,npar,1,npar);
      }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     for(jk=1,pos=0; jk <=nlstate ; jk++)    free_ivector(indx,1,npar);
       pos += pp[jk];    free_matrix(hess,1,npar,1,npar);
     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  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*************** hessian matrix ****************/
       if( i <= (int) agemax){  double hessii( double x[], double delta, int theta, double delti[])
         if(pos>=1.e-5){  {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    int i;
           probs[i][jk][j1]= pp[jk]/pos;    int l=1, lmax=20;
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    double k1,k2;
         }    double p2[NPARMAX+1];
       else    double res;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       }    double fx;
     }    int k=0,kmax=10;
     for(jk=-1; jk <=nlstate+ndeath; jk++)    double l1;
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    fx=func(x);
     if(i <= (int) agemax)    for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficresp,"\n");    for(l=0 ; l <=lmax; l++){
     printf("\n");      l1=pow(10,l);
     }      delts=delt;
     }      for(k=1 ; k <kmax; k=k+1){
  }        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
   fclose(ficresp);        k1=func(p2)-fx;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        p2[theta]=x[theta]-delt;
   free_vector(pp,1,nlstate);        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 }  /* End of Freq */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
 /************ Prevalence ********************/  #ifdef DEBUG
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)        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);
 {  /* Some frequencies */        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   double ***freq; /* Frequencies */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   double *pp;          k=kmax;
   double pos;        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   pp=vector(1,nlstate);          k=kmax; l=lmax*10.;
   probs= ma3x(1,130 ,1,8, 1,8);        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          delts=delt;
   j1=0;        }
        }
   j=cptcoveff;    }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    delti[theta]=delts;
      return res; 
  for(k1=1; k1<=j;k1++){    
     for(i1=1; i1<=ncodemax[k1];i1++){  }
       j1++;  
    double hessij( double x[], double delti[], int thetai,int thetaj)
       for (i=-1; i<=nlstate+ndeath; i++)    {
         for (jk=-1; jk<=nlstate+ndeath; jk++)      int i;
           for(m=agemin; m <= agemax+3; m++)    int l=1, l1, lmax=20;
           freq[i][jk][m]=0;    double k1,k2,k3,k4,res,fx;
          double p2[NPARMAX+1];
       for (i=1; i<=imx; i++) {    int k;
         bool=1;  
         if  (cptcovn>0) {    fx=func(x);
           for (z1=1; z1<=cptcoveff; z1++)    for (k=1; k<=2; k++) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (i=1;i<=npar;i++) p2[i]=x[i];
               bool=0;      p2[thetai]=x[thetai]+delti[thetai]/k;
               }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         if (bool==1) {      k1=func(p2)-fx;
           for(m=fprev1; m<=lprev1; m++){    
             if(agev[m][i]==0) agev[m][i]=agemax+1;      p2[thetai]=x[thetai]+delti[thetai]/k;
             if(agev[m][i]==1) agev[m][i]=agemax+2;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      k2=func(p2)-fx;
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    
           }      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
        for(i=(int)agemin; i <= (int)agemax+3; i++){    
         for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]-delti[thetai]/k;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             pp[jk] += freq[jk][m][i];      k4=func(p2)-fx;
         }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
           for(m=-1, pos=0; m <=0 ; m++)      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);
             pos += freq[jk][m][i];      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         }  #endif
            }
          for(jk=1; jk <=nlstate ; jk++){    return res;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  }
              pp[jk] += freq[jk][m][i];  
          }  /************** Inverse of matrix **************/
            void ludcmp(double **a, int n, int *indx, double *d) 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  { 
     int i,imax,j,k; 
          for(jk=1; jk <=nlstate ; jk++){              double big,dum,sum,temp; 
            if( i <= (int) agemax){    double *vv; 
              if(pos>=1.e-5){   
                probs[i][jk][j1]= pp[jk]/pos;    vv=vector(1,n); 
              }    *d=1.0; 
            }    for (i=1;i<=n;i++) { 
          }      big=0.0; 
                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; 
      } 
      for (j=1;j<=n;j++) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1;i<j;i++) { 
   free_vector(pp,1,nlstate);        sum=a[i][j]; 
          for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 }  /* End of Freq */        a[i][j]=sum; 
 /************* Waves Concatenation ***************/      } 
       big=0.0; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      for (i=j;i<=n;i++) { 
 {        sum=a[i][j]; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for (k=1;k<j;k++) 
      Death is a valid wave (if date is known).          sum -= a[i][k]*a[k][j]; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        a[i][j]=sum; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      and mw[mi+1][i]. dh depends on stepm.          big=dum; 
      */          imax=i; 
         } 
   int i, mi, m;      } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      if (j != imax) { 
      double sum=0., jmean=0.;*/        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
   int j, k=0,jk, ju, jl;          a[imax][k]=a[j][k]; 
   double sum=0.;          a[j][k]=dum; 
   jmin=1e+5;        } 
   jmax=-1;        *d = -(*d); 
   jmean=0.;        vv[imax]=vv[j]; 
   for(i=1; i<=imx; i++){      } 
     mi=0;      indx[j]=imax; 
     m=firstpass;      if (a[j][j] == 0.0) a[j][j]=TINY; 
     while(s[m][i] <= nlstate){      if (j != n) { 
       if(s[m][i]>=1)        dum=1.0/(a[j][j]); 
         mw[++mi][i]=m;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       if(m >=lastpass)      } 
         break;    } 
       else    free_vector(vv,1,n);  /* Doesn't work */
         m++;  ;
     }/* end while */  } 
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */  void lubksb(double **a, int n, int *indx, double b[]) 
       /* if(mi==0)  never been interviewed correctly before death */  { 
          /* Only death is a correct wave */    int i,ii=0,ip,j; 
       mw[mi][i]=m;    double sum; 
     }   
     for (i=1;i<=n;i++) { 
     wav[i]=mi;      ip=indx[i]; 
     if(mi==0)      sum=b[ip]; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      b[ip]=b[i]; 
   }      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   for(i=1; i<=imx; i++){      else if (sum) ii=i; 
     for(mi=1; mi<wav[i];mi++){      b[i]=sum; 
       if (stepm <=0)    } 
         dh[mi][i]=1;    for (i=n;i>=1;i--) { 
       else{      sum=b[i]; 
         if (s[mw[mi+1][i]][i] > nlstate) {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           if (agedc[i] < 2*AGESUP) {      b[i]=sum/a[i][i]; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    } 
           if(j==0) j=1;  /* Survives at least one month after exam */  } 
           k=k+1;  
           if (j >= jmax) jmax=j;  /************ Frequencies ********************/
           if (j <= jmin) jmin=j;  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)
           sum=sum+j;  {  /* Some frequencies */
           /* if (j<10) printf("j=%d num=%d ",j,i); */    
           }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         }    int first;
         else{    double ***freq; /* Frequencies */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double *pp;
           k=k+1;    double pos, k2, dateintsum=0,k2cpt=0;
           if (j >= jmax) jmax=j;    FILE *ficresp;
           else if (j <= jmin)jmin=j;    char fileresp[FILENAMELENGTH];
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    
           sum=sum+j;    pp=vector(1,nlstate);
         }    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
         jk= j/stepm;    strcpy(fileresp,"p");
         jl= j -jk*stepm;    strcat(fileresp,fileres);
         ju= j -(jk+1)*stepm;    if((ficresp=fopen(fileresp,"w"))==NULL) {
         if(jl <= -ju)      printf("Problem with prevalence resultfile: %s\n", fileresp);
           dh[mi][i]=jk;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         else      exit(0);
           dh[mi][i]=jk+1;    }
         if(dh[mi][i]==0)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
           dh[mi][i]=1; /* At least one step */    j1=0;
       }    
     }    j=cptcoveff;
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    first=1;
  }  
 /*********** Tricode ****************************/    for(k1=1; k1<=j;k1++){
 void tricode(int *Tvar, int **nbcode, int imx)      for(i1=1; i1<=ncodemax[k1];i1++){
 {        j1++;
   int Ndum[20],ij=1, k, j, i;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   int cptcode=0;          scanf("%d", i);*/
   cptcoveff=0;        for (i=-1; i<=nlstate+ndeath; i++)  
            for (jk=-1; jk<=nlstate+ndeath; jk++)  
   for (k=0; k<19; k++) Ndum[k]=0;            for(m=agemin; m <= agemax+3; m++)
   for (k=1; k<=7; k++) ncodemax[k]=0;              freq[i][jk][m]=0;
         
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        dateintsum=0;
     for (i=1; i<=imx; i++) {        k2cpt=0;
       ij=(int)(covar[Tvar[j]][i]);        for (i=1; i<=imx; i++) {
       Ndum[ij]++;          bool=1;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          if  (cptcovn>0) {
       if (ij > cptcode) cptcode=ij;            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     for (i=0; i<=cptcode; i++) {          }
       if(Ndum[i]!=0) ncodemax[j]++;          if (bool==1){
     }            for(m=firstpass; m<=lastpass; m++){
     ij=1;              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
     for (i=1; i<=ncodemax[j]; i++) {                if(agev[m][i]==1) agev[m][i]=agemax+2;
       for (k=0; k<=19; k++) {                if (m<lastpass) {
         if (Ndum[k] != 0) {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           nbcode[Tvar[j]][ij]=k;                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
           ij++;                }
         }                
         if (ij > ncodemax[j]) break;                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
       }                    dateintsum=dateintsum+k2;
     }                  k2cpt++;
   }                  }
               }
  for (k=0; k<19; k++) Ndum[k]=0;            }
           }
  for (i=1; i<=ncovmodel-2; i++) {        }
       ij=Tvar[i];         
       Ndum[ij]++;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     }  
         if  (cptcovn>0) {
  ij=1;          fprintf(ficresp, "\n#********** Variable "); 
  for (i=1; i<=10; i++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    if((Ndum[i]!=0) && (i<=ncov)){          fprintf(ficresp, "**********\n#");
      Tvaraff[ij]=i;        }
      ij++;        for(i=1; i<=nlstate;i++) 
    }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
  }        fprintf(ficresp, "\n");
          
     cptcoveff=ij-1;        for(i=(int)agemin; i <= (int)agemax+3; i++){
 }          if(i==(int)agemax+3){
             fprintf(ficlog,"Total");
 /*********** Health Expectancies ****************/          }else{
             if(first==1){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)              first=0;
 {              printf("See log file for details...\n");
   /* Health expectancies */            }
   int i, j, nhstepm, hstepm, h;            fprintf(ficlog,"Age %d", i);
   double age, agelim,hf;          }
   double ***p3mat;          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fprintf(ficreseij,"# Health expectancies\n");              pp[jk] += freq[jk][m][i]; 
   fprintf(ficreseij,"# Age");          }
   for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j<=nlstate;j++)            for(m=-1, pos=0; m <=0 ; m++)
       fprintf(ficreseij," %1d-%1d",i,j);              pos += freq[jk][m][i];
   fprintf(ficreseij,"\n");            if(pp[jk]>=1.e-10){
               if(first==1){
   hstepm=1*YEARM; /*  Every j years of age (in month) */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   agelim=AGESUP;            }else{
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(first==1)
     /* nhstepm age range expressed in number of stepm */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     /* Typically if 20 years = 20*12/6=40 stepm */            }
     if (stepm >= YEARM) hstepm=1;          }
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              pp[jk] += freq[jk][m][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
   
           for(jk=1,pos=0; jk <=nlstate ; jk++)
     for(i=1; i<=nlstate;i++)            pos += pp[jk];
       for(j=1; j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            if(pos>=1.e-5){
           eij[i][j][(int)age] +=p3mat[i][j][h];              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);
     hf=1;            }else{
     if (stepm >= YEARM) hf=stepm/YEARM;              if(first==1)
     fprintf(ficreseij,"%.0f",age );                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<=nlstate;j++){            }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            if( i <= (int) agemax){
       }              if(pos>=1.e-5){
     fprintf(ficreseij,"\n");                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                probs[i][jk][j1]= pp[jk]/pos;
   }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 }              }
               else
 /************ Variance ******************/                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
 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)            }
 {          }
   /* Variance of health expectancies */          
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(jk=-1; jk <=nlstate+ndeath; jk++)
   double **newm;            for(m=-1; m <=nlstate+ndeath; m++)
   double **dnewm,**doldm;              if(freq[jk][m][i] !=0 ) {
   int i, j, nhstepm, hstepm, h;              if(first==1)
   int k, cptcode;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double *xp;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **gp, **gm;              }
   double ***gradg, ***trgradg;          if(i <= (int) agemax)
   double ***p3mat;            fprintf(ficresp,"\n");
   double age,agelim;          if(first==1)
   int theta;            printf("Others in log...\n");
           fprintf(ficlog,"\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");        }
   fprintf(ficresvij,"# Age");      }
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=nlstate;j++)    dateintmean=dateintsum/k2cpt; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);   
   fprintf(ficresvij,"\n");    fclose(ficresp);
     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,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    /* End of Freq */
    }
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /************ Prevalence ********************/
   agelim = AGESUP;  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 (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     if (stepm >= YEARM) hstepm=1;       in each health status at the date of interview (if between dateprev1 and dateprev2).
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       We still use firstpass and lastpass as another selection.
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);   
     gp=matrix(0,nhstepm,1,nlstate);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     gm=matrix(0,nhstepm,1,nlstate);    double ***freq; /* Frequencies */
     double *pp;
     for(theta=1; theta <=npar; theta++){    double pos; 
       for(i=1; i<=npar; i++){ /* Computes gradient */    double  y2; /* in fractional years */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    pp=vector(1,nlstate);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     j1=0;
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    j=cptcoveff;
           prlim[i][i]=probs[(int)age][i][ij];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }    
          for(k1=1; k1<=j;k1++){
       for(j=1; j<= nlstate; j++){      for(i1=1; i1<=ncodemax[k1];i1++){
         for(h=0; h<=nhstepm; h++){        j1++;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for (i=-1; i<=nlstate+ndeath; i++)  
         }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       }            for(m=agemin; m <= agemax+3; m++)
                  freq[i][jk][m]=0;
       for(i=1; i<=npar; i++) /* Computes gradient */       
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (i=1; i<=imx; i++) { /* Each individual */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            bool=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
       if (popbased==1) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         for(i=1; i<=nlstate;i++)                bool=0;
           prlim[i][i]=probs[(int)age][i][ij];          } 
       }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       for(j=1; j<= nlstate; j++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         for(h=0; h<=nhstepm; h++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                if(agev[m][i]==0) agev[m][i]=agemax+1;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                if(agev[m][i]==1) agev[m][i]=agemax+2;
         }                if (m<lastpass) {
       }                  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];
       for(j=1; j<= nlstate; j++)                  else
         for(h=0; h<=nhstepm; h++){                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
         }                }
     } /* End theta */              }
             } /* end selection of waves */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          }
         }
     for(h=0; h<=nhstepm; h++)        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
       for(j=1; j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
         for(theta=1; theta <=npar; theta++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           trgradg[h][j][theta]=gradg[h][theta][j];              pp[jk] += freq[jk][m][i]; 
           }
     for(i=1;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
       for(j=1;j<=nlstate;j++)            for(m=-1, pos=0; m <=0 ; m++)
         vareij[i][j][(int)age] =0.;              pos += freq[jk][m][i];
     for(h=0;h<=nhstepm;h++){          }
       for(k=0;k<=nhstepm;k++){          
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          for(jk=1; jk <=nlstate ; jk++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         for(i=1;i<=nlstate;i++)              pp[jk] += freq[jk][m][i];
           for(j=1;j<=nlstate;j++)          }
             vareij[i][j][(int)age] += doldm[i][j];          
       }          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
     }          
     h=1;          for(jk=1; jk <=nlstate ; jk++){    
     if (stepm >= YEARM) h=stepm/YEARM;            if( i <= (int) agemax){
     fprintf(ficresvij,"%.0f ",age );              if(pos>=1.e-5){
     for(i=1; i<=nlstate;i++)                probs[i][jk][j1]= pp[jk]/pos;
       for(j=1; j<=nlstate;j++){              }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            }
       }          }/* end jk */
     fprintf(ficresvij,"\n");        }/* end i */
     free_matrix(gp,0,nhstepm,1,nlstate);      } /* end i1 */
     free_matrix(gm,0,nhstepm,1,nlstate);    } /* end k1 */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   } /* End age */    free_vector(pp,1,nlstate);
      
   free_vector(xp,1,npar);  }  /* End of Freq */
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /************* Waves Concatenation ***************/
   
 }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
 /************ Variance of prevlim ******************/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 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)       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
   /* Variance of prevalence limit */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       and mw[mi+1][i]. dh depends on stepm.
   double **newm;       */
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;    int i, mi, m;
   int k, cptcode;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double *xp;       double sum=0., jmean=0.;*/
   double *gp, *gm;    int first;
   double **gradg, **trgradg;    int j, k=0,jk, ju, jl;
   double age,agelim;    double sum=0.;
   int theta;    first=0;
        jmin=1e+5;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    jmax=-1;
   fprintf(ficresvpl,"# Age");    jmean=0.;
   for(i=1; i<=nlstate;i++)    for(i=1; i<=imx; i++){
       fprintf(ficresvpl," %1d-%1d",i,i);      mi=0;
   fprintf(ficresvpl,"\n");      m=firstpass;
       while(s[m][i] <= nlstate){
   xp=vector(1,npar);        if(s[m][i]>=1)
   dnewm=matrix(1,nlstate,1,npar);          mw[++mi][i]=m;
   doldm=matrix(1,nlstate,1,nlstate);        if(m >=lastpass)
            break;
   hstepm=1*YEARM; /* Every year of age */        else
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          m++;
   agelim = AGESUP;      }/* end while */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      if (s[m][i] > nlstate){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        mi++;     /* Death is another wave */
     if (stepm >= YEARM) hstepm=1;        /* if(mi==0)  never been interviewed correctly before death */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */           /* Only death is a correct wave */
     gradg=matrix(1,npar,1,nlstate);        mw[mi][i]=m;
     gp=vector(1,nlstate);      }
     gm=vector(1,nlstate);  
       wav[i]=mi;
     for(theta=1; theta <=npar; theta++){      if(mi==0){
       for(i=1; i<=npar; i++){ /* Computes gradient */        if(first==0){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
       }          first=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)        if(first==1){
         gp[i] = prlim[i][i];          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
            }
       for(i=1; i<=npar; i++) /* Computes gradient */      } /* end mi==0 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for(i=1; i<=imx; i++){
         gm[i] = prlim[i][i];      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
       for(i=1;i<=nlstate;i++)          dh[mi][i]=1;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        else{
     } /* End theta */          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
     trgradg =matrix(1,nlstate,1,npar);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */
     for(j=1; j<=nlstate;j++)            k=k+1;
       for(theta=1; theta <=npar; theta++)            if (j >= jmax) jmax=j;
         trgradg[j][theta]=gradg[theta][j];            if (j <= jmin) jmin=j;
             sum=sum+j;
     for(i=1;i<=nlstate;i++)            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       varpl[i][(int)age] =0.;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     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++)          else{
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     fprintf(ficresvpl,"%.0f ",age );            k=k+1;
     for(i=1; i<=nlstate;i++)            if (j >= jmax) jmax=j;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            else if (j <= jmin)jmin=j;
     fprintf(ficresvpl,"\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_vector(gp,1,nlstate);            sum=sum+j;
     free_vector(gm,1,nlstate);          }
     free_matrix(gradg,1,npar,1,nlstate);          jk= j/stepm;
     free_matrix(trgradg,1,nlstate,1,npar);          jl= j -jk*stepm;
   } /* End age */          ju= j -(jk+1)*stepm;
           if(mle <=1){ 
   free_vector(xp,1,npar);            if(jl==0){
   free_matrix(doldm,1,nlstate,1,npar);              dh[mi][i]=jk;
   free_matrix(dnewm,1,nlstate,1,nlstate);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
 }                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
 /************ Variance of one-step probabilities  ******************/              bh[mi][i]=ju;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            }
 {          }else{
   int i, j;            if(jl <= -ju){
   int k=0, cptcode;              dh[mi][i]=jk;
   double **dnewm,**doldm;              bh[mi][i]=jl;       /* bias is positive if real duration
   double *xp;                                   * is higher than the multiple of stepm and negative otherwise.
   double *gp, *gm;                                   */
   double **gradg, **trgradg;            }
   double age,agelim, cov[NCOVMAX];            else{
   int theta;              dh[mi][i]=jk+1;
   char fileresprob[FILENAMELENGTH];              bh[mi][i]=ju;
             }
   strcpy(fileresprob,"prob");            if(dh[mi][i]==0){
   strcat(fileresprob,fileres);              dh[mi][i]=1; /* At least one step */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              bh[mi][i]=ju; /* At least one step */
     printf("Problem with resultfile: %s\n", fileresprob);              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);
   }            }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          }
          } /* end if mle */
       } /* end wave */
   xp=vector(1,npar);    }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    jmean=sum/k;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   cov[1]=1;   }
   for (age=bage; age<=fage; age ++){  
     cov[2]=age;  /*********** Tricode ****************************/
     gradg=matrix(1,npar,1,9);  void tricode(int *Tvar, int **nbcode, int imx)
     trgradg=matrix(1,9,1,npar);  {
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int Ndum[20],ij=1, k, j, i, maxncov=19;
        int cptcode=0;
     for(theta=1; theta <=npar; theta++){    cptcoveff=0; 
       for(i=1; i<=npar; i++)   
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (k=0; k<maxncov; k++) Ndum[k]=0;
          for (k=1; k<=7; k++) ncodemax[k]=0;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
        for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       k=0;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       for(i=1; i<= (nlstate+ndeath); i++){                                 modality*/ 
         for(j=1; j<=(nlstate+ndeath);j++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            k=k+1;        Ndum[ij]++; /*store the modality */
           gp[k]=pmmij[i][j];        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       }                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
       for(i=1; i<=npar; i++)      }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
          for (i=0; i<=cptcode; i++) {
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      }
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){      ij=1; 
         for(j=1; j<=(nlstate+ndeath);j++){      for (i=1; i<=ncodemax[j]; i++) {
           k=k+1;        for (k=0; k<= maxncov; k++) {
           gm[k]=pmmij[i][j];          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(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            ij++;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            }
     }          if (ij > ncodemax[j]) break; 
         }  
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      } 
       for(theta=1; theta <=npar; theta++)    }  
       trgradg[j][theta]=gradg[theta][j];  
     for (k=0; k< maxncov; k++) Ndum[k]=0;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      pmij(pmmij,cov,ncovmodel,x,nlstate);     ij=Tvar[i];
      Ndum[ij]++;
      k=0;   }
      for(i=1; i<=(nlstate+ndeath); i++){  
        for(j=1; j<=(nlstate+ndeath);j++){   ij=1;
          k=k+1;   for (i=1; i<= maxncov; i++) {
          gm[k]=pmmij[i][j];     if((Ndum[i]!=0) && (i<=ncovcol)){
         }       Tvaraff[ij]=i; /*For printing */
      }       ij++;
           }
      /*printf("\n%d ",(int)age);   }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){   
           cptcoveff=ij-1; /*Number of simple covariates*/
   }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/  /*********** Health Expectancies ****************/
   
   fprintf(ficresprob,"\n%d ",(int)age);  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  {
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* Health expectancies */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   }    double age, agelim, hf;
     double ***p3mat,***varhe;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double **dnewm,**doldm;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double *xp;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double **gp, **gm;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double ***gradg, ***trgradg;
 }    int theta;
  free_vector(xp,1,npar);  
 fclose(ficresprob);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
  exit(0);    xp=vector(1,npar);
 }    dnewm=matrix(1,nlstate*2,1,npar);
     doldm=matrix(1,nlstate*2,1,nlstate*2);
 /***********************************************/    
 /**************** Main Program *****************/    fprintf(ficreseij,"# Health expectancies\n");
 /***********************************************/    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
 /*int main(int argc, char *argv[])*/      for(j=1; j<=nlstate;j++)
 int main()        fprintf(ficreseij," %1d-%1d (SE)",i,j);
 {    fprintf(ficreseij,"\n");
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    if(estepm < stepm){
   double agedeb, agefin,hf;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double agemin=1.e20, agemax=-1.e20;    }
     else  hstepm=estepm;   
   double fret;    /* We compute the life expectancy from trapezoids spaced every estepm months
   double **xi,tmp,delta;     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
   double dum; /* Dummy variable */     * we are calculating an estimate of the Life Expectancy assuming a linear 
   double ***p3mat;     * progression in between and thus overestimating or underestimating according
   int *indx;     * to the curvature of the survival function. If, for the same date, we 
   char line[MAXLINE], linepar[MAXLINE];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   char title[MAXLINE];     * to compare the new estimate of Life expectancy with the same linear 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];     * hypothesis. A more precise result, taking into account a more precise
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];     * curvature will be obtained if estepm is as small as stepm. */
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    /* For example we decided to compute the life expectancy with the smallest unit */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int firstobs=1, lastobs=10;       nhstepm is the number of hstepm from age to agelim 
   int sdeb, sfin; /* Status at beginning and end */       nstepm is the number of stepm from age to agelin. 
   int c,  h , cpt,l;       Look at hpijx to understand the reason of that which relies in memory size
   int ju,jl, mi;       and note for a fixed period like estepm months */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;       survival function given by stepm (the optimization length). Unfortunately it
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;       means that if the survival funtion is printed only each two years of age and if
   int hstepm, nhstepm;       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.
   double bage, fage, age, agelim, agebase;    */
   double ftolpl=FTOL;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double **prlim;  
   double *severity;    agelim=AGESUP;
   double ***param; /* Matrix of parameters */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double  *p;      /* nhstepm age range expressed in number of stepm */
   double **matcov; /* Matrix of covariance */      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   double ***delti3; /* Scale */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double *delti; /* Scale */      /* if (stepm >= YEARM) hstepm=1;*/
   double ***eij, ***vareij;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double **varpl; /* Variances of prevalence limits by age */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *epj, vepp;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   double kk1;      gp=matrix(0,nhstepm,1,nlstate*2);
       gm=matrix(0,nhstepm,1,nlstate*2);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   char z[1]="c", occ;   
 #include <sys/time.h>  
 #include <time.h>      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
   /* long total_usecs;      /* Computing Variances of health expectancies */
   struct timeval start_time, end_time;  
         for(theta=1; theta <=npar; theta++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   printf("\nIMACH, Version 0.64b");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   printf("\nEnter the parameter file name: ");    
         cptj=0;
 #ifdef windows        for(j=1; j<= nlstate; j++){
   scanf("%s",pathtot);          for(i=1; i<=nlstate; i++){
   getcwd(pathcd, size);            cptj=cptj+1;
   /*cygwin_split_path(pathtot,path,optionfile);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   /* cutv(path,optionfile,pathtot,'\\');*/            }
           }
 split(pathtot, path,optionfile);        }
   chdir(path);       
   replace(pathc,path);       
 #endif        for(i=1; i<=npar; i++) 
 #ifdef unix          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   scanf("%s",optionfile);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #endif        
         cptj=0;
 /*-------- arguments in the command line --------*/        for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
   strcpy(fileres,"r");            cptj=cptj+1;
   strcat(fileres, optionfile);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   /*---------arguments file --------*/            }
           }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        }
     printf("Problem with optionfile %s\n",optionfile);        for(j=1; j<= nlstate*2; j++)
     goto end;          for(h=0; h<=nhstepm-1; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   strcpy(filereso,"o");       } 
   strcat(filereso,fileres);     
   if((ficparo=fopen(filereso,"w"))==NULL) {  /* End theta */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   
   /* Reads comments: lines beginning with '#' */       for(h=0; h<=nhstepm-1; h++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<=nlstate*2;j++)
     ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++)
     fgets(line, MAXLINE, ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
     puts(line);       
     fputs(line,ficparo);  
   }       for(i=1;i<=nlstate*2;i++)
   ungetc(c,ficpar);        for(j=1;j<=nlstate*2;j++)
           varhe[i][j][(int)age] =0.;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);       printf("%d|",(int)age);fflush(stdout);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 while((c=getc(ficpar))=='#' && c!= EOF){       for(h=0;h<=nhstepm-1;h++){
     ungetc(c,ficpar);        for(k=0;k<=nhstepm-1;k++){
     fgets(line, MAXLINE, ficpar);          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
     puts(line);          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     fputs(line,ficparo);          for(i=1;i<=nlstate*2;i++)
   }            for(j=1;j<=nlstate*2;j++)
   ungetc(c,ficpar);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);      }
  while((c=getc(ficpar))=='#' && c!= EOF){      /* Computing expectancies */
     ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++)
     puts(line);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     fputs(line,ficparo);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   }            
   ungetc(c,ficpar);  /* 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]);*/
    
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);          }
    
   covar=matrix(0,NCOVMAX,1,n);      fprintf(ficreseij,"%3.0f",age );
   cptcovn=0;      cptj=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   ncovmodel=2+cptcovn;          cptj++;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
          }
   /* Read guess parameters */      fprintf(ficreseij,"\n");
   /* Reads comments: lines beginning with '#' */     
   while((c=getc(ficpar))=='#' && c!= EOF){      free_matrix(gm,0,nhstepm,1,nlstate*2);
     ungetc(c,ficpar);      free_matrix(gp,0,nhstepm,1,nlstate*2);
     fgets(line, MAXLINE, ficpar);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
     puts(line);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     fputs(line,ficparo);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    }
   ungetc(c,ficpar);    printf("\n");
      fprintf(ficlog,"\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    free_vector(xp,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(dnewm,1,nlstate*2,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
       fprintf(ficparo,"%1d%1d",i1,j1);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
       printf("%1d%1d",i,j);  }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  /************ Variance ******************/
         printf(" %lf",param[i][j][k]);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
         fprintf(ficparo," %lf",param[i][j][k]);  {
       }    /* Variance of health expectancies */
       fscanf(ficpar,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       printf("\n");    /* double **newm;*/
       fprintf(ficparo,"\n");    double **dnewm,**doldm;
     }    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    int k, cptcode;
     double *xp;
   p=param[1][1];    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
   /* Reads comments: lines beginning with '#' */    double **gradgp, **trgradgp; /* for var p point j */
   while((c=getc(ficpar))=='#' && c!= EOF){    double *gpp, *gmp; /* for var p point j */
     ungetc(c,ficpar);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     fgets(line, MAXLINE, ficpar);    double ***p3mat;
     puts(line);    double age,agelim, hf;
     fputs(line,ficparo);    double ***mobaverage;
   }    int theta;
   ungetc(c,ficpar);    char digit[4];
     char digitp[25];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    char fileresprobmorprev[FILENAMELENGTH];
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){    if(popbased==1){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      if(mobilav!=0)
       printf("%1d%1d",i,j);        strcpy(digitp,"-populbased-mobilav-");
       fprintf(ficparo,"%1d%1d",i1,j1);      else strcpy(digitp,"-populbased-nomobil-");
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar,"%le",&delti3[i][j][k]);    else 
         printf(" %le",delti3[i][j][k]);      strcpy(digitp,"-stablbased-");
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    if (mobilav!=0) {
       fscanf(ficpar,"\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("\n");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficparo,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   }      }
   delti=delti3[1][1];    }
    
   /* Reads comments: lines beginning with '#' */    strcpy(fileresprobmorprev,"prmorprev"); 
   while((c=getc(ficpar))=='#' && c!= EOF){    sprintf(digit,"%-d",ij);
     ungetc(c,ficpar);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     puts(line);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     fputs(line,ficparo);    strcat(fileresprobmorprev,fileres);
   }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   matcov=matrix(1,npar,1,npar);    }
   for(i=1; i <=npar; i++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fscanf(ficpar,"%s",&str);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     printf("%s",str);    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(ficparo,"%s",str);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=1; j <=i; j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar," %le",&matcov[i][j]);      fprintf(ficresprobmorprev," p.%-d SE",j);
       printf(" %.5le",matcov[i][j]);      for(i=1; i<=nlstate;i++)
       fprintf(ficparo," %.5le",matcov[i][j]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
     fscanf(ficpar,"\n");    fprintf(ficresprobmorprev,"\n");
     printf("\n");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     fprintf(ficparo,"\n");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   for(i=1; i <=npar; i++)      exit(0);
     for(j=i+1;j<=npar;j++)    }
       matcov[i][j]=matcov[j][i];    else{
          fprintf(ficgp,"\n# Routine varevsij");
   printf("\n");    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
     /*-------- data file ----------*/      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     if((ficres =fopen(fileres,"w"))==NULL) {      exit(0);
       printf("Problem with resultfile: %s\n", fileres);goto end;    }
     }    else{
     fprintf(ficres,"#%s\n",version);      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");
          fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     if((fic=fopen(datafile,"r"))==NULL)    {    }
       printf("Problem with datafile: %s\n", datafile);goto end;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }  
     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");
     n= lastobs;    fprintf(ficresvij,"# Age");
     severity = vector(1,maxwav);    for(i=1; i<=nlstate;i++)
     outcome=imatrix(1,maxwav+1,1,n);      for(j=1; j<=nlstate;j++)
     num=ivector(1,n);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     moisnais=vector(1,n);    fprintf(ficresvij,"\n");
     annais=vector(1,n);  
     moisdc=vector(1,n);    xp=vector(1,npar);
     andc=vector(1,n);    dnewm=matrix(1,nlstate,1,npar);
     agedc=vector(1,n);    doldm=matrix(1,nlstate,1,nlstate);
     cod=ivector(1,n);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     weight=vector(1,n);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  
     mint=matrix(1,maxwav,1,n);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     anint=matrix(1,maxwav,1,n);    gpp=vector(nlstate+1,nlstate+ndeath);
     s=imatrix(1,maxwav+1,1,n);    gmp=vector(nlstate+1,nlstate+ndeath);
     adl=imatrix(1,maxwav+1,1,n);        trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     tab=ivector(1,NCOVMAX);    
     ncodemax=ivector(1,8);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     i=1;    }
     while (fgets(line, MAXLINE, fic) != NULL)    {    else  hstepm=estepm;   
       if ((i >= firstobs) && (i <=lastobs)) {    /* 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 (j=maxwav;j>=1;j--){       nhstepm is the number of hstepm from age to agelim 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);       nstepm is the number of stepm from age to agelin. 
           strcpy(line,stra);       Look at hpijx to understand the reason of that which relies in memory size
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       and note for a fixed period like k years */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         }       survival function given by stepm (the optimization length). Unfortunately it
               means that if the survival funtion is printed every two years of age and if
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       results. So we changed our mind and took the option of the best precision.
     */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         for (j=ncov;j>=1;j--){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         num[i]=atol(stra);      gp=matrix(0,nhstepm,1,nlstate);
              gm=matrix(0,nhstepm,1,nlstate);
         /*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;}*/  
       for(theta=1; theta <=npar; theta++){
         i=i+1;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }        }
     /* printf("ii=%d", ij);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        scanf("%d",i);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   imx=i-1; /* Number of individuals */  
         if (popbased==1) {
   /* for (i=1; i<=imx; i++){          if(mobilav ==0){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            for(i=1; i<=nlstate;i++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              prlim[i][i]=probs[(int)age][i][ij];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++) 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]));*/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);    
   Tprod=ivector(1,15);        for(j=1; j<= nlstate; j++){
   Tvaraff=ivector(1,15);          for(h=0; h<=nhstepm; h++){
   Tvard=imatrix(1,15,1,2);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   Tage=ivector(1,15);                    gp[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
   if (strlen(model) >1){        }
     j=0, j1=0, k1=1, k2=1;        /* This for computing probability of death (h=1 means
     j=nbocc(model,'+');           computed over hstepm matrices product = hstepm*stepm months) 
     j1=nbocc(model,'*');           as a weighted average of prlim.
     cptcovn=j+1;        */
     cptcovprod=j1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gpp[j]=0.; i<= nlstate; i++)
                gpp[j] += prlim[i][i]*p3mat[i][j][1];
     strcpy(modelsav,model);        }    
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        /* end probability of death */
       printf("Error. Non available option model=%s ",model);  
       goto end;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(i=(j+1); i>=1;i--){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       cutv(stra,strb,modelsav,'+');   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        if (popbased==1) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          if(mobilav ==0){
       /*scanf("%d",i);*/            for(i=1; i<=nlstate;i++)
       if (strchr(strb,'*')) {              prlim[i][i]=probs[(int)age][i][ij];
         cutv(strd,strc,strb,'*');          }else{ /* mobilav */ 
         if (strcmp(strc,"age")==0) {            for(i=1; i<=nlstate;i++)
           cptcovprod--;              prlim[i][i]=mobaverage[(int)age][i][ij];
           cutv(strb,stre,strd,'V');          }
           Tvar[i]=atoi(stre);        }
           cptcovage++;  
             Tage[cptcovage]=i;        for(j=1; j<= nlstate; j++){
             /*printf("stre=%s ", stre);*/          for(h=0; h<=nhstepm; h++){
         }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         else if (strcmp(strd,"age")==0) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           cptcovprod--;          }
           cutv(strb,stre,strc,'V');        }
           Tvar[i]=atoi(stre);        /* This for computing probability of death (h=1 means
           cptcovage++;           computed over hstepm matrices product = hstepm*stepm months) 
           Tage[cptcovage]=i;           as a weighted average of prlim.
         }        */
         else {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cutv(strb,stre,strc,'V');          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           Tvar[i]=ncov+k1;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           cutv(strb,strc,strd,'V');        }    
           Tprod[k1]=i;        /* end probability of death */
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);        for(j=1; j<= nlstate; j++) /* vareij */
           Tvar[cptcovn+k2]=Tvard[k1][1];          for(h=0; h<=nhstepm; h++){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           for (k=1; k<=lastobs;k++)          }
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           k2=k2+2;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }        }
       }  
       else {      } /* End theta */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);      for(h=0; h<=nhstepm; h++) /* veij */
       }        for(j=1; j<=nlstate;j++)
       strcpy(modelsav,stra);            for(theta=1; theta <=npar; theta++)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            trgradg[h][j][theta]=gradg[h][theta][j];
         scanf("%d",i);*/  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 }        for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fclose(fic);      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
     /*  if(mle==1){*/          vareij[i][j][(int)age] =0.;
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;      for(h=0;h<=nhstepm;h++){
     }        for(k=0;k<=nhstepm;k++){
     /*-calculation of age at interview from date of interview and age at death -*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     agev=matrix(1,maxwav,1,imx);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
    for (i=1; i<=imx; i++)            for(j=1;j<=nlstate;j++)
      for(m=2; (m<= maxwav); m++)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        }
          anint[m][i]=9999;      }
          s[m][i]=-1;  
        }      /* pptj */
          matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     for (i=1; i<=imx; i++)  {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   
       for(m=1; (m<= maxwav); m++){     for(j=nlstate+1;j<=nlstate+ndeath;j++)
         if(s[m][i] >0){       for(i=nlstate+1;i<=nlstate+ndeath;i++){
           if (s[m][i] == nlstate+1) {          varppt[j][i]=doldmp[j][i];
             if(agedc[i]>0)      /* end ppptj */
               if(moisdc[i]!=99 && andc[i]!=9999)      /*  x centered again */
               agev[m][i]=agedc[i];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             else {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               if (andc[i]!=9999){   
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      if (popbased==1) {
               agev[m][i]=-1;        if(mobilav ==0){
               }          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=probs[(int)age][i][ij];
           }        }else{ /* mobilav */ 
           else if(s[m][i] !=9){ /* Should no more exist */          for(i=1; i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            prlim[i][i]=mobaverage[(int)age][i][ij];
             if(mint[m][i]==99 || anint[m][i]==9999)        }
               agev[m][i]=1;      }
             else if(agev[m][i] <agemin){      
               agemin=agev[m][i];      /* This for computing probability of death (h=1 means
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
             }         as a weighted average of prlim.
             else if(agev[m][i] >agemax){      */
               agemax=agev[m][i];      for(j=nlstate+1;j<=nlstate+ndeath;j++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
             }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
             /*agev[m][i]=anint[m][i]-annais[i];*/      }    
             /*   agev[m][i] = age[i]+2*m;*/      /* end probability of death */
           }  
           else { /* =9 */      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             agev[m][i]=1;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             s[m][i]=-1;        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]);
         else /*= 0 Unknown */        }
           agev[m][i]=1;      } 
       }      fprintf(ficresprobmorprev,"\n");
      
     }      fprintf(ficresvij,"%.0f ",age );
     for (i=1; i<=imx; i++)  {      for(i=1; i<=nlstate;i++)
       for(m=1; (m<= maxwav); m++){        for(j=1; j<=nlstate;j++){
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           printf("Error: Wrong value in nlstate or ndeath\n");          }
           goto end;      fprintf(ficresvij,"\n");
         }      free_matrix(gp,0,nhstepm,1,nlstate);
       }      free_matrix(gm,0,nhstepm,1,nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(severity,1,maxwav);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_imatrix(outcome,1,maxwav+1,1,n);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_vector(moisnais,1,n);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_vector(annais,1,n);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_matrix(mint,1,maxwav,1,n);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     free_matrix(anint,1,maxwav,1,n);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     free_vector(moisdc,1,n);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     free_vector(andc,1,n);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     wav=ivector(1,imx);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     /* Concatenates waves */    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    /*  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);
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    free_vector(xp,1,npar);
       ncodemax[1]=1;    free_matrix(doldm,1,nlstate,1,nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    free_matrix(dnewm,1,nlstate,1,npar);
          free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    codtab=imatrix(1,100,1,10);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
    h=0;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    m=pow(2,cptcoveff);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
    for(k=1;k<=cptcoveff; k++){    fclose(ficgp);
      for(i=1; i <=(m/pow(2,k));i++){    fclose(fichtm);
        for(j=1; j <= ncodemax[k]; j++){  }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;  /************ Variance of prevlim ******************/
            if (h>m) h=1;codtab[h][k]=j;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
          }  {
        }    /* Variance of prevalence limit */
      }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    }    double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
    /*for(i=1; i <=m ;i++){    int k, cptcode;
      for(k=1; k <=cptcovn; k++){    double *xp;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    double *gp, *gm;
      }    double **gradg, **trgradg;
      printf("\n");    double age,agelim;
    }    int theta;
    scanf("%d",i);*/     
        fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
    /* Calculates basic frequencies. Computes observed prevalence at single age    fprintf(ficresvpl,"# Age");
        and prints on file fileres'p'. */    for(i=1; i<=nlstate;i++)
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xp=vector(1,npar);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    dnewm=matrix(1,nlstate,1,npar);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    doldm=matrix(1,nlstate,1,nlstate);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
          hstepm=1*YEARM; /* Every year of age */
     /* For Powell, parameters are in a vector p[] starting at p[1]    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    agelim = AGESUP;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if(mle==1){      if (stepm >= YEARM) hstepm=1;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     }      gradg=matrix(1,npar,1,nlstate);
          gp=vector(1,nlstate);
     /*--------- results files --------------*/      gm=vector(1,nlstate);
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  
          for(theta=1; theta <=npar; theta++){
    jk=1;        for(i=1; i<=npar; i++){ /* Computes gradient */
    fprintf(ficres,"# Parameters\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    printf("# Parameters\n");        }
    for(i=1,jk=1; i <=nlstate; i++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      for(k=1; k <=(nlstate+ndeath); k++){        for(i=1;i<=nlstate;i++)
        if (k != i)          gp[i] = prlim[i][i];
          {      
            printf("%d%d ",i,k);        for(i=1; i<=npar; i++) /* Computes gradient */
            fprintf(ficres,"%1d%1d ",i,k);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            for(j=1; j <=ncovmodel; j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              printf("%f ",p[jk]);        for(i=1;i<=nlstate;i++)
              fprintf(ficres,"%f ",p[jk]);          gm[i] = prlim[i][i];
              jk++;  
            }        for(i=1;i<=nlstate;i++)
            printf("\n");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
            fprintf(ficres,"\n");      } /* End theta */
          }  
      }      trgradg =matrix(1,nlstate,1,npar);
    }  
  if(mle==1){      for(j=1; j<=nlstate;j++)
     /* Computing hessian and covariance matrix */        for(theta=1; theta <=npar; theta++)
     ftolhess=ftol; /* Usually correct */          trgradg[j][theta]=gradg[theta][j];
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }      for(i=1;i<=nlstate;i++)
     fprintf(ficres,"# Scales\n");        varpl[i][(int)age] =0.;
     printf("# Scales\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
      for(i=1,jk=1; i <=nlstate; i++){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(j=1; j <=nlstate+ndeath; j++){      for(i=1;i<=nlstate;i++)
         if (j!=i) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);      fprintf(ficresvpl,"%.0f ",age );
           for(k=1; k<=ncovmodel;k++){      for(i=1; i<=nlstate;i++)
             printf(" %.5e",delti[jk]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             fprintf(ficres," %.5e",delti[jk]);      fprintf(ficresvpl,"\n");
             jk++;      free_vector(gp,1,nlstate);
           }      free_vector(gm,1,nlstate);
           printf("\n");      free_matrix(gradg,1,npar,1,nlstate);
           fprintf(ficres,"\n");      free_matrix(trgradg,1,nlstate,1,npar);
         }    } /* End age */
       }  
       }    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,npar);
     k=1;    free_matrix(dnewm,1,nlstate,1,nlstate);
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");  }
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;  /************ Variance of one-step probabilities  ******************/
       i1=(i-1)/(ncovmodel*nlstate)+1;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  {
       printf("%s%d%d",alph[k],i1,tab[i]);*/    int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficres,"%3d",i);    int k2, l2, j1,  z1;
       printf("%3d",i);    int k=0,l, cptcode;
       for(j=1; j<=i;j++){    int first=1, first1;
         fprintf(ficres," %.5e",matcov[i][j]);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         printf(" %.5e",matcov[i][j]);    double **dnewm,**doldm;
       }    double *xp;
       fprintf(ficres,"\n");    double *gp, *gm;
       printf("\n");    double **gradg, **trgradg;
       k++;    double **mu;
     }    double age,agelim, cov[NCOVMAX];
        double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     while((c=getc(ficpar))=='#' && c!= EOF){    int theta;
       ungetc(c,ficpar);    char fileresprob[FILENAMELENGTH];
       fgets(line, MAXLINE, ficpar);    char fileresprobcov[FILENAMELENGTH];
       puts(line);    char fileresprobcor[FILENAMELENGTH];
       fputs(line,ficparo);  
     }    double ***varpij;
     ungetc(c,ficpar);  
      strcpy(fileresprob,"prob"); 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     if (fage <= 2) {      printf("Problem with resultfile: %s\n", fileresprob);
       bage = agemin;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       fage = agemax;    }
     }    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
        }
 /*------------ gnuplot -------------*/    strcpy(fileresprobcor,"probcor"); 
 chdir(pathcd);    strcat(fileresprobcor,fileres);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with file graph.gp");goto end;      printf("Problem with resultfile: %s\n", fileresprobcor);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 #ifdef windows    }
   fprintf(ficgp,"cd \"%s\" \n",pathc);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 #endif    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 m=pow(2,cptcoveff);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  /* 1eme*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    for (k1=1; k1<= m ; k1 ++) {    
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 #ifdef windows    fprintf(ficresprob,"# Age");
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 #endif    fprintf(ficresprobcov,"# Age");
 #ifdef unix    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    fprintf(ficresprobcov,"# Age");
 #endif  
   
 for (i=1; i<= nlstate ; i ++) {    for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(j=1; j<=(nlstate+ndeath);j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     for (i=1; i<= nlstate ; i ++) {      }  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   /* fprintf(ficresprob,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresprobcov,"\n");
 }    fprintf(ficresprobcor,"\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);   */
      for (i=1; i<= nlstate ; i ++) {   xp=vector(1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 }      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
 #ifdef unix    first=1;
 fprintf(ficgp,"\nset ter gif small size 400,300");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 #endif      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
    }      exit(0);
   }    }
   /*2 eme*/    else{
       fprintf(ficgp,"\n# Routine varprob");
   for (k1=1; k1<= m ; k1 ++) {    }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
          printf("Problem with html file: %s\n", optionfilehtm);
     for (i=1; i<= nlstate+1 ; i ++) {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       k=2*i;      exit(0);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    }
       for (j=1; j<= nlstate+1 ; j ++) {    else{
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(fichtm,"\n");
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      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");
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      cov[1]=1;
       fprintf(ficgp,"\" t\"\" w l 0,");    tj=cptcoveff;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       for (j=1; j<= nlstate+1 ; j ++) {    j1=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for(t=1; t<=tj;t++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i1=1; i1<=ncodemax[t];i1++){ 
 }          j1++;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        if  (cptcovn>0) {
       else fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresprob, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*3eme*/          fprintf(ficresprobcov, "**********\n#\n");
           
   for (k1=1; k1<= m ; k1 ++) {          fprintf(ficgp, "\n#********** Variable "); 
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=2+nlstate*(cpt-1);          fprintf(ficgp, "**********\n#\n");
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          
       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+i,cpt,i+1);          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]]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     }          
   }          fprintf(ficresprobcor, "\n#********** Variable ");    
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* CV preval stat */          fprintf(ficresprobcor, "**********\n#");    
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<nlstate ; cpt ++) {        
       k=3;        for (age=bage; age<=fage; age ++){ 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          cov[2]=age;
       for (i=1; i< nlstate ; i ++)          for (k=1; k<=cptcovn;k++) {
         fprintf(ficgp,"+$%d",k+i+1);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          }
                for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       l=3+(nlstate+ndeath)*cpt;          for (k=1; k<=cptcovprod;k++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (i=1; i< nlstate ; i ++) {          
         l=3+(nlstate+ndeath)*cpt;          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         fprintf(ficgp,"+$%d",l+i+1);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       }          gp=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            gm=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      
     }          for(theta=1; theta <=npar; theta++){
   }              for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* proba elementaires */            
    for(i=1,jk=1; i <=nlstate; i++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     for(k=1; k <=(nlstate+ndeath); k++){            
       if (k != i) {            k=0;
         for(j=1; j <=ncovmodel; j++){            for(i=1; i<= (nlstate); i++){
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/              for(j=1; j<=(nlstate+ndeath);j++){
           /*fprintf(ficgp,"%s",alph[1]);*/                k=k+1;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                gp[k]=pmmij[i][j];
           jk++;              }
           fprintf(ficgp,"\n");            }
         }            
       }            for(i=1; i<=npar; i++)
     }              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for(jk=1; jk <=m; jk++) {            k=0;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);            for(i=1; i<=(nlstate); i++){
    i=1;              for(j=1; j<=(nlstate+ndeath);j++){
    for(k2=1; k2<=nlstate; k2++) {                k=k+1;
      k3=i;                gm[k]=pmmij[i][j];
      for(k=1; k<=(nlstate+ndeath); k++) {              }
        if (k != k2){            }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       
 ij=1;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         for(j=3; j <=ncovmodel; j++) {              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
           }            for(theta=1; theta <=npar; theta++)
           else              trgradg[j][theta]=gradg[theta][j];
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          
         }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           fprintf(ficgp,")/(1");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                  free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         for(k1=1; k1 <=nlstate; k1++){            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 ij=1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          pmij(pmmij,cov,ncovmodel,x,nlstate);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          
             ij++;          k=0;
           }          for(i=1; i<=(nlstate); i++){
           else            for(j=1; j<=(nlstate+ndeath);j++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              k=k+1;
           }              mu[k][(int) age]=pmmij[i][j];
           fprintf(ficgp,")");            }
         }          }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         i=i+ncovmodel;              varpij[i][j][(int)age] = doldm[i][j];
        }  
      }          /*printf("\n%d ",(int)age);
    }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            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]));
                }*/
   fclose(ficgp);  
              fprintf(ficresprob,"\n%d ",(int)age);
 chdir(path);          fprintf(ficresprobcov,"\n%d ",(int)age);
              fprintf(ficresprobcor,"\n%d ",(int)age);
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     free_ivector(num,1,n);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     free_vector(agedc,1,n);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     fclose(ficparo);          }
     fclose(ficres);          i=0;
     /*  }*/          for (k=1; k<=(nlstate);k++){
                for (l=1; l<=(nlstate+ndeath);l++){ 
    /*________fin mle=1_________*/              i=i++;
                  fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
     /* No more information from the sample is required now */                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /* Reads comments: lines beginning with '#' */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   while((c=getc(ficpar))=='#' && c!= EOF){              }
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          }/* end of loop for state */
     puts(line);        } /* end of loop for age */
     fputs(line,ficparo);  
   }        /* Confidence intervalle of pij  */
   ungetc(c,ficpar);        /*
            fprintf(ficgp,"\nset noparametric;unset label");
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          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);
 /*--------- index.htm --------*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   strcpy(optionfilehtm,optionfile);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   strcat(optionfilehtm,".htm");        */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm);goto end;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   }        first1=1;
         for (k2=1; k2<=(nlstate);k2++){
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>            if(l2==k2) continue;
 Total number of observations=%d <br>            j=(k2-1)*(nlstate+ndeath)+l2;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>            for (k1=1; k1<=(nlstate);k1++){
 <hr  size=\"2\" color=\"#EC5E5E\">              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 <li>Outputs files<br><br>\n                if(l1==k1) continue;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                i=(k1-1)*(nlstate+ndeath)+l1;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                if(i<=j) continue;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                for (age=bage; age<=fage; age ++){ 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                  if ((int)age %5==0){
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                    mu1=mu[i][(int) age]/stepm*YEARM ;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                    mu2=mu[j][(int) age]/stepm*YEARM;
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>                    c12=cv12/sqrt(v1*v2);
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  fprintf(fichtm," <li>Graphs</li><p>");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
  m=cptcoveff;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                    /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
  j1=0;                    v12=-v21;
  for(k1=1; k1<=m;k1++){                    v22=v11;
    for(i1=1; i1<=ncodemax[k1];i1++){                    tnalp=v21/v11;
        j1++;                    if(first1==1){
        if (cptcovn > 0) {                      first1=0;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
          for (cpt=1; cpt<=cptcoveff;cpt++)                    }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);                    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);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                    /*printf(fignu*/
        }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                        if(first==1){
        for(cpt=1; cpt<nlstate;cpt++){                      first=0;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>                      fprintf(ficgp,"\nset parametric;unset label");
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
        }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     for(cpt=1; cpt<=nlstate;cpt++) {                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
 interval) in state (%d): v%s%d%d.gif <br>                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
      }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
      for(cpt=1; cpt<=nlstate;cpt++) {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>                      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",\
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
      }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                    }else{
 health expectancies in states (1) and (2): e%s%d.gif<br>                      first=0;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
 fprintf(fichtm,"\n</body>");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
  }                      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",\
 fclose(fichtm);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   /*--------------- Prevalence limit --------------*/                    }/* if first */
                    } /* age mod 5 */
   strcpy(filerespl,"pl");                } /* end loop age */
   strcat(filerespl,fileres);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                first=1;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              } /*l12 */
   }            } /* k12 */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          } /*l1 */
   fprintf(ficrespl,"#Prevalence limit\n");        }/* k1 */
   fprintf(ficrespl,"#Age ");      } /* loop covariates */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   prlim=matrix(1,nlstate,1,nlstate);    free_vector(xp,1,npar);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprob);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprobcov);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprobcor);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficgp);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fclose(fichtm);
   k=0;  }
   agebase=agemin;  
   agelim=agemax;  
   ftolpl=1.e-10;  /******************* Printing html file ***********/
   i1=cptcoveff;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   if (cptcovn < 1){i1=1;}                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   for(cptcov=1;cptcov<=i1;cptcov++){                    int popforecast, int estepm ,\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    double jprev1, double mprev1,double anprev1, \
         k=k+1;                    double jprev2, double mprev2,double anprev2){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    int jj1, k1, i1, cpt;
         fprintf(ficrespl,"\n#******");    /*char optionfilehtm[FILENAMELENGTH];*/
         for(j=1;j<=cptcoveff;j++)    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with %s \n",optionfilehtm), exit(0);
         fprintf(ficrespl,"******\n");      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
            }
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
           fprintf(ficrespl,"%.0f",age );   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
           for(i=1; i<=nlstate;i++)   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
           fprintf(ficrespl," %.5f", prlim[i][i]);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
           fprintf(ficrespl,"\n");   - Life expectancies by age and initial health status (estepm=%2d months): 
         }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
       }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     }  
   fclose(ficrespl);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   /*------------- h Pij x at various ages ------------*/   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {   jj1=0;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
   printf("Computing pij: result on file '%s' \n", filerespij);       jj1++;
         if (cptcovn > 0) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /*if (stepm<=24) stepsize=2;*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   agelim=AGESUP;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   hstepm=stepsize*YEARM; /* Every year of age */       }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       /* 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>
   k=0;  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   for(cptcov=1;cptcov<=i1;cptcov++){       /* Quasi-incidences */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       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>
       k=k+1;  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
         fprintf(ficrespij,"\n#****** ");         /* Stable prevalence in each health state */
         for(j=1;j<=cptcoveff;j++)         for(cpt=1; cpt<nlstate;cpt++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
         fprintf(ficrespij,"******\n");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
                 }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       for(cpt=1; cpt<=nlstate;cpt++) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       }
           oldm=oldms;savm=savms;       fprintf(fichtm,"\n<br>- Total life expectancy by age and
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    health expectancies in states (1) and (2): e%s%d.png<br>
           fprintf(ficrespij,"# Age");  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
           for(i=1; i<=nlstate;i++)     } /* end i1 */
             for(j=1; j<=nlstate+ndeath;j++)   }/* End k1 */
               fprintf(ficrespij," %1d-%1d",i,j);   fprintf(fichtm,"</ul>");
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
             for(i=1; i<=nlstate;i++)   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
               for(j=1; j<=nlstate+ndeath;j++)   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
             fprintf(ficrespij,"\n");   - 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 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
           fprintf(ficrespij,"\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);
         }  
     }   if(popforecast==1) fprintf(fichtm,"\n
   }   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          <br>",fileres,fileres,fileres,fileres);
    else 
   fclose(ficrespij);     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   /*---------- Forecasting ------------------*/  
    m=cptcoveff;
   strcpy(fileresf,"f");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {   jj1=0;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);       jj1++;
        if (cptcovn > 0) {
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
  free_matrix(agev,1,maxwav,1,imx);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /* Mobile average */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   if (mobilav==1) {  interval) in state (%d): v%s%d%d.png <br>
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)       }
       for (i=1; i<=nlstate;i++)     } /* end i1 */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   }/* End k1 */
           mobaverage[(int)agedeb][i][cptcod]=0.;   fprintf(fichtm,"</ul>");
      fclose(fichtm);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){  }
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /******************* Gnuplot file **************/
           for (cpt=0;cpt<=4;cpt++){  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int ng;
         }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       }      printf("Problem with file %s",optionfilegnuplot);
     }        fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   }    }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*#ifdef windows */
   if (stepm<=12) stepsize=1;      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   agelim=AGESUP;  m=pow(2,cptcoveff);
   hstepm=stepsize*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
    k=0;     for (k1=1; k1<= m ; k1 ++) {
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       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);
       k=k+1;  
       fprintf(ficresf,"\n#****** ");       for (i=1; i<= nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       }
       fprintf(ficresf,"******\n");       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);
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");       for (i=1; i<= nlstate ; i ++) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for (agedeb=fage; agedeb>=bage; agedeb--){       } 
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        if (mobilav==1) {       for (i=1; i<= nlstate ; i ++) {
         for(j=1; j<=nlstate;j++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }       }  
         else {       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
           for(j=1; j<=nlstate;j++)     }
           fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);    }
         }      /*2 eme*/
       for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");    
       }    for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nforecast;cpt++)        fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
              
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for (i=1; i<= nlstate+1 ; i ++) {
         nhstepm = nhstepm/hstepm;        k=2*i;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         oldm=oldms;savm=savms;          else fprintf(ficgp," \%%*lf (\%%*lf)");
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }   
                        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         for (h=0; h<=nhstepm; h++){        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);
          if (h*hstepm/YEARM*stepm==cpt)        for (j=1; j<= nlstate+1 ; j ++) {
             fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                    else fprintf(ficgp," \%%*lf (\%%*lf)");
                  }   
           for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficgp,"\" t\"\" w l 0,");
             kk1=0.;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
             for(i=1; i<=nlstate;i++) {                for (j=1; j<= nlstate+1 ; j ++) {
               if (mobilav==1)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];          else fprintf(ficgp," \%%*lf (\%%*lf)");
               else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];        }   
             }            if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);        else fprintf(ficgp,"\" t\"\" w l 0,");
           }      }
         }    }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
       }    /*3eme*/
     }    
   }    for (k1=1; k1<= m ; k1 ++) { 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (cpt=1; cpt<= nlstate ; cpt ++) {
   free_imatrix(s,1,maxwav+1,1,n);        k=2+nlstate*(2*cpt-2);
   free_vector(weight,1,n);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   fclose(ficresf);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   /*---------- Health expectancies and variances ------------*/        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   strcpy(filerest,"t");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   strcat(filerest,fileres);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   if((ficrest=fopen(filerest,"w"))==NULL) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   }          
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        */
         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);
   strcpy(filerese,"e");          
   strcat(filerese,fileres);        } 
   if((ficreseij=fopen(filerese,"w"))==NULL) {      }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }    
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
  strcpy(fileresv,"v");      for (cpt=1; cpt<nlstate ; cpt ++) {
   strcat(fileresv,fileres);        k=3;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   }        
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
   k=0;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   for(cptcov=1;cptcov<=i1;cptcov++){        
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        l=3+(nlstate+ndeath)*cpt;
       k=k+1;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
       fprintf(ficrest,"\n#****** ");        for (i=1; i< nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++)          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"+$%d",l+i+1);
       fprintf(ficrest,"******\n");        }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       fprintf(ficreseij,"\n#****** ");      } 
       for(j=1;j<=cptcoveff;j++)    }  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficresvij,"\n#****** ");      for(k=1; k <=(nlstate+ndeath); k++){
       for(j=1;j<=cptcoveff;j++)        if (k != i) {
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for(j=1; j <=ncovmodel; j++){
       fprintf(ficresvij,"******\n");            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            fprintf(ficgp,"\n");
       oldm=oldms;savm=savms;          }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      }
       oldm=oldms;savm=savms;     }
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
           for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");       for(jk=1; jk <=m; jk++) {
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       fprintf(ficrest,"\n");         if (ng==2)
                   fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       hf=1;         else
       if (stepm >= YEARM) hf=stepm/YEARM;           fprintf(ficgp,"\nset title \"Probability\"\n");
       epj=vector(1,nlstate+1);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
       for(age=bage; age <=fage ;age++){         i=1;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         for(k2=1; k2<=nlstate; k2++) {
         if (popbased==1) {           k3=i;
           for(i=1; i<=nlstate;i++)           for(k=1; k<=(nlstate+ndeath); k++) {
             prlim[i][i]=probs[(int)age][i][k];             if (k != k2){
         }               if(ng==2)
                         fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
         fprintf(ficrest," %.0f",age);               else
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {               ij=1;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];               for(j=3; j <=ncovmodel; j++) {
           }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           epj[nlstate+1] +=epj[j];                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
         }                   ij++;
         for(i=1, vepp=0.;i <=nlstate;i++)                 }
           for(j=1;j <=nlstate;j++)                 else
             vepp += vareij[i][j][(int)age];                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));               }
         for(j=1;j <=nlstate;j++){               fprintf(ficgp,")/(1");
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));               
         }               for(k1=1; k1 <=nlstate; k1++){   
         fprintf(ficrest,"\n");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       }                 ij=1;
     }                 for(j=3; j <=ncovmodel; j++){
   }                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                             ij++;
                    }
                    else
  fclose(ficreseij);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  fclose(ficresvij);                 }
   fclose(ficrest);                 fprintf(ficgp,")");
   fclose(ficpar);               }
   free_vector(epj,1,nlstate+1);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   /*  scanf("%d ",i); */               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
   /*------- Variance limit prevalence------*/               }
            } /* end k */
 strcpy(fileresvpl,"vpl");         } /* end k2 */
   strcat(fileresvpl,fileres);       } /* end jk */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     } /* end ng */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     fclose(ficgp); 
     exit(0);  }  /* end gnuplot */
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
   /*************** Moving average **************/
  k=0;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
  for(cptcov=1;cptcov<=i1;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, cpt, cptcod;
      k=k+1;    int modcovmax =1;
      fprintf(ficresvpl,"\n#****** ");    int mobilavrange, mob;
      for(j=1;j<=cptcoveff;j++)    double age;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                                   a covariate has 2 modalities */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
      oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
    }      if(mobilav==1) mobilavrange=5; /* default */
  }      else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
   fclose(ficresvpl);        for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
   /*---------- End : free ----------------*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      /* We keep the original values on the extreme ages bage, fage and for 
           fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         we use a 5 terms etc. until the borders are no more concerned. 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          for (i=1; i<=nlstate;i++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   free_matrix(matcov,1,npar,1,npar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   free_vector(delti,1,npar);                }
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            }
           }
   printf("End of Imach\n");        }/* end age */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      }/* end mob */
      }else return -1;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    return 0;
   /*printf("Total time was %d uSec.\n", total_usecs);*/  }/* End movingaverage */
   /*------ End -----------*/  
   
   /************** Forecasting ******************/
  end:  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){
 #ifdef windows    /* proj1, year, month, day of starting projection 
  chdir(pathcd);       agemin, agemax range of age
 #endif       dateprev1 dateprev2 range of dates during which prevalence is computed
         
  system("..\\gp37mgw\\wgnuplot graph.plt");    */
     int yearp, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 #ifdef windows    int *popage;
   while (z[0] != 'q') {    double calagedatem, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     chdir(pathcd);    double *popeffectif,*popcount;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    double ***p3mat;
     scanf("%s",z);    double ***mobaverage;
     if (z[0] == 'c') system("./imach");    char fileresf[FILENAMELENGTH];
     else if (z[0] == 'e') {  
       chdir(path);    agelim=AGESUP;
       system(optionfilehtm);    calagedatem=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; /* offset
     }        from the mean date of interviews between dateprev1 and dateprev2
     else if (z[0] == 'q') exit(0);        (in fractional years converted to fractional months) */
   }    /* Computing age-specific starting prevalence between exact 
 #endif       dateprev1 and dateprev2 (in float years) and
 }   shifting ages from calagedatem.
     */
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedatem);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f ",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     for(cptcov=1, k=0;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*yearp)) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                   
                 }
                 if (h==(int)(calagedatem+12*yearp)){
                   fprintf(ficresf," %.3f", kk1);
                           
                 }
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       }
     }
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   /************** Forecasting ******************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedatem;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    
     /* 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 */
   }
   
   

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changed lines
  Added in v.1.69


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