Diff for /imach/src/imach.c between versions 1.10 and 1.72

version 1.10, 2001/05/09 14:25:42 version 1.72, 2003/03/28 13:33:56
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      /* $Id$
 /*********************** 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 */
   #define AGESUP 130
 int *wav; /* Number of waves for this individuual 0 is possible */  #define AGEBASE 40
 int maxwav; /* Maxim number of waves */  #ifdef windows
 int jmin, jmax; /* min, max spacing between 2 waves */  #define DIRSEPARATOR '\\'
 int mle, weightopt;  #define ODIRSEPARATOR '/'
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #else
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define DIRSEPARATOR '/'
 double jmean; /* Mean space between 2 waves */  #define ODIRSEPARATOR '\\'
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #endif
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  char version[80]="Imach version 0.93, February 2003, INED-EUROREVES ";
 FILE *ficgp, *fichtm;  int erreur; /* Error number */
 FILE *ficreseij;  int nvar;
   char filerese[FILENAMELENGTH];  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
  FILE  *ficresvij;  int npar=NPARMAX;
   char fileresv[FILENAMELENGTH];  int nlstate=2; /* Number of live states */
  FILE  *ficresvpl;  int ndeath=1; /* Number of dead states */
   char fileresvpl[FILENAMELENGTH];  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 #define NR_END 1  
 #define FREE_ARG char*  int *wav; /* Number of waves for this individuual 0 is possible */
 #define FTOL 1.0e-10  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 #define NRANSI  int mle, weightopt;
 #define ITMAX 200  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define TOL 2.0e-4  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 #define CGOLD 0.3819660  double jmean; /* Mean space between 2 waves */
 #define ZEPS 1.0e-10  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define GOLD 1.618034  FILE *ficlog;
 #define GLIMIT 100.0  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define TINY 1.0e-20  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 static double maxarg1,maxarg2;  FILE *ficreseij;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char filerese[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvij;
    char fileresv[FILENAMELENGTH];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  FILE  *ficresvpl;
 #define rint(a) floor(a+0.5)  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 static double sqrarg;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 int imx;  char filelog[FILENAMELENGTH]; /* Log file */
 int stepm;  char filerest[FILENAMELENGTH];
 /* Stepm, step in month: minimum step interpolation*/  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij;  #define NR_END 1
   #define FREE_ARG char*
 double *weight;  #define FTOL 1.0e-10
 int **s; /* Status */  
 double *agedc, **covar, idx;  #define NRANSI 
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define ITMAX 200 
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define TOL 2.0e-4 
 double ftolhess; /* Tolerance for computing hessian */  
   #define CGOLD 0.3819660 
 /**************** split *************************/  #define ZEPS 1.0e-10 
 static  int split( char *path, char *dirc, char *name )  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
    char *s;                             /* pointer */  #define GOLD 1.618034 
    int  l1, l2;                         /* length counters */  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  static double maxarg1,maxarg2;
    s = strrchr( path, '\\' );           /* find last / */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    if ( s == NULL ) {                   /* no directory, so use current */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #if     defined(__bsd__)                /* get current working directory */    
       extern char       *getwd( );  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
       if ( getwd( dirc ) == NULL ) {  
 #else  static double sqrarg;
       extern char       *getcwd( );  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  int imx; 
          return( GLOCK_ERROR_GETCWD );  int stepm;
       }  /* Stepm, step in month: minimum step interpolation*/
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  int estepm;
       s++;                              /* after this, the filename */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int m,nb;
       strcpy( name, s );                /* save file name */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       dirc[l1-l2] = 0;                  /* add zero */  double **pmmij, ***probs;
    }  double dateintmean=0;
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  double *weight;
    return( 0 );                         /* we're done */  int **s; /* Status */
 }  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 *************************/
   int i;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int lg=20;  {
   i=0;    char  *ss;                            /* pointer */
   lg=strlen(t);    int   l1, l2;                         /* length counters */
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    l1 = strlen(path );                   /* length of path */
     if (t[i]== '\\') s[i]='/';    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 int nbocc(char *s, char occ)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 {  #if     defined(__bsd__)                /* get current working directory */
   int i,j=0;      extern char *getwd( );
   int lg=20;  
   i=0;      if ( getwd( dirc ) == NULL ) {
   lg=strlen(s);  #else
   for(i=0; i<= lg; i++) {      extern char *getcwd( );
   if  (s[i] == occ ) j++;  
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   return j;  #endif
 }        return( GLOCK_ERROR_GETCWD );
       }
 void cutv(char *u,char *v, char*t, char occ)      strcpy( name, path );               /* we've got it */
 {    } else {                              /* strip direcotry from path */
   int i,lg,j,p=0;      ss++;                               /* after this, the filename */
   i=0;      l2 = strlen( ss );                  /* length of filename */
   for(j=0; j<=strlen(t)-1; j++) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      strcpy( name, ss );         /* save file name */
   }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   lg=strlen(t);    }
   for(j=0; j<p; j++) {    l1 = strlen( dirc );                  /* length of directory */
     (u[j] = t[j]);  #ifdef windows
   }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
      u[p]='\0';  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    for(j=0; j<= lg; j++) {  #endif
     if (j>=(p+1))(v[j-p-1] = t[j]);    ss = strrchr( name, '.' );            /* find last / */
   }    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 /********************** nrerror ********************/    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 void nrerror(char error_text[])    finame[l1-l2]= 0;
 {    return( 0 );                          /* we're done */
   fprintf(stderr,"ERREUR ...\n");  }
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  
 }  /******************************************/
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  void replace(char *s, char*t)
 {  {
   double *v;    int i;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    int lg=20;
   if (!v) nrerror("allocation failure in vector");    i=0;
   return v-nl+NR_END;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /************************ free vector ******************/      if (t[i]== '\\') s[i]='/';
 void free_vector(double*v, int nl, int nh)    }
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  int nbocc(char *s, char occ)
   {
 /************************ivector *******************************/    int i,j=0;
 int *ivector(long nl,long nh)    int lg=20;
 {    i=0;
   int *v;    lg=strlen(s);
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    for(i=0; i<= lg; i++) {
   if (!v) nrerror("allocation failure in ivector");    if  (s[i] == occ ) j++;
   return v-nl+NR_END;    }
 }    return j;
   }
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  void cutv(char *u,char *v, char*t, char occ)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    /* cuts string t into u and v where u is ended by char occ excluding it
 }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
        gives u="abcedf" and v="ghi2j" */
 /******************* imatrix *******************************/    int i,lg,j,p=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    i=0;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    for(j=0; j<=strlen(t)-1; j++) {
 {      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);
   /* allocate pointers to rows */    for(j=0; j<p; j++) {
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));      (u[j] = t[j]);
   if (!m) nrerror("allocation failure 1 in matrix()");    }
   m += NR_END;       u[p]='\0';
   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()");  
   m[nrl] += NR_END;  /********************** nrerror ********************/
   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");
   /* return pointer to array of pointers to rows */    fprintf(stderr,"%s\n",error_text);
   return m;    exit(EXIT_FAILURE);
 }  }
   /*********************** vector *******************/
 /****************** free_imatrix *************************/  double *vector(int nl, int nh)
 void free_imatrix(m,nrl,nrh,ncl,nch)  {
       int **m;    double *v;
       long nch,ncl,nrh,nrl;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      /* free an int matrix allocated by imatrix() */    if (!v) nrerror("allocation failure in vector");
 {    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 *******************************/  {
 double **matrix(long nrl, long nrh, long ncl, long nch)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  /************************ivector *******************************/
   int *ivector(long nl,long nh)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    int *v;
   m += NR_END;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m -= nrl;    if (!v) nrerror("allocation failure in ivector");
     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()");  
   m[nrl] += NR_END;  /******************free ivector **************************/
   m[nrl] -= ncl;  void free_ivector(int *v, long nl, long nh)
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    free((FREE_ARG)(v+nl-NR_END));
   return m;  }
 }  
   /******************* imatrix *******************************/
 /*************************free matrix ************************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG)(m+nrl-NR_END));    int **m; 
 }    
     /* allocate pointers to rows */ 
 /******************* ma3x *******************************/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()"); 
 {    m += NR_END; 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m -= nrl; 
   double ***m;    
     
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    /* allocate rows and set pointers to them */ 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m += NR_END;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m -= nrl;    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    /* return pointer to array of pointers to rows */ 
     return m; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  } 
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /****************** free_imatrix *************************/
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  void free_imatrix(m,nrl,nrh,ncl,nch)
   m[nrl][ncl] += NR_END;        int **m;
   m[nrl][ncl] -= nll;        long nch,ncl,nrh,nrl; 
   for (j=ncl+1; j<=nch; j++)       /* free an int matrix allocated by imatrix() */ 
     m[nrl][j]=m[nrl][j-1]+nlay;  { 
      free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for (i=nrl+1; i<=nrh; i++) {    free((FREE_ARG) (m+nrl-NR_END)); 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  } 
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  /******************* matrix *******************************/
   }  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 ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m += NR_END;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m -= nrl;
   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()");
 /***************** f1dim *************************/    m[nrl] += NR_END;
 extern int ncom;    m[nrl] -= ncl;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      return m;
 double f1dim(double x)  }
 {  
   int j;  /*************************free matrix ************************/
   double f;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double *xt;  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
   xt=vector(1,ncom);    free((FREE_ARG)(m+nrl-NR_END));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  }
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  /******************* ma3x *******************************/
   return f;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 }  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 /*****************brent *************************/    double ***m;
 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*)));
   int iter;    if (!m) nrerror("allocation failure 1 in matrix()");
   double a,b,d,etemp;    m += NR_END;
   double fu,fv,fw,fx;    m -= nrl;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double e=0.0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
   a=(ax < cx ? ax : cx);    m[nrl] -= ncl;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     xm=0.5*(a+b);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl][ncl] += NR_END;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl][ncl] -= nll;
     printf(".");fflush(stdout);    for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG      m[nrl][j]=m[nrl][j-1]+nlay;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    for (i=nrl+1; i<=nrh; i++) {
 #endif      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      for (j=ncl+1; j<=nch; j++) 
       *xmin=x;        m[i][j]=m[i][j-1]+nlay;
       return fx;    }
     }    return m;
     ftemp=fu;  }
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /*************************free ma3x ************************/
       q=(x-v)*(fx-fw);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if (q > 0.0) p = -p;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       q=fabs(q);    free((FREE_ARG)(m+nrl-NR_END));
       etemp=e;  }
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /***************** f1dim *************************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern int ncom; 
       else {  extern double *pcom,*xicom;
         d=p/q;  extern double (*nrfunc)(double []); 
         u=x+d;   
         if (u-a < tol2 || b-u < tol2)  double f1dim(double x) 
           d=SIGN(tol1,xm-x);  { 
       }    int j; 
     } else {    double f;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    double *xt; 
     }   
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    xt=vector(1,ncom); 
     fu=(*f)(u);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     if (fu <= fx) {    f=(*nrfunc)(xt); 
       if (u >= x) a=x; else b=x;    free_vector(xt,1,ncom); 
       SHFT(v,w,x,u)    return f; 
         SHFT(fv,fw,fx,fu)  } 
         } else {  
           if (u < x) a=u; else b=u;  /*****************brent *************************/
           if (fu <= fw || w == x) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
             v=w;  { 
             w=u;    int iter; 
             fv=fw;    double a,b,d,etemp;
             fw=fu;    double fu,fv,fw,fx;
           } else if (fu <= fv || v == x || v == w) {    double ftemp;
             v=u;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             fv=fu;    double e=0.0; 
           }   
         }    a=(ax < cx ? ax : cx); 
   }    b=(ax > cx ? ax : cx); 
   nrerror("Too many iterations in brent");    x=w=v=bx; 
   *xmin=x;    fw=fv=fx=(*f)(x); 
   return fx;    for (iter=1;iter<=ITMAX;iter++) { 
 }      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 /****************** mnbrak ***********************/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      fprintf(ficlog,".");fflush(ficlog);
             double (*func)(double))  #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);
   double ulim,u,r,q, dum;      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 fu;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
    #endif
   *fa=(*func)(*ax);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   *fb=(*func)(*bx);        *xmin=x; 
   if (*fb > *fa) {        return fx; 
     SHFT(dum,*ax,*bx,dum)      } 
       SHFT(dum,*fb,*fa,dum)      ftemp=fu;
       }      if (fabs(e) > tol1) { 
   *cx=(*bx)+GOLD*(*bx-*ax);        r=(x-w)*(fx-fv); 
   *fc=(*func)(*cx);        q=(x-v)*(fx-fw); 
   while (*fb > *fc) {        p=(x-v)*q-(x-w)*r; 
     r=(*bx-*ax)*(*fb-*fc);        q=2.0*(q-r); 
     q=(*bx-*cx)*(*fb-*fa);        if (q > 0.0) p = -p; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        q=fabs(q); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        etemp=e; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        e=d; 
     if ((*bx-u)*(u-*cx) > 0.0) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       fu=(*func)(u);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        else { 
       fu=(*func)(u);          d=p/q; 
       if (fu < *fc) {          u=x+d; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))          if (u-a < tol2 || b-u < tol2) 
           SHFT(*fb,*fc,fu,(*func)(u))            d=SIGN(tol1,xm-x); 
           }        } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      } else { 
       u=ulim;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       fu=(*func)(u);      } 
     } else {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       u=(*cx)+GOLD*(*cx-*bx);      fu=(*f)(u); 
       fu=(*func)(u);      if (fu <= fx) { 
     }        if (u >= x) a=x; else b=x; 
     SHFT(*ax,*bx,*cx,u)        SHFT(v,w,x,u) 
       SHFT(*fa,*fb,*fc,fu)          SHFT(fv,fw,fx,fu) 
       }          } else { 
 }            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
 /*************** linmin ************************/              v=w; 
               w=u; 
 int ncom;              fv=fw; 
 double *pcom,*xicom;              fw=fu; 
 double (*nrfunc)(double []);            } else if (fu <= fv || v == x || v == w) { 
                v=u; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))              fv=fu; 
 {            } 
   double brent(double ax, double bx, double cx,          } 
                double (*f)(double), double tol, double *xmin);    } 
   double f1dim(double x);    nrerror("Too many iterations in brent"); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    *xmin=x; 
               double *fc, double (*func)(double));    return fx; 
   int j;  } 
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /****************** mnbrak ***********************/
    
   ncom=n;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   pcom=vector(1,n);              double (*func)(double)) 
   xicom=vector(1,n);  { 
   nrfunc=func;    double ulim,u,r,q, dum;
   for (j=1;j<=n;j++) {    double fu; 
     pcom[j]=p[j];   
     xicom[j]=xi[j];    *fa=(*func)(*ax); 
   }    *fb=(*func)(*bx); 
   ax=0.0;    if (*fb > *fa) { 
   xx=1.0;      SHFT(dum,*ax,*bx,dum) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        SHFT(dum,*fb,*fa,dum) 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        } 
 #ifdef DEBUG    *cx=(*bx)+GOLD*(*bx-*ax); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *fc=(*func)(*cx); 
 #endif    while (*fb > *fc) { 
   for (j=1;j<=n;j++) {      r=(*bx-*ax)*(*fb-*fc); 
     xi[j] *= xmin;      q=(*bx-*cx)*(*fb-*fa); 
     p[j] += xi[j];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   free_vector(xicom,1,n);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   free_vector(pcom,1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
 }        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 /*************** powell ************************/        fu=(*func)(u); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        if (fu < *fc) { 
             double (*func)(double []))          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 {            SHFT(*fb,*fc,fu,(*func)(u)) 
   void linmin(double p[], double xi[], int n, double *fret,            } 
               double (*func)(double []));      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int i,ibig,j;        u=ulim; 
   double del,t,*pt,*ptt,*xit;        fu=(*func)(u); 
   double fp,fptt;      } else { 
   double *xits;        u=(*cx)+GOLD*(*cx-*bx); 
   pt=vector(1,n);        fu=(*func)(u); 
   ptt=vector(1,n);      } 
   xit=vector(1,n);      SHFT(*ax,*bx,*cx,u) 
   xits=vector(1,n);        SHFT(*fa,*fb,*fc,fu) 
   *fret=(*func)(p);        } 
   for (j=1;j<=n;j++) pt[j]=p[j];  } 
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /*************** linmin ************************/
     ibig=0;  
     del=0.0;  int ncom; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double *pcom,*xicom;
     for (i=1;i<=n;i++)  double (*nrfunc)(double []); 
       printf(" %d %.12f",i, p[i]);   
     printf("\n");  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (i=1;i<=n;i++) {  { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double brent(double ax, double bx, double cx, 
       fptt=(*fret);                 double (*f)(double), double tol, double *xmin); 
 #ifdef DEBUG    double f1dim(double x); 
       printf("fret=%lf \n",*fret);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #endif                double *fc, double (*func)(double)); 
       printf("%d",i);fflush(stdout);    int j; 
       linmin(p,xit,n,fret,func);    double xx,xmin,bx,ax; 
       if (fabs(fptt-(*fret)) > del) {    double fx,fb,fa;
         del=fabs(fptt-(*fret));   
         ibig=i;    ncom=n; 
       }    pcom=vector(1,n); 
 #ifdef DEBUG    xicom=vector(1,n); 
       printf("%d %.12e",i,(*fret));    nrfunc=func; 
       for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      pcom[j]=p[j]; 
         printf(" x(%d)=%.12e",j,xit[j]);      xicom[j]=xi[j]; 
       }    } 
       for(j=1;j<=n;j++)    ax=0.0; 
         printf(" p=%.12e",p[j]);    xx=1.0; 
       printf("\n");    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 #endif    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #ifdef DEBUG    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       int k[2],l;  #endif
       k[0]=1;    for (j=1;j<=n;j++) { 
       k[1]=-1;      xi[j] *= xmin; 
       printf("Max: %.12e",(*func)(p));      p[j] += xi[j]; 
       for (j=1;j<=n;j++)    } 
         printf(" %.12e",p[j]);    free_vector(xicom,1,n); 
       printf("\n");    free_vector(pcom,1,n); 
       for(l=0;l<=1;l++) {  } 
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /*************** powell ************************/
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         }              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, 
 #endif                double (*func)(double [])); 
     int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
       free_vector(xit,1,n);    double fp,fptt;
       free_vector(xits,1,n);    double *xits;
       free_vector(ptt,1,n);    pt=vector(1,n); 
       free_vector(pt,1,n);    ptt=vector(1,n); 
       return;    xit=vector(1,n); 
     }    xits=vector(1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    *fret=(*func)(p); 
     for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
       ptt[j]=2.0*p[j]-pt[j];    for (*iter=1;;++(*iter)) { 
       xit[j]=p[j]-pt[j];      fp=(*fret); 
       pt[j]=p[j];      ibig=0; 
     }      del=0.0; 
     fptt=(*func)(ptt);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     if (fptt < fp) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      for (i=1;i<=n;i++) 
       if (t < 0.0) {        printf(" %d %.12f",i, p[i]);
         linmin(p,xit,n,fret,func);      fprintf(ficlog," %d %.12f",i, p[i]);
         for (j=1;j<=n;j++) {      printf("\n");
           xi[j][ibig]=xi[j][n];      fprintf(ficlog,"\n");
           xi[j][n]=xit[j];      for (i=1;i<=n;i++) { 
         }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 #ifdef DEBUG        fptt=(*fret); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #ifdef DEBUG
         for(j=1;j<=n;j++)        printf("fret=%lf \n",*fret);
           printf(" %.12e",xit[j]);        fprintf(ficlog,"fret=%lf \n",*fret);
         printf("\n");  #endif
 #endif        printf("%d",i);fflush(stdout);
       }        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
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        printf("%d %.12e",i,(*fret));
 {        fprintf(ficlog,"%d %.12e",i,(*fret));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        for (j=1;j<=n;j++) {
      matrix by transitions matrix until convergence is reached */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   int i, ii,j,k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double min, max, maxmin, maxmax,sumnew=0.;        }
   double **matprod2();        for(j=1;j<=n;j++) {
   double **out, cov[NCOVMAX], **pmij();          printf(" p=%.12e",p[j]);
   double **newm;          fprintf(ficlog," p=%.12e",p[j]);
   double agefin, delaymax=50 ; /* Max number of years to converge */        }
         printf("\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)        fprintf(ficlog,"\n");
     for (j=1;j<=nlstate+ndeath;j++){  #endif
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
    cov[1]=1.;        int k[2],l;
          k[0]=1;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        k[1]=-1;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        printf("Max: %.12e",(*func)(p));
     newm=savm;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     /* Covariates have to be included here again */        for (j=1;j<=n;j++) {
      cov[2]=agefin;          printf(" %.12e",p[j]);
            fprintf(ficlog," %.12e",p[j]);
       for (k=1; k<=cptcovn;k++) {        }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        printf("\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]);*/        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
       for (k=1; k<=cptcovage;k++)          for (j=1;j<=n;j++) {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for (k=1; k<=cptcovprod;k++)            printf("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]]];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          printf("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]);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #endif
   
     savm=oldm;  
     oldm=newm;        free_vector(xit,1,n); 
     maxmax=0.;        free_vector(xits,1,n); 
     for(j=1;j<=nlstate;j++){        free_vector(ptt,1,n); 
       min=1.;        free_vector(pt,1,n); 
       max=0.;        return; 
       for(i=1; i<=nlstate; i++) {      } 
         sumnew=0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      for (j=1;j<=n;j++) { 
         prlim[i][j]= newm[i][j]/(1-sumnew);        ptt[j]=2.0*p[j]-pt[j]; 
         max=FMAX(max,prlim[i][j]);        xit[j]=p[j]-pt[j]; 
         min=FMIN(min,prlim[i][j]);        pt[j]=p[j]; 
       }      } 
       maxmin=max-min;      fptt=(*func)(ptt); 
       maxmax=FMAX(maxmax,maxmin);      if (fptt < fp) { 
     }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     if(maxmax < ftolpl){        if (t < 0.0) { 
       return prlim;          linmin(p,xit,n,fret,func); 
     }          for (j=1;j<=n;j++) { 
   }            xi[j][ibig]=xi[j][n]; 
 }            xi[j][n]=xit[j]; 
           }
 /*************** transition probabilities **********/  #ifdef DEBUG
           printf("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 )          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {          for(j=1;j<=n;j++){
   double s1, s2;            printf(" %.12e",xit[j]);
   /*double t34;*/            fprintf(ficlog," %.12e",xit[j]);
   int i,j,j1, nc, ii, jj;          }
           printf("\n");
     for(i=1; i<= nlstate; i++){          fprintf(ficlog,"\n");
     for(j=1; j<i;j++){  #endif
       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);*/  } 
       }  
       ps[i][j]=s2;  /**** Prevalence limit (stable prevalence)  ****************/
       /*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++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];       matrix by transitions matrix until convergence is reached */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }    int i, ii,j,k;
       ps[i][j]=s2;    double min, max, maxmin, maxmax,sumnew=0.;
     }    double **matprod2();
   }    double **out, cov[NCOVMAX], **pmij();
   for(i=1; i<= nlstate; i++){    double **newm;
      s1=0;    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=i+1; j<=nlstate+ndeath; j++)      for (j=1;j<=nlstate+ndeath;j++){
       s1+=exp(ps[i][j]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     ps[i][i]=1./(s1+1.);      }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];     cov[1]=1.;
     for(j=i+1; j<=nlstate+ndeath; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   } /* end i */      newm=savm;
       /* Covariates have to be included here again */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){       cov[2]=agefin;
     for(jj=1; jj<= nlstate+ndeath; jj++){    
       ps[ii][jj]=0;        for (k=1; k<=cptcovn;k++) {
       ps[ii][ii]=1;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   }        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        for (k=1; k<=cptcovprod;k++)
     for(jj=1; jj<= nlstate+ndeath; jj++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      printf("%lf ",ps[ii][jj]);  
    }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     printf("\n ");        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     printf("\n ");printf("%lf ",cov[2]);*/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      savm=oldm;
   goto end;*/      oldm=newm;
     return ps;      maxmax=0.;
 }      for(j=1;j<=nlstate;j++){
         min=1.;
 /**************** Product of 2 matrices ******************/        max=0.;
         for(i=1; i<=nlstate; i++) {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          sumnew=0;
 {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          prlim[i][j]= newm[i][j]/(1-sumnew);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          max=FMAX(max,prlim[i][j]);
   /* in, b, out are matrice of pointers which should have been initialized          min=FMIN(min,prlim[i][j]);
      before: only the contents of out is modified. The function returns        }
      a pointer to pointers identical to out */        maxmin=max-min;
   long i, j, k;        maxmax=FMAX(maxmax,maxmin);
   for(i=nrl; i<= nrh; i++)      }
     for(k=ncolol; k<=ncoloh; k++)      if(maxmax < ftolpl){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        return prlim;
         out[i][k] +=in[i][j]*b[j][k];      }
     }
   return out;  }
 }  
   /*************** transition probabilities ***************/ 
   
 /************* Higher Matrix Product ***************/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double s1, s2;
 {    /*double t34;*/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int i,j,j1, nc, ii, jj;
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      for(i=1; i<= nlstate; i++){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      for(j=1; j<i;j++){
      (typically every 2 years instead of every month which is too big).        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      Model is determined by parameters x and covariates have to be          /*s2 += param[i][j][nc]*cov[nc];*/
      included manually here.          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      */        }
         ps[i][j]=s2;
   int i, j, d, h, k;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double **out, cov[NCOVMAX];      }
   double **newm;      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Hstepm could be zero and should return the unit matrix */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for (i=1;i<=nlstate+ndeath;i++)          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     for (j=1;j<=nlstate+ndeath;j++){        }
       oldm[i][j]=(i==j ? 1.0 : 0.0);        ps[i][j]=s2;
       po[i][j][0]=(i==j ? 1.0 : 0.0);      }
     }    }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      /*ps[3][2]=1;*/
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){    for(i=1; i<= nlstate; i++){
       newm=savm;       s1=0;
       /* Covariates have to be included here again */      for(j=1; j<i; j++)
       cov[1]=1.;        s1+=exp(ps[i][j]);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      for(j=i+1; j<=nlstate+ndeath; j++)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        s1+=exp(ps[i][j]);
 for (k=1; k<=cptcovage;k++)      ps[i][i]=1./(s1+1.);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for(j=1; j<i; j++)
    for (k=1; k<=cptcovprod;k++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    } /* end i */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      for(jj=1; jj<= nlstate+ndeath; jj++){
       savm=oldm;        ps[ii][jj]=0;
       oldm=newm;        ps[ii][ii]=1;
     }      }
     for(i=1; i<=nlstate+ndeath; i++)    }
       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]);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
          */      for(jj=1; jj<= nlstate+ndeath; jj++){
       }       printf("%lf ",ps[ii][jj]);
   } /* end h */     }
   return po;      printf("\n ");
 }      }
       printf("\n ");printf("%lf ",cov[2]);*/
   /*
 /*************** log-likelihood *************/    for(i=1; i<= npar; i++) printf("%f ",x[i]);
 double func( double *x)    goto end;*/
 {      return ps;
   int i, ii, j, k, mi, d, kk;  }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /**************** Product of 2 matrices ******************/
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   long ipmx;  {
   /*extern weight */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   /* We are differentiating ll according to initial status */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* in, b, out are matrice of pointers which should have been initialized 
   /*for(i=1;i<imx;i++)       before: only the contents of out is modified. The function returns
     printf(" %d\n",s[4][i]);       a pointer to pointers identical to out */
   */    long i, j, k;
   cov[1]=1.;    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
   for(k=1; k<=nlstate; k++) ll[k]=0.;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          out[i][k] +=in[i][j]*b[j][k];
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){    return out;
       for (ii=1;ii<=nlstate+ndeath;ii++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /************* Higher Matrix Product ***************/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  {
         }    /* Computes the transition matrix starting at age 'age' over 
               'nhstepm*hstepm*stepm' months (i.e. until
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       nhstepm*hstepm matrices. 
         savm=oldm;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         oldm=newm;       (typically every 2 years instead of every month which is too big 
               for the memory).
               Model is determined by parameters x and covariates have to be 
       } /* end mult */       included manually here. 
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;    int i, j, d, h, k;
       sw += weight[i];    double **out, cov[NCOVMAX];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double **newm;
     } /* end of wave */  
   } /* end of individual */    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      for (j=1;j<=nlstate+ndeath;j++){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   return -l;      }
 }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 /*********** Maximum Likelihood Estimation ***************/        newm=savm;
         /* Covariates have to be included here again */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        cov[1]=1.;
 {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int i,j, iter;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double **xi,*delti;        for (k=1; k<=cptcovage;k++)
   double fret;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   xi=matrix(1,npar,1,npar);        for (k=1; k<=cptcovprod;k++)
   for (i=1;i<=npar;i++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   powell(p,xi,npar,ftol,&iter,&fret,func);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        savm=oldm;
         oldm=newm;
 }      }
       for(i=1; i<=nlstate+ndeath; i++)
 /**** Computes Hessian and covariance matrix ***/        for(j=1;j<=nlstate+ndeath;j++) {
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          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]);
   double  **a,**y,*x,pd;           */
   double **hess;        }
   int i, j,jk;    } /* end h */
   int *indx;    return po;
   }
   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[]) ;  /*************** log-likelihood *************/
   void ludcmp(double **a, int npar, int *indx, double *d) ;  double func( double *x)
   {
     int i, ii, j, k, mi, d, kk;
   hess=matrix(1,npar,1,npar);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double sw; /* Sum of weights */
   for (i=1;i<=npar;i++){    double lli; /* Individual log likelihood */
     printf("%d",i);fflush(stdout);    int s1, s2;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double bbh, survp;
     /*printf(" %f ",p[i]);*/    long ipmx;
   }    /*extern weight */
     /* We are differentiating ll according to initial status */
   for (i=1;i<=npar;i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for (j=1;j<=npar;j++)  {    /*for(i=1;i<imx;i++) 
       if (j>i) {      printf(" %d\n",s[4][i]);
         printf(".%d%d",i,j);fflush(stdout);    */
         hess[i][j]=hessij(p,delti,i,j);    cov[1]=1.;
         hess[j][i]=hess[i][j];  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
   }    if(mle==1){
   printf("\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   a=matrix(1,npar,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   y=matrix(1,npar,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   x=vector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   indx=ivector(1,npar);            }
   for (i=1;i<=npar;i++)          for(d=0; d<dh[mi][i]; d++){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            newm=savm;
   ludcmp(a,npar,indx,&pd);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   for (j=1;j<=npar;j++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=1;i<=npar;i++) x[i]=0;            }
     x[j]=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     lubksb(a,npar,indx,x);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1;i<=npar;i++){            savm=oldm;
       matcov[i][j]=x[i];            oldm=newm;
     }          } /* end mult */
   }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   printf("\n#Hessian matrix#\n");          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (i=1;i<=npar;i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (j=1;j<=npar;j++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       printf("%.3e ",hess[i][j]);           * 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");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   /* Recompute Inverse */           * -stepm/2 to stepm/2 .
   for (i=1;i<=npar;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           * For stepm > 1 the results are less biased than in previous versions. 
   ludcmp(a,npar,indx,&pd);           */
           s1=s[mw[mi][i]][i];
   /*  printf("\n#Hessian matrix recomputed#\n");          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   for (j=1;j<=npar;j++) {          /* bias is positive if real duration
     for (i=1;i<=npar;i++) x[i]=0;           * is higher than the multiple of stepm and negative otherwise.
     x[j]=1;           */
     lubksb(a,npar,indx,x);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for (i=1;i<=npar;i++){          if( s2 > nlstate){ 
       y[i][j]=x[i];            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       printf("%.3e ",y[i][j]);               to the likelihood is the probability to die between last step unit time and current 
     }               step unit time, which is also the differences between probability to die before dh 
     printf("\n");               and probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   */          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
   free_matrix(a,1,npar,1,npar);          and not the date of a change in health state. The former idea was
   free_matrix(y,1,npar,1,npar);          to consider that at each interview the state was recorded
   free_vector(x,1,npar);          (healthy, disable or death) and IMaCh was corrected; but when we
   free_ivector(indx,1,npar);          introduced the exact date of death then we should have modified
   free_matrix(hess,1,npar,1,npar);          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 }          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
 /*************** hessian matrix ****************/          probability to die within a month. Thanks to Chris
 double hessii( double x[], double delta, int theta, double delti[])          Jackson for correcting this bug.  Former versions increased
 {          mortality artificially. The bad side is that we add another loop
   int i;          which slows down the processing. The difference can be up to 10%
   int l=1, lmax=20;          lower mortality.
   double k1,k2;            */
   double p2[NPARMAX+1];            lli=log(out[s1][s2] - savm[s1][s2]);
   double res;          }else{
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double fx;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   int k=0,kmax=10;          } 
   double l1;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   fx=func(x);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   for (i=1;i<=npar;i++) p2[i]=x[i];          ipmx +=1;
   for(l=0 ; l <=lmax; l++){          sw += weight[i];
     l1=pow(10,l);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     delts=delt;        } /* end of wave */
     for(k=1 ; k <kmax; k=k+1){      } /* end of individual */
       delt = delta*(l1*k);    }  else if(mle==2){
       p2[theta]=x[theta] +delt;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       k1=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       p2[theta]=x[theta]-delt;        for(mi=1; mi<= wav[i]-1; mi++){
       k2=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
       /*res= (k1-2.0*fx+k2)/delt/delt; */            for (j=1;j<=nlstate+ndeath;j++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                    savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef DEBUG            }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          for(d=0; d<=dh[mi][i]; d++){
 #endif            newm=savm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            for (kk=1; kk<=cptcovage;kk++) {
         k=kmax;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         k=kmax; l=lmax*10.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            oldm=newm;
         delts=delt;          } /* end mult */
       }        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
   delti[theta]=delts;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   return res;           * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
 }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 double hessij( double x[], double delti[], int thetai,int thetaj)           * probability in order to take into account the bias as a fraction of the way
 {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int i;           * -stepm/2 to stepm/2 .
   int l=1, l1, lmax=20;           * For stepm=1 the results are the same as for previous versions of Imach.
   double k1,k2,k3,k4,res,fx;           * For stepm > 1 the results are less biased than in previous versions. 
   double p2[NPARMAX+1];           */
   int k;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   fx=func(x);          bbh=(double)bh[mi][i]/(double)stepm; 
   for (k=1; k<=2; k++) {          /* bias is positive if real duration
     for (i=1;i<=npar;i++) p2[i]=x[i];           * is higher than the multiple of stepm and negative otherwise.
     p2[thetai]=x[thetai]+delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          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 */
     k1=func(p2)-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]));*/
            /*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 */
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*if(lli ==000.0)*/
     k2=func(p2)-fx;          /*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;
     p2[thetai]=x[thetai]-delti[thetai]/k;          sw += weight[i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     k3=func(p2)-fx;        } /* end of wave */
        } /* end of individual */
     p2[thetai]=x[thetai]-delti[thetai]/k;    }  else if(mle==3){  /* exponential inter-extrapolation */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     k4=func(p2)-fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(mi=1; mi<= wav[i]-1; mi++){
 #ifdef DEBUG          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            for (j=1;j<=nlstate+ndeath;j++){
 #endif              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;            }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 /************** Inverse of matrix **************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void ludcmp(double **a, int n, int *indx, double *d)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i,imax,j,k;            }
   double big,dum,sum,temp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *vv;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   vv=vector(1,n);            oldm=newm;
   *d=1.0;          } /* end mult */
   for (i=1;i<=n;i++) {        
     big=0.0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (j=1;j<=n;j++)          /* But now since version 0.9 we anticipate for bias and large stepm.
       if ((temp=fabs(a[i][j])) > big) big=temp;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * (in months) between two waves is not a multiple of stepm, we rounded to 
     vv[i]=1.0/big;           * 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
   for (j=1;j<=n;j++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     for (i=1;i<j;i++) {           * probability in order to take into account the bias as a fraction of the way
       sum=a[i][j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];           * -stepm/2 to stepm/2 .
       a[i][j]=sum;           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
     big=0.0;           */
     for (i=j;i<=n;i++) {          s1=s[mw[mi][i]][i];
       sum=a[i][j];          s2=s[mw[mi+1][i]][i];
       for (k=1;k<j;k++)          bbh=(double)bh[mi][i]/(double)stepm; 
         sum -= a[i][k]*a[k][j];          /* bias is positive if real duration
       a[i][j]=sum;           * is higher than the multiple of stepm and negative otherwise.
       if ( (dum=vv[i]*fabs(sum)) >= big) {           */
         big=dum;          /* 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 */
         imax=i;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
     if (j != imax) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for (k=1;k<=n;k++) {          ipmx +=1;
         dum=a[imax][k];          sw += weight[i];
         a[imax][k]=a[j][k];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         a[j][k]=dum;        } /* end of wave */
       }      } /* end of individual */
       *d = -(*d);    }else{  /* ml=4 no inter-extrapolation */
       vv[imax]=vv[j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     indx[j]=imax;        for(mi=1; mi<= wav[i]-1; mi++){
     if (a[j][j] == 0.0) a[j][j]=TINY;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (j != n) {            for (j=1;j<=nlstate+ndeath;j++){
       dum=1.0/(a[j][j]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
   }          for(d=0; d<dh[mi][i]; d++){
   free_vector(vv,1,n);  /* Doesn't work */            newm=savm;
 ;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void lubksb(double **a, int n, int *indx, double b[])            }
 {          
   int i,ii=0,ip,j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double sum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   for (i=1;i<=n;i++) {            oldm=newm;
     ip=indx[i];          } /* end mult */
     sum=b[ip];        
     b[ip]=b[i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     if (ii)          ipmx +=1;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          sw += weight[i];
     else if (sum) ii=i;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     b[i]=sum;        } /* end of wave */
   }      } /* end of individual */
   for (i=n;i>=1;i--) {    } /* End of if */
     sum=b[i];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     b[i]=sum/a[i][i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   }    return -l;
 }  }
   
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  /*********** Maximum Likelihood Estimation ***************/
 {  /* Some frequencies */  
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    int i,j, iter;
   double *pp;    double **xi,*delti;
   double pos;    double fret;
   FILE *ficresp;    xi=matrix(1,npar,1,npar);
   char fileresp[FILENAMELENGTH];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   pp=vector(1,nlstate);        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(fileresp,"p");    powell(p,xi,npar,ftol,&iter,&fret,func);
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     printf("Problem with prevalence resultfile: %s\n", fileresp);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     exit(0);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
   /**** Computes Hessian and covariance matrix ***/
   j=cptcoveff;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
     double  **a,**y,*x,pd;
   for(k1=1; k1<=j;k1++){    double **hess;
    for(i1=1; i1<=ncodemax[k1];i1++){    int i, j,jk;
        j1++;    int *indx;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
          scanf("%d", i);*/    double hessii(double p[], double delta, int theta, double delti[]);
         for (i=-1; i<=nlstate+ndeath; i++)      double hessij(double p[], double delti[], int i, int j);
          for (jk=-1; jk<=nlstate+ndeath; jk++)      void lubksb(double **a, int npar, int *indx, double b[]) ;
            for(m=agemin; m <= agemax+3; m++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
              freq[i][jk][m]=0;  
            hess=matrix(1,npar,1,npar);
        for (i=1; i<=imx; i++) {  
          bool=1;    printf("\nCalculation of the hessian matrix. Wait...\n");
          if  (cptcovn>0) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
            for (z1=1; z1<=cptcoveff; z1++)    for (i=1;i<=npar;i++){
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      printf("%d",i);fflush(stdout);
                bool=0;      fprintf(ficlog,"%d",i);fflush(ficlog);
          }      hess[i][i]=hessii(p,ftolhess,i,delti);
           if (bool==1) {      /*printf(" %f ",p[i]);*/
            for(m=firstpass; m<=lastpass-1; m++){      /*printf(" %lf ",hess[i][i]);*/
              if(agev[m][i]==0) agev[m][i]=agemax+1;    }
              if(agev[m][i]==1) agev[m][i]=agemax+2;    
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for (i=1;i<=npar;i++) {
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      for (j=1;j<=npar;j++)  {
            }        if (j>i) { 
          }          printf(".%d%d",i,j);fflush(stdout);
        }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         if  (cptcovn>0) {          hess[i][j]=hessij(p,delti,i,j);
          fprintf(ficresp, "\n#********** Variable ");          hess[j][i]=hess[i][j];    
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*printf(" %lf ",hess[i][j]);*/
        fprintf(ficresp, "**********\n#");        }
         }      }
        for(i=1; i<=nlstate;i++)    }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    printf("\n");
        fprintf(ficresp, "\n");    fprintf(ficlog,"\n");
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     if(i==(int)agemax+3)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       printf("Total");    
     else    a=matrix(1,npar,1,npar);
       printf("Age %d", i);    y=matrix(1,npar,1,npar);
     for(jk=1; jk <=nlstate ; jk++){    x=vector(1,npar);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    indx=ivector(1,npar);
         pp[jk] += freq[jk][m][i];    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(jk=1; jk <=nlstate ; jk++){    ludcmp(a,npar,indx,&pd);
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    for (j=1;j<=npar;j++) {
       if(pp[jk]>=1.e-10)      for (i=1;i<=npar;i++) x[i]=0;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      x[j]=1;
       else      lubksb(a,npar,indx,x);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      for (i=1;i<=npar;i++){ 
     }        matcov[i][j]=x[i];
     for(jk=1; jk <=nlstate ; jk++){      }
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    }
         pp[jk] += freq[jk][m][i];  
     }    printf("\n#Hessian matrix#\n");
     for(jk=1,pos=0; jk <=nlstate ; jk++)    fprintf(ficlog,"\n#Hessian matrix#\n");
       pos += pp[jk];    for (i=1;i<=npar;i++) { 
     for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=npar;j++) { 
       if(pos>=1.e-5)        printf("%.3e ",hess[i][j]);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        fprintf(ficlog,"%.3e ",hess[i][j]);
       else      }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      printf("\n");
       if( i <= (int) agemax){      fprintf(ficlog,"\n");
         if(pos>=1.e-5)    }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
       else    /* Recompute Inverse */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     }    ludcmp(a,npar,indx,&pd);
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)    /*  printf("\n#Hessian matrix recomputed#\n");
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)    for (j=1;j<=npar;j++) {
       fprintf(ficresp,"\n");      for (i=1;i<=npar;i++) x[i]=0;
     printf("\n");      x[j]=1;
     }      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
  }        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   fclose(ficresp);        fprintf(ficlog,"%.3e ",y[i][j]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);      printf("\n");
       fprintf(ficlog,"\n");
 }  /* End of Freq */    }
     */
 /************* Waves Concatenation ***************/  
     free_matrix(a,1,npar,1,npar);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    free_matrix(y,1,npar,1,npar);
 {    free_vector(x,1,npar);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    free_ivector(indx,1,npar);
      Death is a valid wave (if date is known).    free_matrix(hess,1,npar,1,npar);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.  }
      */  
   /*************** hessian matrix ****************/
   int i, mi, m;  double hessii( double x[], double delta, int theta, double delti[])
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  {
      double sum=0., jmean=0.;*/    int i;
     int l=1, lmax=20;
 int j, k=0,jk, ju, jl;    double k1,k2;
      double sum=0.;    double p2[NPARMAX+1];
 jmin=1e+5;    double res;
  jmax=-1;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 jmean=0.;    double fx;
   for(i=1; i<=imx; i++){    int k=0,kmax=10;
     mi=0;    double l1;
     m=firstpass;  
     while(s[m][i] <= nlstate){    fx=func(x);
       if(s[m][i]>=1)    for (i=1;i<=npar;i++) p2[i]=x[i];
         mw[++mi][i]=m;    for(l=0 ; l <=lmax; l++){
       if(m >=lastpass)      l1=pow(10,l);
         break;      delts=delt;
       else      for(k=1 ; k <kmax; k=k+1){
         m++;        delt = delta*(l1*k);
     }/* end while */        p2[theta]=x[theta] +delt;
     if (s[m][i] > nlstate){        k1=func(p2)-fx;
       mi++;     /* Death is another wave */        p2[theta]=x[theta]-delt;
       /* if(mi==0)  never been interviewed correctly before death */        k2=func(p2)-fx;
          /* Only death is a correct wave */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       mw[mi][i]=m;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     }        
   #ifdef DEBUG
     wav[i]=mi;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     if(mi==0)        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   for(i=1; i<=imx; i++){          k=kmax;
     for(mi=1; mi<wav[i];mi++){        }
       if (stepm <=0)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         dh[mi][i]=1;          k=kmax; l=lmax*10.;
       else{        }
         if (s[mw[mi+1][i]][i] > nlstate) {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           if (agedc[i] < 2*AGESUP) {          delts=delt;
           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;    delti[theta]=delts;
           else if (j <= jmin)jmin=j;    return res; 
           sum=sum+j;    
           if (j<0) printf("j=%d num=%d ",j,i);  }
           }  
         }  double hessij( double x[], double delti[], int thetai,int thetaj)
         else{  {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int i;
           k=k+1;    int l=1, l1, lmax=20;
           if (j >= jmax) jmax=j;    double k1,k2,k3,k4,res,fx;
           else if (j <= jmin)jmin=j;    double p2[NPARMAX+1];
           sum=sum+j;    int k;
         }  
         jk= j/stepm;    fx=func(x);
         jl= j -jk*stepm;    for (k=1; k<=2; k++) {
         ju= j -(jk+1)*stepm;      for (i=1;i<=npar;i++) p2[i]=x[i];
         if(jl <= -ju)      p2[thetai]=x[thetai]+delti[thetai]/k;
           dh[mi][i]=jk;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         else      k1=func(p2)-fx;
           dh[mi][i]=jk+1;    
         if(dh[mi][i]==0)      p2[thetai]=x[thetai]+delti[thetai]/k;
           dh[mi][i]=1; /* At least one step */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       }      k2=func(p2)-fx;
     }    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
   jmean=sum/k;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      k3=func(p2)-fx;
 }    
 /*********** Tricode ****************************/      p2[thetai]=x[thetai]-delti[thetai]/k;
 void tricode(int *Tvar, int **nbcode, int imx)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 {      k4=func(p2)-fx;
   int Ndum[20],ij=1, k, j, i;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   int cptcode=0;  #ifdef DEBUG
   cptcoveff=0;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        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);
   for (k=0; k<19; k++) Ndum[k]=0;  #endif
   for (k=1; k<=7; k++) ncodemax[k]=0;    }
     return res;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  }
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  /************** Inverse of matrix **************/
       Ndum[ij]++;  void ludcmp(double **a, int n, int *indx, double *d) 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  { 
       if (ij > cptcode) cptcode=ij;    int i,imax,j,k; 
     }    double big,dum,sum,temp; 
     double *vv; 
     for (i=0; i<=cptcode; i++) {   
       if(Ndum[i]!=0) ncodemax[j]++;    vv=vector(1,n); 
     }    *d=1.0; 
     ij=1;    for (i=1;i<=n;i++) { 
       big=0.0; 
       for (j=1;j<=n;j++) 
     for (i=1; i<=ncodemax[j]; i++) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
       for (k=0; k<=19; k++) {      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         if (Ndum[k] != 0) {      vv[i]=1.0/big; 
           nbcode[Tvar[j]][ij]=k;    } 
           ij++;    for (j=1;j<=n;j++) { 
         }      for (i=1;i<j;i++) { 
         if (ij > ncodemax[j]) break;        sum=a[i][j]; 
       }          for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
   }        } 
       big=0.0; 
  for (k=0; k<19; k++) Ndum[k]=0;      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
  for (i=1; i<=ncovmodel; i++) {        for (k=1;k<j;k++) 
       ij=Tvar[i];          sum -= a[i][k]*a[k][j]; 
       Ndum[ij]++;        a[i][j]=sum; 
     }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
  ij=1;          imax=i; 
  for (i=1; i<=10; i++) {        } 
    if((Ndum[i]!=0) && (i<=ncov)){      } 
      Tvaraff[ij]=i;      if (j != imax) { 
      ij++;        for (k=1;k<=n;k++) { 
    }          dum=a[imax][k]; 
  }          a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
     cptcoveff=ij-1;        } 
 }        *d = -(*d); 
         vv[imax]=vv[j]; 
 /*********** Health Expectancies ****************/      } 
       indx[j]=imax; 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      if (a[j][j] == 0.0) a[j][j]=TINY; 
 {      if (j != n) { 
   /* Health expectancies */        dum=1.0/(a[j][j]); 
   int i, j, nhstepm, hstepm, h;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   double age, agelim,hf;      } 
   double ***p3mat;    } 
      free_vector(vv,1,n);  /* Doesn't work */
   fprintf(ficreseij,"# Health expectancies\n");  ;
   fprintf(ficreseij,"# Age");  } 
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  void lubksb(double **a, int n, int *indx, double b[]) 
       fprintf(ficreseij," %1d-%1d",i,j);  { 
   fprintf(ficreseij,"\n");    int i,ii=0,ip,j; 
     double sum; 
   hstepm=1*YEARM; /*  Every j years of age (in month) */   
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
   agelim=AGESUP;      sum=b[ip]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      b[ip]=b[i]; 
     /* nhstepm age range expressed in number of stepm */      if (ii) 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     /* Typically if 20 years = 20*12/6=40 stepm */      else if (sum) ii=i; 
     if (stepm >= YEARM) hstepm=1;      b[i]=sum; 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    } 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=n;i>=1;i--) { 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      sum=b[i]; 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        b[i]=sum/a[i][i]; 
     } 
   } 
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)  /************ Frequencies ********************/
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  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)
           eij[i][j][(int)age] +=p3mat[i][j][h];  {  /* Some frequencies */
         }    
        int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     hf=1;    int first;
     if (stepm >= YEARM) hf=stepm/YEARM;    double ***freq; /* Frequencies */
     fprintf(ficreseij,"%.0f",age );    double *pp;
     for(i=1; i<=nlstate;i++)    double pos, k2, dateintsum=0,k2cpt=0;
       for(j=1; j<=nlstate;j++){    FILE *ficresp;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    char fileresp[FILENAMELENGTH];
       }    
     fprintf(ficreseij,"\n");    pp=vector(1,nlstate);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    strcpy(fileresp,"p");
 }    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
 /************ Variance ******************/      printf("Problem with prevalence resultfile: %s\n", fileresp);
 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)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 {      exit(0);
   /* Variance of health expectancies */    }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   double **newm;    j1=0;
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    j=cptcoveff;
   int k, cptcode;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    double *xp;  
   double **gp, **gm;    first=1;
   double ***gradg, ***trgradg;  
   double ***p3mat;    for(k1=1; k1<=j;k1++){
   double age,agelim;      for(i1=1; i1<=ncodemax[k1];i1++){
   int theta;        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    fprintf(ficresvij,"# Covariances of life expectancies\n");          scanf("%d", i);*/
   fprintf(ficresvij,"# Age");        for (i=-1; i<=nlstate+ndeath; i++)  
   for(i=1; i<=nlstate;i++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     for(j=1; j<=nlstate;j++)            for(m=agemin; m <= agemax+3; m++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);              freq[i][jk][m]=0;
   fprintf(ficresvij,"\n");        
         dateintsum=0;
   xp=vector(1,npar);        k2cpt=0;
   dnewm=matrix(1,nlstate,1,npar);        for (i=1; i<=imx; i++) {
   doldm=matrix(1,nlstate,1,nlstate);          bool=1;
            if  (cptcovn>0) {
   hstepm=1*YEARM; /* Every year of age */            for (z1=1; z1<=cptcoveff; z1++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   agelim = AGESUP;                bool=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 (bool==1){
     if (stepm >= YEARM) hstepm=1;            for(m=firstpass; m<=lastpass; m++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              k2=anint[m][i]+(mint[m][i]/12.);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                if(agev[m][i]==0) agev[m][i]=agemax+1;
     gp=matrix(0,nhstepm,1,nlstate);                if(agev[m][i]==1) agev[m][i]=agemax+2;
     gm=matrix(0,nhstepm,1,nlstate);                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for(theta=1; theta <=npar; theta++){                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */                }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                
       }                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                    dateintsum=dateintsum+k2;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                  k2cpt++;
       for(j=1; j<= nlstate; j++){                }
         for(h=0; h<=nhstepm; h++){              }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          }
         }        }
       }         
            fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if  (cptcovn>0) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            fprintf(ficresp, "\n#********** Variable "); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(j=1; j<= nlstate; j++){          fprintf(ficresp, "**********\n#");
         for(h=0; h<=nhstepm; h++){        }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for(i=1; i<=nlstate;i++) 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         }        fprintf(ficresp, "\n");
       }        
       for(j=1; j<= nlstate; j++)        for(i=(int)agemin; i <= (int)agemax+3; i++){
         for(h=0; h<=nhstepm; h++){          if(i==(int)agemax+3){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            fprintf(ficlog,"Total");
         }          }else{
     } /* End theta */            if(first==1){
               first=0;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              printf("See log file for details...\n");
             }
     for(h=0; h<=nhstepm; h++)            fprintf(ficlog,"Age %d", i);
       for(j=1; j<=nlstate;j++)          }
         for(theta=1; theta <=npar; theta++)          for(jk=1; jk <=nlstate ; jk++){
           trgradg[h][j][theta]=gradg[h][theta][j];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
     for(i=1;i<=nlstate;i++)          }
       for(j=1;j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
         vareij[i][j][(int)age] =0.;            for(m=-1, pos=0; m <=0 ; m++)
     for(h=0;h<=nhstepm;h++){              pos += freq[jk][m][i];
       for(k=0;k<=nhstepm;k++){            if(pp[jk]>=1.e-10){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              if(first==1){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for(i=1;i<=nlstate;i++)              }
           for(j=1;j<=nlstate;j++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             vareij[i][j][(int)age] += doldm[i][j];            }else{
       }              if(first==1)
     }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     h=1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     if (stepm >= YEARM) h=stepm/YEARM;            }
     fprintf(ficresvij,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       }              pp[jk] += freq[jk][m][i];
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);          for(jk=1,pos=0; jk <=nlstate ; jk++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            pos += pp[jk];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          for(jk=1; jk <=nlstate ; jk++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(pos>=1.e-5){
   } /* End age */              if(first==1)
                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   free_matrix(doldm,1,nlstate,1,npar);            }else{
   free_matrix(dnewm,1,nlstate,1,nlstate);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 /************ Variance of prevlim ******************/            if( i <= (int) agemax){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)              if(pos>=1.e-5){
 {                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
   /* Variance of prevalence limit */                probs[i][jk][j1]= pp[jk]/pos;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                /*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 **newm;              }
   double **dnewm,**doldm;              else
   int i, j, nhstepm, hstepm;                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
   int k, cptcode;            }
   double *xp;          }
   double *gp, *gm;          
   double **gradg, **trgradg;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   double age,agelim;            for(m=-1; m <=nlstate+ndeath; m++)
   int theta;              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficresvpl,"# Age");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   for(i=1; i<=nlstate;i++)              }
       fprintf(ficresvpl," %1d-%1d",i,i);          if(i <= (int) agemax)
   fprintf(ficresvpl,"\n");            fprintf(ficresp,"\n");
           if(first==1)
   xp=vector(1,npar);            printf("Others in log...\n");
   dnewm=matrix(1,nlstate,1,npar);          fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate,1,nlstate);        }
        }
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    dateintmean=dateintsum/k2cpt; 
   agelim = AGESUP;   
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fclose(ficresp);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     if (stepm >= YEARM) hstepm=1;    free_vector(pp,1,nlstate);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
     gradg=matrix(1,npar,1,nlstate);    /* End of Freq */
     gp=vector(1,nlstate);  }
     gm=vector(1,nlstate);  
   /************ Prevalence ********************/
     for(theta=1; theta <=npar; theta++){  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for(i=1; i<=npar; i++){ /* Computes gradient */  {  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       }       in each health status at the date of interview (if between dateprev1 and dateprev2).
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       We still use firstpass and lastpass as another selection.
       for(i=1;i<=nlstate;i++)    */
         gp[i] = prlim[i][i];   
        int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       for(i=1; i<=npar; i++) /* Computes gradient */    double ***freq; /* Frequencies */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double *pp;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double pos; 
       for(i=1;i<=nlstate;i++)    double  y2; /* in fractional years */
         gm[i] = prlim[i][i];  
     pp=vector(1,nlstate);
       for(i=1;i<=nlstate;i++)    
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     } /* End theta */    j1=0;
     
     trgradg =matrix(1,nlstate,1,npar);    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for(j=1; j<=nlstate;j++)    
       for(theta=1; theta <=npar; theta++)    for(k1=1; k1<=j;k1++){
         trgradg[j][theta]=gradg[theta][j];      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
     for(i=1;i<=nlstate;i++)        
       varpl[i][(int)age] =0.;        for (i=-1; i<=nlstate+ndeath; i++)  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for(m=agemin; m <= agemax+3; m++)
     for(i=1;i<=nlstate;i++)              freq[i][jk][m]=0;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       
         for (i=1; i<=imx; i++) { /* Each individual */
     fprintf(ficresvpl,"%.0f ",age );          bool=1;
     for(i=1; i<=nlstate;i++)          if  (cptcovn>0) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            for (z1=1; z1<=cptcoveff; z1++) 
     fprintf(ficresvpl,"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     free_vector(gp,1,nlstate);                bool=0;
     free_vector(gm,1,nlstate);          } 
     free_matrix(gradg,1,npar,1,nlstate);          if (bool==1) { 
     free_matrix(trgradg,1,nlstate,1,npar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   } /* End age */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   free_vector(xp,1,npar);                if(agev[m][i]==0) agev[m][i]=agemax+1;
   free_matrix(doldm,1,nlstate,1,npar);                if(agev[m][i]==1) agev[m][i]=agemax+2;
   free_matrix(dnewm,1,nlstate,1,nlstate);                if (m<lastpass) {
                   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]; 
                 }
               }
             } /* end selection of waves */
 /***********************************************/          }
 /**************** Main Program *****************/        }
 /***********************************************/        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
           for(jk=1; jk <=nlstate ; jk++){
 /*int main(int argc, char *argv[])*/            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 int main()              pp[jk] += freq[jk][m][i]; 
 {          }
           for(jk=1; jk <=nlstate ; jk++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            for(m=-1, pos=0; m <=0 ; m++)
   double agedeb, agefin,hf;              pos += freq[jk][m][i];
   double agemin=1.e20, agemax=-1.e20;          }
           
   double fret;          for(jk=1; jk <=nlstate ; jk++){
   double **xi,tmp,delta;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
   double dum; /* Dummy variable */          }
   double ***p3mat;          
   int *indx;          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
   char line[MAXLINE], linepar[MAXLINE];          
   char title[MAXLINE];          for(jk=1; jk <=nlstate ; jk++){    
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];            if( i <= (int) agemax){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];              if(pos>=1.e-5){
   char filerest[FILENAMELENGTH];                probs[i][jk][j1]= pp[jk]/pos;
   char fileregp[FILENAMELENGTH];              }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            }
   int firstobs=1, lastobs=10;          }/* end jk */
   int sdeb, sfin; /* Status at beginning and end */        }/* end i */
   int c,  h , cpt,l;      } /* end i1 */
   int ju,jl, mi;    } /* end k1 */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    
      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   int hstepm, nhstepm;    free_vector(pp,1,nlstate);
   double bage, fage, age, agelim, agebase;    
   double ftolpl=FTOL;  }  /* End of Freq */
   double **prlim;  
   double *severity;  /************* Waves Concatenation ***************/
   double ***param; /* Matrix of parameters */  
   double  *p;  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)
   double **matcov; /* Matrix of covariance */  {
   double ***delti3; /* Scale */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   double *delti; /* Scale */       Death is a valid wave (if date is known).
   double ***eij, ***vareij;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   double **varpl; /* Variances of prevalence limits by age */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double *epj, vepp;       and mw[mi+1][i]. dh depends on stepm.
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";       */
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
     int i, mi, m;
   char z[1]="c", occ;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 #include <sys/time.h>       double sum=0., jmean=0.;*/
 #include <time.h>    int first;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int j, k=0,jk, ju, jl;
   /* long total_usecs;    double sum=0.;
   struct timeval start_time, end_time;    first=0;
      jmin=1e+5;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    jmax=-1;
     jmean=0.;
     for(i=1; i<=imx; i++){
   printf("\nIMACH, Version 0.64b");      mi=0;
   printf("\nEnter the parameter file name: ");      m=firstpass;
       while(s[m][i] <= nlstate){
 #ifdef windows        if(s[m][i]>=1)
   scanf("%s",pathtot);          mw[++mi][i]=m;
   getcwd(pathcd, size);        if(m >=lastpass)
   /*cygwin_split_path(pathtot,path,optionfile);          break;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        else
   /* cutv(path,optionfile,pathtot,'\\');*/          m++;
       }/* end while */
 split(pathtot, path,optionfile);      if (s[m][i] > nlstate){
   chdir(path);        mi++;     /* Death is another wave */
   replace(pathc,path);        /* if(mi==0)  never been interviewed correctly before death */
 #endif           /* Only death is a correct wave */
 #ifdef unix        mw[mi][i]=m;
   scanf("%s",optionfile);      }
 #endif  
       wav[i]=mi;
 /*-------- arguments in the command line --------*/      if(mi==0){
         if(first==0){
   strcpy(fileres,"r");          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
   strcat(fileres, optionfile);          first=1;
         }
   /*---------arguments file --------*/        if(first==1){
           fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        }
     printf("Problem with optionfile %s\n",optionfile);      } /* end mi==0 */
     goto end;    }
   }  
     for(i=1; i<=imx; i++){
   strcpy(filereso,"o");      for(mi=1; mi<wav[i];mi++){
   strcat(filereso,fileres);        if (stepm <=0)
   if((ficparo=fopen(filereso,"w"))==NULL) {          dh[mi][i]=1;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
   /* Reads comments: lines beginning with '#' */            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   while((c=getc(ficpar))=='#' && c!= EOF){            if(j==0) j=1;  /* Survives at least one month after exam */
     ungetc(c,ficpar);            k=k+1;
     fgets(line, MAXLINE, ficpar);            if (j >= jmax) jmax=j;
     puts(line);            if (j <= jmin) jmin=j;
     fputs(line,ficparo);            sum=sum+j;
   }            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   ungetc(c,ficpar);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   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);          }
   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);          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   covar=matrix(0,NCOVMAX,1,n);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   cptcovn=0;            k=k+1;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
   ncovmodel=2+cptcovn;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            sum=sum+j;
            }
   /* Read guess parameters */          jk= j/stepm;
   /* Reads comments: lines beginning with '#' */          jl= j -jk*stepm;
   while((c=getc(ficpar))=='#' && c!= EOF){          ju= j -(jk+1)*stepm;
     ungetc(c,ficpar);          if(mle <=1){ 
     fgets(line, MAXLINE, ficpar);            if(jl==0){
     puts(line);              dh[mi][i]=jk;
     fputs(line,ficparo);              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
   ungetc(c,ficpar);                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              bh[mi][i]=ju;
     for(i=1; i <=nlstate; i++)            }
     for(j=1; j <=nlstate+ndeath-1; j++){          }else{
       fscanf(ficpar,"%1d%1d",&i1,&j1);            if(jl <= -ju){
       fprintf(ficparo,"%1d%1d",i1,j1);              dh[mi][i]=jk;
       printf("%1d%1d",i,j);              bh[mi][i]=jl;       /* bias is positive if real duration
       for(k=1; k<=ncovmodel;k++){                                   * is higher than the multiple of stepm and negative otherwise.
         fscanf(ficpar," %lf",&param[i][j][k]);                                   */
         printf(" %lf",param[i][j][k]);            }
         fprintf(ficparo," %lf",param[i][j][k]);            else{
       }              dh[mi][i]=jk+1;
       fscanf(ficpar,"\n");              bh[mi][i]=ju;
       printf("\n");            }
       fprintf(ficparo,"\n");            if(dh[mi][i]==0){
     }              dh[mi][i]=1; /* At least one step */
                bh[mi][i]=ju; /* At least one step */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              /*  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);*/
   p=param[1][1];            }
            }
   /* Reads comments: lines beginning with '#' */        } /* end if mle */
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* end wave */
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    jmean=sum/k;
     puts(line);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fputs(line,ficparo);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   }   }
   ungetc(c,ficpar);  
   /*********** Tricode ****************************/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  void tricode(int *Tvar, int **nbcode, int imx)
   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++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int cptcode=0;
       printf("%1d%1d",i,j);    cptcoveff=0; 
       fprintf(ficparo,"%1d%1d",i1,j1);   
       for(k=1; k<=ncovmodel;k++){    for (k=0; k<maxncov; k++) Ndum[k]=0;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for (k=1; k<=7; k++) ncodemax[k]=0;
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       fscanf(ficpar,"\n");                                 modality*/ 
       printf("\n");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       fprintf(ficparo,"\n");        Ndum[ij]++; /*store the modality */
     }        /*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 
   delti=delti3[1][1];                                         Tvar[j]. If V=sex and male is 0 and 
                                           female is 1, then  cptcode=1.*/
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for (i=0; i<=cptcode; i++) {
     fgets(line, MAXLINE, ficpar);        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 */
     puts(line);      }
     fputs(line,ficparo);  
   }      ij=1; 
   ungetc(c,ficpar);      for (i=1; i<=ncodemax[j]; i++) {
          for (k=0; k<= maxncov; k++) {
   matcov=matrix(1,npar,1,npar);          if (Ndum[k] != 0) {
   for(i=1; i <=npar; i++){            nbcode[Tvar[j]][ij]=k; 
     fscanf(ficpar,"%s",&str);            /* 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; */
     printf("%s",str);            
     fprintf(ficparo,"%s",str);            ij++;
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);          if (ij > ncodemax[j]) break; 
       printf(" %.5le",matcov[i][j]);        }  
       fprintf(ficparo," %.5le",matcov[i][j]);      } 
     }    }  
     fscanf(ficpar,"\n");  
     printf("\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
     fprintf(ficparo,"\n");  
   }   for (i=1; i<=ncovmodel-2; i++) { 
   for(i=1; i <=npar; i++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     for(j=i+1;j<=npar;j++)     ij=Tvar[i];
       matcov[i][j]=matcov[j][i];     Ndum[ij]++;
       }
   printf("\n");  
    ij=1;
    for (i=1; i<= maxncov; i++) {
     /*-------- data file ----------*/     if((Ndum[i]!=0) && (i<=ncovcol)){
     if((ficres =fopen(fileres,"w"))==NULL) {       Tvaraff[ij]=i; /*For printing */
       printf("Problem with resultfile: %s\n", fileres);goto end;       ij++;
     }     }
     fprintf(ficres,"#%s\n",version);   }
       
     if((fic=fopen(datafile,"r"))==NULL)    {   cptcoveff=ij-1; /*Number of simple covariates*/
       printf("Problem with datafile: %s\n", datafile);goto end;  }
     }  
   /*********** Health Expectancies ****************/
     n= lastobs;  
     severity = vector(1,maxwav);  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 )
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);  {
     moisnais=vector(1,n);    /* Health expectancies */
     annais=vector(1,n);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     moisdc=vector(1,n);    double age, agelim, hf;
     andc=vector(1,n);    double ***p3mat,***varhe;
     agedc=vector(1,n);    double **dnewm,**doldm;
     cod=ivector(1,n);    double *xp;
     weight=vector(1,n);    double **gp, **gm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double ***gradg, ***trgradg;
     mint=matrix(1,maxwav,1,n);    int theta;
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     adl=imatrix(1,maxwav+1,1,n);        xp=vector(1,npar);
     tab=ivector(1,NCOVMAX);    dnewm=matrix(1,nlstate*2,1,npar);
     ncodemax=ivector(1,8);    doldm=matrix(1,nlstate*2,1,nlstate*2);
     
     i=1;    fprintf(ficreseij,"# Health expectancies\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(ficreseij,"# Age");
       if ((i >= firstobs) && (i <=lastobs)) {    for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++)
         for (j=maxwav;j>=1;j--){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficreseij,"\n");
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if(estepm < stepm){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
            else  hstepm=estepm;   
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    /* We compute the life expectancy from trapezoids spaced every estepm months
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);     * 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
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);     * we are calculating an estimate of the Life Expectancy assuming a linear 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         for (j=ncov;j>=1;j--){     * to compare the new estimate of Life expectancy with the same linear 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);     * hypothesis. A more precise result, taking into account a more precise
         }     * curvature will be obtained if estepm is as small as stepm. */
         num[i]=atol(stra);  
     /* For example we decided to compute the life expectancy with the smallest unit */
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
         i=i+1;       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
     }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     /*scanf("%d",i);*/       survival function given by stepm (the optimization length). Unfortunately it
   imx=i-1; /* Number of individuals */       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /* Calculation of the number of parameter from char model*/       results. So we changed our mind and took the option of the best precision.
   Tvar=ivector(1,15);    */
   Tprod=ivector(1,15);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);    agelim=AGESUP;
   Tage=ivector(1,15);          for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          /* nhstepm age range expressed in number of stepm */
   if (strlen(model) >1){      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     j=0, j1=0, k1=1, k2=1;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     j=nbocc(model,'+');      /* if (stepm >= YEARM) hstepm=1;*/
     j1=nbocc(model,'*');      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     cptcovn=j+1;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     cptcovprod=j1;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
          gp=matrix(0,nhstepm,1,nlstate*2);
          gm=matrix(0,nhstepm,1,nlstate*2);
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       printf("Error. Non available option model=%s ",model);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       goto end;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     }   
      
     for(i=(j+1); i>=1;i--){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      /* Computing Variances of health expectancies */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/       for(theta=1; theta <=npar; theta++){
       if (strchr(strb,'*')) {        for(i=1; i<=npar; i++){ 
         cutv(strd,strc,strb,'*');          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         if (strcmp(strc,"age")==0) {        }
           cptcovprod--;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           cutv(strb,stre,strd,'V');    
           Tvar[i]=atoi(stre);        cptj=0;
           cptcovage++;        for(j=1; j<= nlstate; j++){
             Tage[cptcovage]=i;          for(i=1; i<=nlstate; i++){
             /*printf("stre=%s ", stre);*/            cptj=cptj+1;
         }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         else if (strcmp(strd,"age")==0) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           cptcovprod--;            }
           cutv(strb,stre,strc,'V');          }
           Tvar[i]=atoi(stre);        }
           cptcovage++;       
           Tage[cptcovage]=i;       
         }        for(i=1; i<=npar; i++) 
         else {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           cutv(strb,stre,strc,'V');        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           Tvar[i]=ncov+k1;        
           cutv(strb,strc,strd,'V');        cptj=0;
           Tprod[k1]=i;        for(j=1; j<= nlstate; j++){
           Tvard[k1][1]=atoi(strc);          for(i=1;i<=nlstate;i++){
           Tvard[k1][2]=atoi(stre);            cptj=cptj+1;
           Tvar[cptcovn+k2]=Tvard[k1][1];            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           for (k=1; k<=lastobs;k++)            }
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          }
           k1++;        }
           k2=k2+2;        for(j=1; j<= nlstate*2; j++)
         }          for(h=0; h<=nhstepm-1; h++){
       }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       else {          }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       } 
        /*  scanf("%d",i);*/     
       cutv(strd,strc,strb,'V');  /* End theta */
       Tvar[i]=atoi(strc);  
       }       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       for(h=0; h<=nhstepm-1; h++)
         scanf("%d",i);*/        for(j=1; j<=nlstate*2;j++)
     }          for(theta=1; theta <=npar; theta++)
 }            trgradg[h][j][theta]=gradg[h][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);       for(i=1;i<=nlstate*2;i++)
   scanf("%d ",i);*/        for(j=1;j<=nlstate*2;j++)
     fclose(fic);          varhe[i][j][(int)age] =0.;
   
     /*  if(mle==1){*/       printf("%d|",(int)age);fflush(stdout);
     if (weightopt != 1) { /* Maximisation without weights*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(i=1;i<=n;i++) weight[i]=1.0;       for(h=0;h<=nhstepm-1;h++){
     }        for(k=0;k<=nhstepm-1;k++){
     /*-calculation of age at interview from date of interview and age at death -*/          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
     agev=matrix(1,maxwav,1,imx);          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
              for(i=1;i<=nlstate*2;i++)
     for (i=1; i<=imx; i++)  {            for(j=1;j<=nlstate*2;j++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       for(m=1; (m<= maxwav); m++){        }
         if(s[m][i] >0){      }
           if (s[m][i] == nlstate+1) {      /* Computing expectancies */
             if(agedc[i]>0)      for(i=1; i<=nlstate;i++)
               if(moisdc[i]!=99 && andc[i]!=9999)        for(j=1; j<=nlstate;j++)
               agev[m][i]=agedc[i];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             else {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               if (andc[i]!=9999){            
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  /* 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]);*/
               agev[m][i]=-1;  
               }          }
             }  
           }      fprintf(ficreseij,"%3.0f",age );
           else if(s[m][i] !=9){ /* Should no more exist */      cptj=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      for(i=1; i<=nlstate;i++)
             if(mint[m][i]==99 || anint[m][i]==9999)        for(j=1; j<=nlstate;j++){
               agev[m][i]=1;          cptj++;
             else if(agev[m][i] <agemin){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               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);*/      fprintf(ficreseij,"\n");
             }     
             else if(agev[m][i] >agemax){      free_matrix(gm,0,nhstepm,1,nlstate*2);
               agemax=agev[m][i];      free_matrix(gp,0,nhstepm,1,nlstate*2);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
             }      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
             /*agev[m][i]=anint[m][i]-annais[i];*/      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             /*   agev[m][i] = age[i]+2*m;*/    }
           }    printf("\n");
           else { /* =9 */    fprintf(ficlog,"\n");
             agev[m][i]=1;  
             s[m][i]=-1;    free_vector(xp,1,npar);
           }    free_matrix(dnewm,1,nlstate*2,1,npar);
         }    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
         else /*= 0 Unknown */    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
           agev[m][i]=1;  }
       }  
      /************ Variance ******************/
     }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     for (i=1; i<=imx; i++)  {  {
       for(m=1; (m<= maxwav); m++){    /* Variance of health expectancies */
         if (s[m][i] > (nlstate+ndeath)) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           printf("Error: Wrong value in nlstate or ndeath\n");      /* double **newm;*/
           goto end;    double **dnewm,**doldm;
         }    double **dnewmp,**doldmp;
       }    int i, j, nhstepm, hstepm, h, nstepm ;
     }    int k, cptcode;
     double *xp;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     free_vector(severity,1,maxwav);    double **gradgp, **trgradgp; /* for var p point j */
     free_imatrix(outcome,1,maxwav+1,1,n);    double *gpp, *gmp; /* for var p point j */
     free_vector(moisnais,1,n);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     free_vector(annais,1,n);    double ***p3mat;
     free_matrix(mint,1,maxwav,1,n);    double age,agelim, hf;
     free_matrix(anint,1,maxwav,1,n);    double ***mobaverage;
     free_vector(moisdc,1,n);    int theta;
     free_vector(andc,1,n);    char digit[4];
     char digitp[25];
      
     wav=ivector(1,imx);    char fileresprobmorprev[FILENAMELENGTH];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    if(popbased==1){
          if(mobilav!=0)
     /* Concatenates waves */        strcpy(digitp,"-populbased-mobilav-");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       Tcode=ivector(1,100);      strcpy(digitp,"-stablbased-");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    if (mobilav!=0) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
    codtab=imatrix(1,100,1,10);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
    h=0;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
    m=pow(2,cptcoveff);      }
      }
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    strcpy(fileresprobmorprev,"prmorprev"); 
        for(j=1; j <= ncodemax[k]; j++){    sprintf(digit,"%-d",ij);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
            h++;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
            if (h>m) h=1;codtab[h][k]=j;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
          }    strcat(fileresprobmorprev,fileres);
        }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
      }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
    }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    /*for(i=1; i <=m ;i++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      for(k=1; k <=cptcovn; k++){    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);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      printf("\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
    }      for(i=1; i<=nlstate;i++)
    scanf("%d",i);*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
        }  
    /* Calculates basic frequencies. Computes observed prevalence at single age    fprintf(ficresprobmorprev,"\n");
        and prints on file fileres'p'. */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      exit(0);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    else{
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficgp,"\n# Routine varevsij");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    }
        if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     /* For Powell, parameters are in a vector p[] starting at p[1]      printf("Problem with html file: %s\n", optionfilehtm);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      exit(0);
     }
     if(mle==1){    else{
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      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);
        }
     /*--------- results files --------------*/    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     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);  
        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");
    jk=1;    fprintf(ficresvij,"# Age");
    fprintf(ficres,"# Parameters\n");    for(i=1; i<=nlstate;i++)
    printf("# Parameters\n");      for(j=1; j<=nlstate;j++)
    for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      for(k=1; k <=(nlstate+ndeath); k++){    fprintf(ficresvij,"\n");
        if (k != i)  
          {    xp=vector(1,npar);
            printf("%d%d ",i,k);    dnewm=matrix(1,nlstate,1,npar);
            fprintf(ficres,"%1d%1d ",i,k);    doldm=matrix(1,nlstate,1,nlstate);
            for(j=1; j <=ncovmodel; j++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
              printf("%f ",p[jk]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
            }    gpp=vector(nlstate+1,nlstate+ndeath);
            printf("\n");    gmp=vector(nlstate+1,nlstate+ndeath);
            fprintf(ficres,"\n");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
          }    
      }    if(estepm < stepm){
    }      printf ("Problem %d lower than %d\n",estepm, stepm);
  if(mle==1){    }
     /* Computing hessian and covariance matrix */    else  hstepm=estepm;   
     ftolhess=ftol; /* Usually correct */    /* For example we decided to compute the life expectancy with the smallest unit */
     hesscov(matcov, p, npar, delti, ftolhess, func);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  }       nhstepm is the number of hstepm from age to agelim 
     fprintf(ficres,"# Scales\n");       nstepm is the number of stepm from age to agelin. 
     printf("# Scales\n");       Look at hpijx to understand the reason of that which relies in memory size
      for(i=1,jk=1; i <=nlstate; i++){       and note for a fixed period like k years */
       for(j=1; j <=nlstate+ndeath; j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         if (j!=i) {       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficres,"%1d%1d",i,j);       means that if the survival funtion is printed every two years of age and if
           printf("%1d%1d",i,j);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for(k=1; k<=ncovmodel;k++){       results. So we changed our mind and took the option of the best precision.
             printf(" %.5e",delti[jk]);    */
             fprintf(ficres," %.5e",delti[jk]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             jk++;    agelim = AGESUP;
           }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           printf("\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           fprintf(ficres,"\n");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       }      gp=matrix(0,nhstepm,1,nlstate);
          gm=matrix(0,nhstepm,1,nlstate);
     k=1;  
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");      for(theta=1; theta <=npar; theta++){
     for(i=1;i<=npar;i++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       /*  if (k>nlstate) k=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       i1=(i-1)/(ncovmodel*nlstate)+1;        }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);        if (popbased==1) {
       for(j=1; j<=i;j++){          if(mobilav ==0){
         fprintf(ficres," %.5e",matcov[i][j]);            for(i=1; i<=nlstate;i++)
         printf(" %.5e",matcov[i][j]);              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
       fprintf(ficres,"\n");            for(i=1; i<=nlstate;i++)
       printf("\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
       k++;          }
     }        }
        
     while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<= nlstate; j++){
       ungetc(c,ficpar);          for(h=0; h<=nhstepm; h++){
       fgets(line, MAXLINE, ficpar);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       puts(line);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       fputs(line,ficparo);          }
     }        }
     ungetc(c,ficpar);        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);           as a weighted average of prlim.
            */
     if (fage <= 2) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       bage = agemin;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       fage = agemax;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
         /* end probability of death */
     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\n",agemin,agemax,bage,fage);        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);  
 /*------------ gnuplot -------------*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 chdir(pathcd);   
   if((ficgp=fopen("graph.plt","w"))==NULL) {        if (popbased==1) {
     printf("Problem with file graph.gp");goto end;          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
 #ifdef windows              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficgp,"cd \"%s\" \n",pathc);          }else{ /* mobilav */ 
 #endif            for(i=1; i<=nlstate;i++)
 m=pow(2,cptcoveff);              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
  /* 1eme*/        }
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
 #ifdef windows            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     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);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 #endif          }
 #ifdef unix        }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        /* This for computing probability of death (h=1 means
 #endif           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
 for (i=1; i<= nlstate ; i ++) {        */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
 }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        }    
     for (i=1; i<= nlstate ; i ++) {        /* end probability of death */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate; j++) /* vareij */
 }          for(h=0; h<=nhstepm; h++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
      for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 }            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");      } /* End theta */
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    }  
   }      for(h=0; h<=nhstepm; h++) /* veij */
   /*2 eme*/        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   for (k1=1; k1<= m ; k1 ++) {            trgradg[h][j][theta]=gradg[h][theta][j];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
          for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for (i=1; i<= nlstate+1 ; i ++) {        for(theta=1; theta <=npar; theta++)
       k=2*i;          trgradgp[j][theta]=gradgp[theta][j];
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1;i<=nlstate;i++)
 }          for(j=1;j<=nlstate;j++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          vareij[i][j][(int)age] =0.;
       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);      for(h=0;h<=nhstepm;h++){
       for (j=1; j<= nlstate+1 ; j ++) {        for(k=0;k<=nhstepm;k++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         else fprintf(ficgp," \%%*lf (\%%*lf)");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 }            for(i=1;i<=nlstate;i++)
       fprintf(ficgp,"\" t\"\" w l 0,");            for(j=1;j<=nlstate;j++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }        /* pptj */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       else fprintf(ficgp,"\" t\"\" w l 0,");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
        /* end ppptj */
   /*3eme*/      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   for (k1=1; k1<= m ; k1 ++) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for (cpt=1; cpt<= nlstate ; cpt ++) {   
       k=2+nlstate*(cpt-1);      if (popbased==1) {
       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);        if(mobilav ==0){
       for (i=1; i< nlstate ; i ++) {          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);            prlim[i][i]=probs[(int)age][i][ij];
       }        }else{ /* mobilav */ 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(i=1; i<=nlstate;i++)
     }            prlim[i][i]=mobaverage[(int)age][i][ij];
   }        }
        }
   /* CV preval stat */               
   for (k1=1; k1<= m ; k1 ++) {      /* This for computing probability of death (h=1 means
     for (cpt=1; cpt<nlstate ; cpt ++) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       k=3;         as a weighted average of prlim.
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      */
       for (i=1; i< nlstate ; i ++)      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficgp,"+$%d",k+i+1);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
            }    
       l=3+(nlstate+ndeath)*cpt;      /* end probability of death */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         l=3+(nlstate+ndeath)*cpt;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficgp,"+$%d",l+i+1);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       }        for(i=1; i<=nlstate;i++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
     }      } 
   }      fprintf(ficresprobmorprev,"\n");
   
   /* proba elementaires */      fprintf(ficresvij,"%.0f ",age );
    for(i=1,jk=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
     for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<=nlstate;j++){
       if (k != i) {          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         for(j=1; j <=ncovmodel; j++){        }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      fprintf(ficresvij,"\n");
           /*fprintf(ficgp,"%s",alph[1]);*/      free_matrix(gp,0,nhstepm,1,nlstate);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      free_matrix(gm,0,nhstepm,1,nlstate);
           jk++;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           fprintf(ficgp,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    } /* End age */
     }    free_vector(gpp,nlstate+1,nlstate+ndeath);
     }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   for(jk=1; jk <=m; jk++) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
    i=1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
    for(k2=1; k2<=nlstate; k2++) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      k3=i;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      for(k=1; k<=(nlstate+ndeath); k++) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
        if (k != k2){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
 ij=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
         for(j=3; j <=ncovmodel; j++) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
             ij++;    /*  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);
           }  */
           else    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         }    free_vector(xp,1,npar);
           fprintf(ficgp,")/(1");    free_matrix(doldm,1,nlstate,1,nlstate);
            free_matrix(dnewm,1,nlstate,1,npar);
         for(k1=1; k1 <=nlstate; k1++){      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 ij=1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(j=3; j <=ncovmodel; j++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fclose(ficresprobmorprev);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fclose(ficgp);
             ij++;    fclose(fichtm);
           }  }  
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  /************ Variance of prevlim ******************/
           }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
           fprintf(ficgp,")");  {
         }    /* Variance of prevalence limit */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double **newm;
         i=i+ncovmodel;    double **dnewm,**doldm;
        }    int i, j, nhstepm, hstepm;
      }    int k, cptcode;
    }    double *xp;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    double *gp, *gm;
   }    double **gradg, **trgradg;
        double age,agelim;
   fclose(ficgp);    int theta;
         
 chdir(path);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     free_matrix(agev,1,maxwav,1,imx);    fprintf(ficresvpl,"# Age");
     free_ivector(wav,1,imx);    for(i=1; i<=nlstate;i++)
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        fprintf(ficresvpl," %1d-%1d",i,i);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    fprintf(ficresvpl,"\n");
      
     free_imatrix(s,1,maxwav+1,1,n);    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     free_ivector(num,1,n);    
     free_vector(agedc,1,n);    hstepm=1*YEARM; /* Every year of age */
     free_vector(weight,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    agelim = AGESUP;
     fclose(ficparo);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fclose(ficres);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     /*  }*/      if (stepm >= YEARM) hstepm=1;
          nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    /*________fin mle=1_________*/      gradg=matrix(1,npar,1,nlstate);
          gp=vector(1,nlstate);
       gm=vector(1,nlstate);
    
     /* No more information from the sample is required now */      for(theta=1; theta <=npar; theta++){
   /* Reads comments: lines beginning with '#' */        for(i=1; i<=npar; i++){ /* Computes gradient */
   while((c=getc(ficpar))=='#' && c!= EOF){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     puts(line);        for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);          gp[i] = prlim[i][i];
   }      
   ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        for(i=1;i<=nlstate;i++)
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          gm[i] = prlim[i][i];
 /*--------- index.htm --------*/  
         for(i=1;i<=nlstate;i++)
   strcpy(optionfilehtm,optionfile);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   strcat(optionfilehtm,".htm");      } /* End theta */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm);goto end;      trgradg =matrix(1,nlstate,1,npar);
   }  
       for(j=1; j<=nlstate;j++)
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">        for(theta=1; theta <=npar; theta++)
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          trgradg[j][theta]=gradg[theta][j];
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      for(i=1;i<=nlstate;i++)
 <hr  size=\"2\" color=\"#EC5E5E\">        varpl[i][(int)age] =0.;
 <li>Outputs files<br><br>\n      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      for(i=1;i<=nlstate;i++)
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      fprintf(ficresvpl,"%.0f ",age );
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      for(i=1; i<=nlstate;i++)
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      fprintf(ficresvpl,"\n");
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><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);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
  fprintf(fichtm," <li>Graphs</li><p>");      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
  m=cptcoveff;    } /* End age */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
     free_vector(xp,1,npar);
  j1=0;    free_matrix(doldm,1,nlstate,1,npar);
  for(k1=1; k1<=m;k1++){    free_matrix(dnewm,1,nlstate,1,nlstate);
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;  }
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  /************ Variance of one-step probabilities  ******************/
          for (cpt=1; cpt<=cptcoveff;cpt++)  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  {
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int i, j=0,  i1, k1, l1, t, tj;
        }    int k2, l2, j1,  z1;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    int k=0,l, cptcode;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        int first=1, first1;
        for(cpt=1; cpt<nlstate;cpt++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double **dnewm,**doldm;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    double *xp;
        }    double *gp, *gm;
     for(cpt=1; cpt<=nlstate;cpt++) {    double **gradg, **trgradg;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double **mu;
 interval) in state (%d): v%s%d%d.gif <br>    double age,agelim, cov[NCOVMAX];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      }    int theta;
      for(cpt=1; cpt<=nlstate;cpt++) {    char fileresprob[FILENAMELENGTH];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    char fileresprobcov[FILENAMELENGTH];
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    char fileresprobcor[FILENAMELENGTH];
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double ***varpij;
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    strcpy(fileresprob,"prob"); 
 fprintf(fichtm,"\n</body>");    strcat(fileresprob,fileres);
    }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
  }      printf("Problem with resultfile: %s\n", fileresprob);
 fclose(fichtm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   /*--------------- Prevalence limit --------------*/    strcpy(fileresprobcov,"probcov"); 
      strcat(fileresprobcov,fileres);
   strcpy(filerespl,"pl");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   strcat(filerespl,fileres);      printf("Problem with resultfile: %s\n", fileresprobcov);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
   }    strcpy(fileresprobcor,"probcor"); 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    strcat(fileresprobcor,fileres);
   fprintf(ficrespl,"#Prevalence limit\n");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   fprintf(ficrespl,"#Age ");      printf("Problem with resultfile: %s\n", fileresprobcor);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   fprintf(ficrespl,"\n");    }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
   k=0;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   agebase=agemin;    fprintf(ficresprob,"# Age");
   agelim=agemax;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   ftolpl=1.e-10;    fprintf(ficresprobcov,"# Age");
   i1=cptcoveff;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if (cptcovn < 1){i1=1;}    fprintf(ficresprobcov,"# Age");
   
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1; i<=nlstate;i++)
         k=k+1;      for(j=1; j<=(nlstate+ndeath);j++){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficrespl,"\n#******");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         for(j=1;j<=cptcoveff;j++)        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }  
         fprintf(ficrespl,"******\n");   /* fprintf(ficresprob,"\n");
            fprintf(ficresprobcov,"\n");
         for (age=agebase; age<=agelim; age++){    fprintf(ficresprobcor,"\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   */
           fprintf(ficrespl,"%.0f",age );   xp=vector(1,npar);
           for(i=1; i<=nlstate;i++)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           fprintf(ficrespl,"\n");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       }    first=1;
     }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   fclose(ficrespl);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   /*------------- h Pij x at various ages ------------*/      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        exit(0);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    else{
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      fprintf(ficgp,"\n# Routine varprob");
   }    }
   printf("Computing pij: result on file '%s' \n", filerespij);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        printf("Problem with html file: %s\n", optionfilehtm);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   if (stepm<=24) stepsize=2;      exit(0);
     }
   agelim=AGESUP;    else{
   hstepm=stepsize*YEARM; /* Every year of age */      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      fprintf(fichtm,"\n");
    
   k=0;      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   for(cptcov=1;cptcov<=i1;cptcov++){      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");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      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");
       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]]);    cov[1]=1;
         fprintf(ficrespij,"******\n");    tj=cptcoveff;
            if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    j1=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for(t=1; t<=tj;t++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for(i1=1; i1<=ncodemax[t];i1++){ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;
           oldm=oldms;savm=savms;        if  (cptcovn>0) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresprob, "\n#********** Variable "); 
           fprintf(ficrespij,"# Age");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(i=1; i<=nlstate;i++)          fprintf(ficresprob, "**********\n#\n");
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficresprobcov, "\n#********** Variable "); 
               fprintf(ficrespij," %1d-%1d",i,j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficrespij,"\n");          fprintf(ficresprobcov, "**********\n#\n");
           for (h=0; h<=nhstepm; h++){          
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          fprintf(ficgp, "\n#********** Variable "); 
             for(i=1; i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp, "**********\n#\n");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          
             fprintf(ficrespij,"\n");          
           }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficrespij,"\n");          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]]);
           fprintf(ficresprobcor, "**********\n#");    
   fclose(ficrespij);        }
         
   /*---------- Health expectancies and variances ------------*/        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   strcpy(filerest,"t");          for (k=1; k<=cptcovn;k++) {
   strcat(filerest,fileres);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   if((ficrest=fopen(filerest,"w"))==NULL) {          }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }          for (k=1; k<=cptcovprod;k++)
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   strcpy(filerese,"e");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   strcat(filerese,fileres);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   if((ficreseij=fopen(filerese,"w"))==NULL) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      
   }          for(theta=1; theta <=npar; theta++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:0);
  strcpy(fileresv,"v");            
   strcat(fileresv,fileres);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            k=0;
   }            for(i=1; i<= (nlstate); i++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   k=0;                gp[k]=pmmij[i][j];
   for(cptcov=1;cptcov<=i1;cptcov++){              }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            }
       k=k+1;            
       fprintf(ficrest,"\n#****** ");            for(i=1; i<=npar; i++)
       for(j=1;j<=cptcoveff;j++)              xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
       fprintf(ficrest,"******\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
       fprintf(ficreseij,"\n#****** ");            for(i=1; i<=(nlstate); i++){
       for(j=1;j<=cptcoveff;j++)              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                k=k+1;
       fprintf(ficreseij,"******\n");                gm[k]=pmmij[i][j];
               }
       fprintf(ficresvij,"\n#****** ");            }
       for(j=1;j<=cptcoveff;j++)       
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       fprintf(ficresvij,"******\n");              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
           }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);              for(theta=1; theta <=npar; theta++)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              trgradg[j][theta]=gradg[theta][j];
       oldm=oldms;savm=savms;          
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficrest,"\n");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                  free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;          pmij(pmmij,cov,ncovmodel,x,nlstate);
       epj=vector(1,nlstate+1);          
       for(age=bage; age <=fage ;age++){          k=0;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(i=1; i<=(nlstate); i++){
         fprintf(ficrest," %.0f",age);            for(j=1; j<=(nlstate+ndeath);j++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              k=k+1;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              mu[k][(int) age]=pmmij[i][j];
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];            }
           }          }
           epj[nlstate+1] +=epj[j];          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         for(i=1, vepp=0.;i <=nlstate;i++)              varpij[i][j][(int)age] = doldm[i][j];
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];          /*printf("\n%d ",(int)age);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         for(j=1;j <=nlstate;j++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         }            }*/
         fprintf(ficrest,"\n");  
       }          fprintf(ficresprob,"\n%d ",(int)age);
     }          fprintf(ficresprobcov,"\n%d ",(int)age);
   }          fprintf(ficresprobcor,"\n%d ",(int)age);
          
  fclose(ficreseij);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
  fclose(ficresvij);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   fclose(ficrest);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   fclose(ficpar);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   free_vector(epj,1,nlstate+1);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   /*  scanf("%d ",i); */          }
           i=0;
   /*------- Variance limit prevalence------*/            for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
 strcpy(fileresvpl,"vpl");              i=i++;
   strcat(fileresvpl,fileres);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              for (j=1; j<=i;j++){
     exit(0);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);              }
             }
  k=0;          }/* end of loop for state */
  for(cptcov=1;cptcov<=i1;cptcov++){        } /* end of loop for age */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;        /* Confidence intervalle of pij  */
      fprintf(ficresvpl,"\n#****** ");        /*
      for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"\nset noparametric;unset label");
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
      fprintf(ficresvpl,"******\n");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
      oldm=oldms;savm=savms;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
    }        */
  }  
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   fclose(ficresvpl);        first1=1;
         for (k2=1; k2<=(nlstate);k2++){
   /*---------- End : free ----------------*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            if(l2==k2) continue;
              j=(k2-1)*(nlstate+ndeath)+l2;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for (k1=1; k1<=(nlstate);k1++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  if(l1==k1) continue;
                  i=(k1-1)*(nlstate+ndeath)+l1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                if(i<=j) continue;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                for (age=bage; age<=fage; age ++){ 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                  if ((int)age %5==0){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   free_matrix(matcov,1,npar,1,npar);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   free_vector(delti,1,npar);                    mu1=mu[i][(int) age]/stepm*YEARM ;
                      mu2=mu[j][(int) age]/stepm*YEARM;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
   printf("End of Imach\n");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                      /* Eigen vectors */
   /* 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);*/                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   /*printf("Total time was %d uSec.\n", total_usecs);*/                    /*v21=sqrt(1.-v11*v11); *//* error */
   /*------ End -----------*/                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
  end:                    v22=v11;
 #ifdef windows                    tnalp=v21/v11;
  chdir(pathcd);                    if(first1==1){
 #endif                      first1=0;
  /*system("wgnuplot graph.plt");*/                      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);
  system("../gp37mgw/wgnuplot graph.plt");                    }
                     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);
 #ifdef windows                    /*printf(fignu*/
   while (z[0] != 'q') {                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     chdir(pathcd);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                    if(first==1){
     scanf("%s",z);                      first=0;
     if (z[0] == 'c') system("./imach");                      fprintf(ficgp,"\nset parametric;unset label");
     else if (z[0] == 'e') {                      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);
       chdir(path);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       system(optionfilehtm);                      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,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
     else if (z[0] == 'q') exit(0);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   }                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
 #endif                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
     if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* 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>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
    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
           <br>",fileres,fileres,fileres,fileres);
    else 
      fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",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+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    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
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* 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
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     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;
     
     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 \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
     for(cptcov=1, k=0;cptcov<=cptcoveff;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, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,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+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (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,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h==(int)(YEARM*yearp))
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                 }
                 if (h==(int)(YEARM*yearp)){
                   fprintf(ficresf," %.3f", ppij);
                 }
               }
             }
             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 *****not tested NB*************/
   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, firstpass, lastpass);
     
     
     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;
   
     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]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       if(stepm ==1){
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
       } 
       else{
         erreur=108;
         printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
         fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       }
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.10  
changed lines
  Added in v.1.72


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