Diff for /imach/src/imach.c between versions 1.21 and 1.73

version 1.21, 2002/02/21 18:42:24 version 1.73, 2003/04/08 14:06:50
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status    
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
   Also this programme outputs the covariance matrix of the parameters but also    conditional to the observed state i at age x. The delay 'h' can be
   of the life expectancies. It also computes the prevalence limits.    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is modelled as a multinomial logistic.  The hPx
            Institut national d'études démographiques, Paris.    matrix is simply the matrix product of nh*stepm elementary matrices
   This software have been partly granted by Euro-REVES, a concerted action    and the contribution of each individual to the likelihood is simply
   from the European Union.    hPijx.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Also this programme outputs the covariance matrix of the parameters but also
   can be accessed at http://euroreves.ined.fr/imach .    of the life expectancies. It also computes the stable prevalence. 
   **********************************************************************/    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <math.h>             Institut national d'études démographiques, Paris.
 #include <stdio.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdlib.h>    from the European Union.
 #include <unistd.h>    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXLINE 256    can be accessed at http://euroreves.ined.fr/imach .
 #define FILENAMELENGTH 80    **********************************************************************/
 /*#define DEBUG*/   
 #define windows  #include <math.h>
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #include <stdio.h>
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #include <stdlib.h>
   #include <unistd.h>
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 #define NINTERVMAX 8  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define FILENAMELENGTH 80
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  /*#define DEBUG*/
 #define NCOVMAX 8 /* Maximum number of covariates */  #define windows
 #define MAXN 20000  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define YEARM 12. /* Number of months per year */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define AGESUP 130  
 #define AGEBASE 40  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int erreur; /* Error number */  #define NINTERVMAX 8
 int nvar;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int npar=NPARMAX;  #define NCOVMAX 8 /* Maximum number of covariates */
 int nlstate=2; /* Number of live states */  #define MAXN 20000
 int ndeath=1; /* Number of dead states */  #define YEARM 12. /* Number of months per year */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #define AGESUP 130
 int popbased=0;  #define AGEBASE 40
   #ifdef windows
 int *wav; /* Number of waves for this individuual 0 is possible */  #define DIRSEPARATOR '\\'
 int maxwav; /* Maxim number of waves */  #define ODIRSEPARATOR '/'
 int jmin, jmax; /* min, max spacing between 2 waves */  #else
 int mle, weightopt;  #define DIRSEPARATOR '/'
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define ODIRSEPARATOR '\\'
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #endif
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  char version[80]="Imach version 0.94, February 2003, INED-EUROREVES ";
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int erreur; /* Error number */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  int nvar;
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 FILE *ficreseij;  int npar=NPARMAX;
   char filerese[FILENAMELENGTH];  int nlstate=2; /* Number of live states */
  FILE  *ficresvij;  int ndeath=1; /* Number of dead states */
   char fileresv[FILENAMELENGTH];  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
  FILE  *ficresvpl;  int popbased=0;
   char fileresvpl[FILENAMELENGTH];  
   int *wav; /* Number of waves for this individuual 0 is possible */
 #define NR_END 1  int maxwav; /* Maxim number of waves */
 #define FREE_ARG char*  int jmin, jmax; /* min, max spacing between 2 waves */
 #define FTOL 1.0e-10  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define NRANSI  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define ITMAX 200  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 TOL 2.0e-4  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define CGOLD 0.3819660  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define ZEPS 1.0e-10  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *ficlog;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define GOLD 1.618034  FILE *ficresprobmorprev;
 #define GLIMIT 100.0  FILE *fichtm; /* Html File */
 #define TINY 1.0e-20  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 static double maxarg1,maxarg2;  FILE  *ficresvij;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileresv[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char title[MAXLINE];
 #define rint(a) floor(a+0.5)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 int imx;  char fileregp[FILENAMELENGTH];
 int stepm;  char popfile[FILENAMELENGTH];
 /* Stepm, step in month: minimum step interpolation*/  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define NR_END 1
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define FREE_ARG char*
 double **pmmij, ***probs, ***mobaverage;  #define FTOL 1.0e-10
 double dateintmean=0;  
   #define NRANSI 
 double *weight;  #define ITMAX 200 
 int **s; /* Status */  
 double *agedc, **covar, idx;  #define TOL 2.0e-4 
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #define CGOLD 0.3819660 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define ZEPS 1.0e-10 
 double ftolhess; /* Tolerance for computing hessian */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /**************** split *************************/  #define GOLD 1.618034 
 static  int split( char *path, char *dirc, char *name )  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    l1 = strlen( path );                 /* length of path */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    
    s = strrchr( path, '\\' );           /* find last / */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    if ( s == NULL ) {                   /* no directory, so use current */  #define rint(a) floor(a+0.5)
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       if ( getwd( dirc ) == NULL ) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #else  
       extern char       *getcwd( );  int imx; 
   int stepm;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /* Stepm, step in month: minimum step interpolation*/
 #endif  
          return( GLOCK_ERROR_GETCWD );  int estepm;
       }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  int m,nb;
       s++;                              /* after this, the filename */  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       l2 = strlen( s );                 /* length of filename */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double **pmmij, ***probs;
       strcpy( name, s );                /* save file name */  double dateintmean=0;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  double *weight;
    }  int **s; /* Status */
    l1 = strlen( dirc );                 /* length of directory */  double *agedc, **covar, idx;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    return( 0 );                         /* we're done */  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   
 /******************************************/  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void replace(char *s, char*t)  {
 {    char  *ss;                            /* pointer */
   int i;    int   l1, l2;                         /* length counters */
   int lg=20;  
   i=0;    l1 = strlen(path );                   /* length of path */
   lg=strlen(t);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(i=0; i<= lg; i++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     (s[i] = t[i]);    if ( ss == NULL ) {                   /* no directory, so use current */
     if (t[i]== '\\') s[i]='/';      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }  #if     defined(__bsd__)                /* get current working directory */
       extern char *getwd( );
 int nbocc(char *s, char occ)  
 {      if ( getwd( dirc ) == NULL ) {
   int i,j=0;  #else
   int lg=20;      extern char *getcwd( );
   i=0;  
   lg=strlen(s);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for(i=0; i<= lg; i++) {  #endif
   if  (s[i] == occ ) j++;        return( GLOCK_ERROR_GETCWD );
   }      }
   return j;      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 void cutv(char *u,char *v, char*t, char occ)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,lg,j,p=0;      strcpy( name, ss );         /* save file name */
   i=0;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for(j=0; j<=strlen(t)-1; j++) {      dirc[l1-l2] = 0;                    /* add zero */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    }
   }    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
   lg=strlen(t);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   for(j=0; j<p; j++) {  #else
     (u[j] = t[j]);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   }  #endif
      u[p]='\0';    ss = strrchr( name, '.' );            /* find last / */
     ss++;
    for(j=0; j<= lg; j++) {    strcpy(ext,ss);                       /* save extension */
     if (j>=(p+1))(v[j-p-1] = t[j]);    l1= strlen( name);
   }    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /********************** nrerror ********************/    return( 0 );                          /* we're done */
   }
 void nrerror(char error_text[])  
 {  
   fprintf(stderr,"ERREUR ...\n");  /******************************************/
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  void replace(char *s, char*t)
 }  {
 /*********************** vector *******************/    int i;
 double *vector(int nl, int nh)    int lg=20;
 {    i=0;
   double *v;    lg=strlen(t);
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    for(i=0; i<= lg; i++) {
   if (!v) nrerror("allocation failure in vector");      (s[i] = t[i]);
   return v-nl+NR_END;      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  int nbocc(char *s, char occ)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    int i,j=0;
 }    int lg=20;
     i=0;
 /************************ivector *******************************/    lg=strlen(s);
 int *ivector(long nl,long nh)    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   int *v;    }
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    return j;
   if (!v) nrerror("allocation failure in ivector");  }
   return v-nl+NR_END;  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /******************free ivector **************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 void free_ivector(int *v, long nl, long nh)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   free((FREE_ARG)(v+nl-NR_END));    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /******************* imatrix *******************************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    lg=strlen(t);
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    for(j=0; j<p; j++) {
   int **m;      (u[j] = t[j]);
      }
   /* allocate pointers to rows */       u[p]='\0';
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");     for(j=0; j<= lg; j++) {
   m += NR_END;      if (j>=(p+1))(v[j-p-1] = t[j]);
   m -= nrl;    }
    }
    
   /* allocate rows and set pointers to them */  /********************** nrerror ********************/
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void nrerror(char error_text[])
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    exit(EXIT_FAILURE);
    }
   /* return pointer to array of pointers to rows */  /*********************** vector *******************/
   return m;  double *vector(int nl, int nh)
 }  {
     double *v;
 /****************** free_imatrix *************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 void free_imatrix(m,nrl,nrh,ncl,nch)    if (!v) nrerror("allocation failure in vector");
       int **m;    return v-nl+NR_END;
       long nch,ncl,nrh,nrl;  }
      /* free an int matrix allocated by imatrix() */  
 {  /************************ free vector ******************/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  void free_vector(double*v, int nl, int nh)
   free((FREE_ARG) (m+nrl-NR_END));  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /************************ivector *******************************/
 {  int *ivector(long nl,long nh)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  {
   double **m;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (!v) nrerror("allocation failure in ivector");
   if (!m) nrerror("allocation failure 1 in matrix()");    return v-nl+NR_END;
   m += NR_END;  }
   m -= nrl;  
   /******************free ivector **************************/
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void free_ivector(int *v, long nl, long nh)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /******************* imatrix *******************************/
   return m;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
 /*************************free matrix ************************/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    int **m; 
 {    
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    /* allocate pointers to rows */ 
   free((FREE_ARG)(m+nrl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 /******************* ma3x *******************************/    m -= nrl; 
 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;    /* allocate rows and set pointers to them */ 
   double ***m;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl] += NR_END; 
   if (!m) nrerror("allocation failure 1 in matrix()");    m[nrl] -= ncl; 
   m += NR_END;    
   m -= nrl;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    /* return pointer to array of pointers to rows */ 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return m; 
   m[nrl] += NR_END;  } 
   m[nrl] -= ncl;  
   /****************** free_imatrix *************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));        long nch,ncl,nrh,nrl; 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");       /* free an int matrix allocated by imatrix() */ 
   m[nrl][ncl] += NR_END;  { 
   m[nrl][ncl] -= nll;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for (j=ncl+1; j<=nch; j++)    free((FREE_ARG) (m+nrl-NR_END)); 
     m[nrl][j]=m[nrl][j-1]+nlay;  } 
    
   for (i=nrl+1; i<=nrh; i++) {  /******************* matrix *******************************/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  double **matrix(long nrl, long nrh, long ncl, long nch)
     for (j=ncl+1; j<=nch; j++)  {
       m[i][j]=m[i][j-1]+nlay;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   }    double **m;
   return m;  
 }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /*************************free ma3x ************************/    m += NR_END;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m -= nrl;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /***************** f1dim *************************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern int ncom;    return m;
 extern double *pcom,*xicom;  }
 extern double (*nrfunc)(double []);  
    /*************************free matrix ************************/
 double f1dim(double x)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 {  {
   int j;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double f;    free((FREE_ARG)(m+nrl-NR_END));
   double *xt;  }
    
   xt=vector(1,ncom);  /******************* ma3x *******************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   f=(*nrfunc)(xt);  {
   free_vector(xt,1,ncom);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   return f;    double ***m;
 }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /*****************brent *************************/    if (!m) nrerror("allocation failure 1 in matrix()");
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m += NR_END;
 {    m -= nrl;
   int iter;  
   double a,b,d,etemp;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double fu,fv,fw,fx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double ftemp;    m[nrl] += NR_END;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m[nrl] -= ncl;
   double e=0.0;  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   x=w=v=bx;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   fw=fv=fx=(*f)(x);    m[nrl][ncl] += NR_END;
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl][ncl] -= nll;
     xm=0.5*(a+b);    for (j=ncl+1; j<=nch; j++) 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      m[nrl][j]=m[nrl][j-1]+nlay;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    
     printf(".");fflush(stdout);    for (i=nrl+1; i<=nrh; i++) {
 #ifdef DEBUG      m[i][ncl]=m[i-1l][ncl]+ncol*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);      for (j=ncl+1; j<=nch; j++) 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */        m[i][j]=m[i][j-1]+nlay;
 #endif    }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    return m;
       *xmin=x;  }
       return fx;  
     }  /*************************free ma3x ************************/
     ftemp=fu;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     if (fabs(e) > tol1) {  {
       r=(x-w)*(fx-fv);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       q=(x-v)*(fx-fw);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG)(m+nrl-NR_END));
       q=2.0*(q-r);  }
       if (q > 0.0) p = -p;  
       q=fabs(q);  /***************** f1dim *************************/
       etemp=e;  extern int ncom; 
       e=d;  extern double *pcom,*xicom;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  extern double (*nrfunc)(double []); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));   
       else {  double f1dim(double x) 
         d=p/q;  { 
         u=x+d;    int j; 
         if (u-a < tol2 || b-u < tol2)    double f;
           d=SIGN(tol1,xm-x);    double *xt; 
       }   
     } else {    xt=vector(1,ncom); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     }    f=(*nrfunc)(xt); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    free_vector(xt,1,ncom); 
     fu=(*f)(u);    return f; 
     if (fu <= fx) {  } 
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  /*****************brent *************************/
         SHFT(fv,fw,fx,fu)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         } else {  { 
           if (u < x) a=u; else b=u;    int iter; 
           if (fu <= fw || w == x) {    double a,b,d,etemp;
             v=w;    double fu,fv,fw,fx;
             w=u;    double ftemp;
             fv=fw;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             fw=fu;    double e=0.0; 
           } else if (fu <= fv || v == x || v == w) {   
             v=u;    a=(ax < cx ? ax : cx); 
             fv=fu;    b=(ax > cx ? ax : cx); 
           }    x=w=v=bx; 
         }    fw=fv=fx=(*f)(x); 
   }    for (iter=1;iter<=ITMAX;iter++) { 
   nrerror("Too many iterations in brent");      xm=0.5*(a+b); 
   *xmin=x;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   return fx;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 /****************** mnbrak ***********************/  #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);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      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 (*func)(double))      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 {  #endif
   double ulim,u,r,q, dum;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double fu;        *xmin=x; 
          return fx; 
   *fa=(*func)(*ax);      } 
   *fb=(*func)(*bx);      ftemp=fu;
   if (*fb > *fa) {      if (fabs(e) > tol1) { 
     SHFT(dum,*ax,*bx,dum)        r=(x-w)*(fx-fv); 
       SHFT(dum,*fb,*fa,dum)        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
   *cx=(*bx)+GOLD*(*bx-*ax);        q=2.0*(q-r); 
   *fc=(*func)(*cx);        if (q > 0.0) p = -p; 
   while (*fb > *fc) {        q=fabs(q); 
     r=(*bx-*ax)*(*fb-*fc);        etemp=e; 
     q=(*bx-*cx)*(*fb-*fa);        e=d; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        else { 
     if ((*bx-u)*(u-*cx) > 0.0) {          d=p/q; 
       fu=(*func)(u);          u=x+d; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {          if (u-a < tol2 || b-u < tol2) 
       fu=(*func)(u);            d=SIGN(tol1,xm-x); 
       if (fu < *fc) {        } 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      } else { 
           SHFT(*fb,*fc,fu,(*func)(u))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           }      } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       u=ulim;      fu=(*f)(u); 
       fu=(*func)(u);      if (fu <= fx) { 
     } else {        if (u >= x) a=x; else b=x; 
       u=(*cx)+GOLD*(*cx-*bx);        SHFT(v,w,x,u) 
       fu=(*func)(u);          SHFT(fv,fw,fx,fu) 
     }          } else { 
     SHFT(*ax,*bx,*cx,u)            if (u < x) a=u; else b=u; 
       SHFT(*fa,*fb,*fc,fu)            if (fu <= fw || w == x) { 
       }              v=w; 
 }              w=u; 
               fv=fw; 
 /*************** linmin ************************/              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 int ncom;              v=u; 
 double *pcom,*xicom;              fv=fu; 
 double (*nrfunc)(double []);            } 
            } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    } 
 {    nrerror("Too many iterations in brent"); 
   double brent(double ax, double bx, double cx,    *xmin=x; 
                double (*f)(double), double tol, double *xmin);    return fx; 
   double f1dim(double x);  } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  /****************** mnbrak ***********************/
   int j;  
   double xx,xmin,bx,ax;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double fx,fb,fa;              double (*func)(double)) 
    { 
   ncom=n;    double ulim,u,r,q, dum;
   pcom=vector(1,n);    double fu; 
   xicom=vector(1,n);   
   nrfunc=func;    *fa=(*func)(*ax); 
   for (j=1;j<=n;j++) {    *fb=(*func)(*bx); 
     pcom[j]=p[j];    if (*fb > *fa) { 
     xicom[j]=xi[j];      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
   ax=0.0;        } 
   xx=1.0;    *cx=(*bx)+GOLD*(*bx-*ax); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    *fc=(*func)(*cx); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    while (*fb > *fc) { 
 #ifdef DEBUG      r=(*bx-*ax)*(*fb-*fc); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      q=(*bx-*cx)*(*fb-*fa); 
 #endif      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for (j=1;j<=n;j++) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     xi[j] *= xmin;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     p[j] += xi[j];      if ((*bx-u)*(u-*cx) > 0.0) { 
   }        fu=(*func)(u); 
   free_vector(xicom,1,n);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   free_vector(pcom,1,n);        fu=(*func)(u); 
 }        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 /*************** powell ************************/            SHFT(*fb,*fc,fu,(*func)(u)) 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,            } 
             double (*func)(double []))      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 {        u=ulim; 
   void linmin(double p[], double xi[], int n, double *fret,        fu=(*func)(u); 
               double (*func)(double []));      } else { 
   int i,ibig,j;        u=(*cx)+GOLD*(*cx-*bx); 
   double del,t,*pt,*ptt,*xit;        fu=(*func)(u); 
   double fp,fptt;      } 
   double *xits;      SHFT(*ax,*bx,*cx,u) 
   pt=vector(1,n);        SHFT(*fa,*fb,*fc,fu) 
   ptt=vector(1,n);        } 
   xit=vector(1,n);  } 
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************** linmin ************************/
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  int ncom; 
     fp=(*fret);  double *pcom,*xicom;
     ibig=0;  double (*nrfunc)(double []); 
     del=0.0;   
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (i=1;i<=n;i++)  { 
       printf(" %d %.12f",i, p[i]);    double brent(double ax, double bx, double cx, 
     printf("\n");                 double (*f)(double), double tol, double *xmin); 
     for (i=1;i<=n;i++) {    double f1dim(double x); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       fptt=(*fret);                double *fc, double (*func)(double)); 
 #ifdef DEBUG    int j; 
       printf("fret=%lf \n",*fret);    double xx,xmin,bx,ax; 
 #endif    double fx,fb,fa;
       printf("%d",i);fflush(stdout);   
       linmin(p,xit,n,fret,func);    ncom=n; 
       if (fabs(fptt-(*fret)) > del) {    pcom=vector(1,n); 
         del=fabs(fptt-(*fret));    xicom=vector(1,n); 
         ibig=i;    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
 #ifdef DEBUG      pcom[j]=p[j]; 
       printf("%d %.12e",i,(*fret));      xicom[j]=xi[j]; 
       for (j=1;j<=n;j++) {    } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    ax=0.0; 
         printf(" x(%d)=%.12e",j,xit[j]);    xx=1.0; 
       }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       for(j=1;j<=n;j++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         printf(" p=%.12e",p[j]);  #ifdef DEBUG
       printf("\n");    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    for (j=1;j<=n;j++) { 
 #ifdef DEBUG      xi[j] *= xmin; 
       int k[2],l;      p[j] += xi[j]; 
       k[0]=1;    } 
       k[1]=-1;    free_vector(xicom,1,n); 
       printf("Max: %.12e",(*func)(p));    free_vector(pcom,1,n); 
       for (j=1;j<=n;j++)  } 
         printf(" %.12e",p[j]);  
       printf("\n");  /*************** powell ************************/
       for(l=0;l<=1;l++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         for (j=1;j<=n;j++) {              double (*func)(double [])) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    void linmin(double p[], double xi[], int n, double *fret, 
         }                double (*func)(double [])); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int i,ibig,j; 
       }    double del,t,*pt,*ptt,*xit;
 #endif    double fp,fptt;
     double *xits;
     pt=vector(1,n); 
       free_vector(xit,1,n);    ptt=vector(1,n); 
       free_vector(xits,1,n);    xit=vector(1,n); 
       free_vector(ptt,1,n);    xits=vector(1,n); 
       free_vector(pt,1,n);    *fret=(*func)(p); 
       return;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      fp=(*fret); 
     for (j=1;j<=n;j++) {      ibig=0; 
       ptt[j]=2.0*p[j]-pt[j];      del=0.0; 
       xit[j]=p[j]-pt[j];      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       pt[j]=p[j];      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      for (i=1;i<=n;i++) 
     fptt=(*func)(ptt);        printf(" %d %.12f",i, p[i]);
     if (fptt < fp) {      fprintf(ficlog," %d %.12f",i, p[i]);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      printf("\n");
       if (t < 0.0) {      fprintf(ficlog,"\n");
         linmin(p,xit,n,fret,func);      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           xi[j][ibig]=xi[j][n];        fptt=(*fret); 
           xi[j][n]=xit[j];  #ifdef DEBUG
         }        printf("fret=%lf \n",*fret);
 #ifdef DEBUG        fprintf(ficlog,"fret=%lf \n",*fret);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #endif
         for(j=1;j<=n;j++)        printf("%d",i);fflush(stdout);
           printf(" %.12e",xit[j]);        fprintf(ficlog,"%d",i);fflush(ficlog);
         printf("\n");        linmin(p,xit,n,fret,func); 
 #endif        if (fabs(fptt-(*fret)) > del) { 
       }          del=fabs(fptt-(*fret)); 
     }          ibig=i; 
   }        } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 /**** Prevalence limit ****************/        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 {          printf(" x(%d)=%.12e",j,xit[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
      matrix by transitions matrix until convergence is reached */        }
         for(j=1;j<=n;j++) {
   int i, ii,j,k;          printf(" p=%.12e",p[j]);
   double min, max, maxmin, maxmax,sumnew=0.;          fprintf(ficlog," p=%.12e",p[j]);
   double **matprod2();        }
   double **out, cov[NCOVMAX], **pmij();        printf("\n");
   double **newm;        fprintf(ficlog,"\n");
   double agefin, delaymax=50 ; /* Max number of years to converge */  #endif
       } 
   for (ii=1;ii<=nlstate+ndeath;ii++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for (j=1;j<=nlstate+ndeath;j++){  #ifdef DEBUG
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        int k[2],l;
     }        k[0]=1;
         k[1]=-1;
    cov[1]=1.;        printf("Max: %.12e",(*func)(p));
          fprintf(ficlog,"Max: %.12e",(*func)(p));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        for (j=1;j<=n;j++) {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){          printf(" %.12e",p[j]);
     newm=savm;          fprintf(ficlog," %.12e",p[j]);
     /* Covariates have to be included here again */        }
      cov[2]=agefin;        printf("\n");
          fprintf(ficlog,"\n");
       for (k=1; k<=cptcovn;k++) {        for(l=0;l<=1;l++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          for (j=1;j<=n;j++) {
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (k=1; k<=cptcovage;k++)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
       for (k=1; k<=cptcovprod;k++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #endif
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
     savm=oldm;        free_vector(ptt,1,n); 
     oldm=newm;        free_vector(pt,1,n); 
     maxmax=0.;        return; 
     for(j=1;j<=nlstate;j++){      } 
       min=1.;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       max=0.;      for (j=1;j<=n;j++) { 
       for(i=1; i<=nlstate; i++) {        ptt[j]=2.0*p[j]-pt[j]; 
         sumnew=0;        xit[j]=p[j]-pt[j]; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        pt[j]=p[j]; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      } 
         max=FMAX(max,prlim[i][j]);      fptt=(*func)(ptt); 
         min=FMIN(min,prlim[i][j]);      if (fptt < fp) { 
       }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       maxmin=max-min;        if (t < 0.0) { 
       maxmax=FMAX(maxmax,maxmin);          linmin(p,xit,n,fret,func); 
     }          for (j=1;j<=n;j++) { 
     if(maxmax < ftolpl){            xi[j][ibig]=xi[j][n]; 
       return prlim;            xi[j][n]=xit[j]; 
     }          }
   }  #ifdef DEBUG
 }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 /*************** transition probabilities ***************/          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )            fprintf(ficlog," %.12e",xit[j]);
 {          }
   double s1, s2;          printf("\n");
   /*double t34;*/          fprintf(ficlog,"\n");
   int i,j,j1, nc, ii, jj;  #endif
         }
     for(i=1; i<= nlstate; i++){      } 
     for(j=1; j<i;j++){    } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  } 
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /**** Prevalence limit (stable prevalence)  ****************/
         /*printf("Int j<i 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)
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    int i, ii,j,k;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double min, max, maxmin, maxmax,sumnew=0.;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double **matprod2();
       }    double **out, cov[NCOVMAX], **pmij();
       ps[i][j]=(s2);    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
   }  
     /*ps[3][2]=1;*/    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<= nlstate; i++){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      s1=0;      }
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);     cov[1]=1.;
     for(j=i+1; j<=nlstate+ndeath; j++)   
       s1+=exp(ps[i][j]);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     ps[i][i]=1./(s1+1.);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(j=1; j<i; j++)      newm=savm;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      /* Covariates have to be included here again */
     for(j=i+1; j<=nlstate+ndeath; j++)       cov[2]=agefin;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        for (k=1; k<=cptcovn;k++) {
   } /* end i */          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(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        }
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ps[ii][jj]=0;        for (k=1; k<=cptcovprod;k++)
       ps[ii][ii]=1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
   }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*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]);*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);      savm=oldm;
    }      oldm=newm;
     printf("\n ");      maxmax=0.;
     }      for(j=1;j<=nlstate;j++){
     printf("\n ");printf("%lf ",cov[2]);*/        min=1.;
 /*        max=0.;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        for(i=1; i<=nlstate; i++) {
   goto end;*/          sumnew=0;
     return ps;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 }          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
 /**************** Product of 2 matrices ******************/          min=FMIN(min,prlim[i][j]);
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        maxmin=max-min;
 {        maxmax=FMAX(maxmax,maxmin);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      if(maxmax < ftolpl){
   /* in, b, out are matrice of pointers which should have been initialized        return prlim;
      before: only the contents of out is modified. The function returns      }
      a pointer to pointers identical to out */    }
   long i, j, k;  }
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /*************** transition probabilities ***************/ 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   return out;    double s1, s2;
 }    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   
 /************* Higher Matrix Product ***************/      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {          /*s2 += param[i][j][nc]*cov[nc];*/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      duration (i.e. until          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        }
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        ps[i][j]=s2;
      (typically every 2 years instead of every month which is too big).        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
      Model is determined by parameters x and covariates have to be      }
      included manually here.      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   int i, j, d, h, k;        }
   double **out, cov[NCOVMAX];        ps[i][j]=s2;
   double **newm;      }
     }
   /* Hstepm could be zero and should return the unit matrix */      /*ps[3][2]=1;*/
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){    for(i=1; i<= nlstate; i++){
       oldm[i][j]=(i==j ? 1.0 : 0.0);       s1=0;
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for(j=1; j<i; j++)
     }        s1+=exp(ps[i][j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for(j=i+1; j<=nlstate+ndeath; j++)
   for(h=1; h <=nhstepm; h++){        s1+=exp(ps[i][j]);
     for(d=1; d <=hstepm; d++){      ps[i][i]=1./(s1+1.);
       newm=savm;      for(j=1; j<i; j++)
       /* Covariates have to be included here again */        ps[i][j]= exp(ps[i][j])*ps[i][i];
       cov[1]=1.;      for(j=i+1; j<=nlstate+ndeath; j++)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for (k=1; k<=cptcovage;k++)    } /* end i */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;
         ps[ii][ii]=1;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      }
       /*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,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       oldm=newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
     }       printf("%lf ",ps[ii][jj]);
     for(i=1; i<=nlstate+ndeath; i++)     }
       for(j=1;j<=nlstate+ndeath;j++) {      printf("\n ");
         po[i][j][h]=newm[i][j];      }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      printf("\n ");printf("%lf ",cov[2]);*/
          */  /*
       }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   } /* end h */    goto end;*/
   return po;      return ps;
 }  }
   
   /**************** Product of 2 matrices ******************/
 /*************** log-likelihood *************/  
 double func( double *x)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 {  {
   int i, ii, j, k, mi, d, kk;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double **out;    /* in, b, out are matrice of pointers which should have been initialized 
   double sw; /* Sum of weights */       before: only the contents of out is modified. The function returns
   double lli; /* Individual log likelihood */       a pointer to pointers identical to out */
   long ipmx;    long i, j, k;
   /*extern weight */    for(i=nrl; i<= nrh; i++)
   /* We are differentiating ll according to initial status */      for(k=ncolol; k<=ncoloh; k++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   /*for(i=1;i<imx;i++)          out[i][k] +=in[i][j]*b[j][k];
     printf(" %d\n",s[4][i]);  
   */    return out;
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /************* Higher Matrix Product ***************/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for (ii=1;ii<=nlstate+ndeath;ii++)  {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /* Computes the transition matrix starting at age 'age' over 
       for(d=0; d<dh[mi][i]; d++){       'nhstepm*hstepm*stepm' months (i.e. until
         newm=savm;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       nhstepm*hstepm matrices. 
         for (kk=1; kk<=cptcovage;kk++) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       (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 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       included manually here. 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;       */
         oldm=newm;  
            int i, j, d, h, k;
            double **out, cov[NCOVMAX];
       } /* end mult */    double **newm;
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    /* Hstepm could be zero and should return the unit matrix */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    for (i=1;i<=nlstate+ndeath;i++)
       ipmx +=1;      for (j=1;j<=nlstate+ndeath;j++){
       sw += weight[i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        po[i][j][0]=(i==j ? 1.0 : 0.0);
     } /* end of wave */      }
   } /* end of individual */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      for(d=1; d <=hstepm; d++){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        newm=savm;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        /* Covariates have to be included here again */
   return -l;        cov[1]=1.;
 }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 /*********** Maximum Likelihood Estimation ***************/          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 {  
   int i,j, iter;  
   double **xi,*delti;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double fret;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   xi=matrix(1,npar,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   for (i=1;i<=npar;i++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (j=1;j<=npar;j++)        savm=oldm;
       xi[i][j]=(i==j ? 1.0 : 0.0);        oldm=newm;
   printf("Powell\n");      }
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          po[i][j][h]=newm[i][j];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
 }        }
     } /* end h */
 /**** Computes Hessian and covariance matrix ***/    return po;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  
   double **hess;  /*************** log-likelihood *************/
   int i, j,jk;  double func( double *x)
   int *indx;  {
     int i, ii, j, k, mi, d, kk;
   double hessii(double p[], double delta, int theta, double delti[]);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double hessij(double p[], double delti[], int i, int j);    double **out;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double sw; /* Sum of weights */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double lli; /* Individual log likelihood */
     int s1, s2;
   hess=matrix(1,npar,1,npar);    double bbh, survp;
     long ipmx;
   printf("\nCalculation of the hessian matrix. Wait...\n");    /*extern weight */
   for (i=1;i<=npar;i++){    /* We are differentiating ll according to initial status */
     printf("%d",i);fflush(stdout);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     hess[i][i]=hessii(p,ftolhess,i,delti);    /*for(i=1;i<imx;i++) 
     /*printf(" %f ",p[i]);*/      printf(" %d\n",s[4][i]);
     /*printf(" %lf ",hess[i][i]);*/    */
   }    cov[1]=1.;
    
   for (i=1;i<=npar;i++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (j=1;j<=npar;j++)  {  
       if (j>i) {    if(mle==1){
         printf(".%d%d",i,j);fflush(stdout);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         hess[i][j]=hessij(p,delti,i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         hess[j][i]=hess[i][j];            for(mi=1; mi<= wav[i]-1; mi++){
         /*printf(" %lf ",hess[i][j]);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\n");            }
           for(d=0; d<dh[mi][i]; d++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   a=matrix(1,npar,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   y=matrix(1,npar,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   x=vector(1,npar);            }
   indx=ivector(1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (i=1;i<=npar;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            savm=oldm;
   ludcmp(a,npar,indx,&pd);            oldm=newm;
           } /* end mult */
   for (j=1;j<=npar;j++) {        
     for (i=1;i<=npar;i++) x[i]=0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     x[j]=1;          /* But now since version 0.9 we anticipate for bias and large stepm.
     lubksb(a,npar,indx,x);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<=npar;i++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
       matcov[i][j]=x[i];           * 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
            * probability in order to take into account the bias as a fraction of the way
   printf("\n#Hessian matrix#\n");           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=npar;i++) {           * -stepm/2 to stepm/2 .
     for (j=1;j<=npar;j++) {           * For stepm=1 the results are the same as for previous versions of Imach.
       printf("%.3e ",hess[i][j]);           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
     printf("\n");          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   /* Recompute Inverse */          /* bias is positive if real duration
   for (i=1;i<=npar;i++)           * is higher than the multiple of stepm and negative otherwise.
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];           */
   ludcmp(a,npar,indx,&pd);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   /*  printf("\n#Hessian matrix recomputed#\n");            /* i.e. if s2 is a death state and if the date of death is known then the contribution
                to the likelihood is the probability to die between last step unit time and current 
   for (j=1;j<=npar;j++) {               step unit time, which is also the differences between probability to die before dh 
     for (i=1;i<=npar;i++) x[i]=0;               and probability to die before dh-stepm . 
     x[j]=1;               In version up to 0.92 likelihood was computed
     lubksb(a,npar,indx,x);          as if date of death was unknown. Death was treated as any other
     for (i=1;i<=npar;i++){          health state: the date of the interview describes the actual state
       y[i][j]=x[i];          and not the date of a change in health state. The former idea was
       printf("%.3e ",y[i][j]);          to consider that at each interview the state was recorded
     }          (healthy, disable or death) and IMaCh was corrected; but when we
     printf("\n");          introduced the exact date of death then we should have modified
   }          the contribution of an exact death to the likelihood. This new
   */          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
   free_matrix(a,1,npar,1,npar);          and month of death but the probability to survive from last
   free_matrix(y,1,npar,1,npar);          interview up to one month before death multiplied by the
   free_vector(x,1,npar);          probability to die within a month. Thanks to Chris
   free_ivector(indx,1,npar);          Jackson for correcting this bug.  Former versions increased
   free_matrix(hess,1,npar,1,npar);          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
           lower mortality.
 }            */
             lli=log(out[s1][s2] - savm[s1][s2]);
 /*************** hessian matrix ****************/          }else{
 double hessii( double x[], double delta, int theta, double delti[])            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 {            /*  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 i;          } 
   int l=1, lmax=20;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double k1,k2;          /*if(lli ==000.0)*/
   double p2[NPARMAX+1];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   double res;          ipmx +=1;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          sw += weight[i];
   double fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int k=0,kmax=10;        } /* end of wave */
   double l1;      } /* end of individual */
     }  else if(mle==2){
   fx=func(x);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(l=0 ; l <=lmax; l++){        for(mi=1; mi<= wav[i]-1; mi++){
     l1=pow(10,l);          for (ii=1;ii<=nlstate+ndeath;ii++)
     delts=delt;            for (j=1;j<=nlstate+ndeath;j++){
     for(k=1 ; k <kmax; k=k+1){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       delt = delta*(l1*k);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       p2[theta]=x[theta] +delt;            }
       k1=func(p2)-fx;          for(d=0; d<=dh[mi][i]; d++){
       p2[theta]=x[theta]-delt;            newm=savm;
       k2=func(p2)-fx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /*res= (k1-2.0*fx+k2)/delt/delt; */            for (kk=1; kk<=cptcovage;kk++) {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
 #ifdef DEBUG            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       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);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #endif            savm=oldm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            oldm=newm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          } /* end mult */
         k=kmax;        
       }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          /* But now since version 0.9 we anticipate for bias and large stepm.
         k=kmax; l=lmax*10.;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * the nearest (and in case of equal distance, to the lowest) interval but now
         delts=delt;           * 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
     }           * 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
   delti[theta]=delts;           * -stepm/2 to stepm/2 .
   return res;           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
 }           */
           s1=s[mw[mi][i]][i];
 double hessij( double x[], double delti[], int thetai,int thetaj)          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   int i;          /* bias is positive if real duration
   int l=1, l1, lmax=20;           * is higher than the multiple of stepm and negative otherwise.
   double k1,k2,k3,k4,res,fx;           */
   double p2[NPARMAX+1];          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;          /* 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 */
   fx=func(x);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (k=1; k<=2; k++) {          /*if(lli ==000.0)*/
     for (i=1;i<=npar;i++) p2[i]=x[i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          ipmx +=1;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          sw += weight[i];
     k1=func(p2)-fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
     p2[thetai]=x[thetai]+delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    }  else if(mle==3){  /* exponential inter-extrapolation */
     k2=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k3=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]-delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            }
     k4=func(p2)-fx;          for(d=0; d<dh[mi][i]; d++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            newm=savm;
 #ifdef DEBUG            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     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 (kk=1; kk<=cptcovage;kk++) {
 #endif              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   return res;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 /************** Inverse of matrix **************/            oldm=newm;
 void ludcmp(double **a, int n, int *indx, double *d)          } /* end mult */
 {        
   int i,imax,j,k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double big,dum,sum,temp;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double *vv;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
   vv=vector(1,n);           * the nearest (and in case of equal distance, to the lowest) interval but now
   *d=1.0;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   for (i=1;i<=n;i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     big=0.0;           * probability in order to take into account the bias as a fraction of the way
     for (j=1;j<=n;j++)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       if ((temp=fabs(a[i][j])) > big) big=temp;           * -stepm/2 to stepm/2 .
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * For stepm=1 the results are the same as for previous versions of Imach.
     vv[i]=1.0/big;           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   for (j=1;j<=n;j++) {          s1=s[mw[mi][i]][i];
     for (i=1;i<j;i++) {          s2=s[mw[mi+1][i]][i];
       sum=a[i][j];          bbh=(double)bh[mi][i]/(double)stepm; 
       for (k=1;k<i;k++) 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.
     }           */
     big=0.0;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     for (i=j;i<=n;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 */
       sum=a[i][j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for (k=1;k<j;k++)          /*if(lli ==000.0)*/
         sum -= a[i][k]*a[k][j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       a[i][j]=sum;          ipmx +=1;
       if ( (dum=vv[i]*fabs(sum)) >= big) {          sw += weight[i];
         big=dum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         imax=i;        } /* end of wave */
       }      } /* end of individual */
     }    }else{  /* ml=4 no inter-extrapolation */
     if (j != imax) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1;k<=n;k++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         dum=a[imax][k];        for(mi=1; mi<= wav[i]-1; mi++){
         a[imax][k]=a[j][k];          for (ii=1;ii<=nlstate+ndeath;ii++)
         a[j][k]=dum;            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       *d = -(*d);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       vv[imax]=vv[j];            }
     }          for(d=0; d<dh[mi][i]; d++){
     indx[j]=imax;            newm=savm;
     if (a[j][j] == 0.0) a[j][j]=TINY;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (j != n) {            for (kk=1; kk<=cptcovage;kk++) {
       dum=1.0/(a[j][j]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            }
     }          
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(vv,1,n);  /* Doesn't work */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 ;            savm=oldm;
 }            oldm=newm;
           } /* end mult */
 void lubksb(double **a, int n, int *indx, double b[])        
 {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   int i,ii=0,ip,j;          ipmx +=1;
   double sum;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (i=1;i<=n;i++) {        } /* end of wave */
     ip=indx[i];      } /* end of individual */
     sum=b[ip];    } /* End of if */
     b[ip]=b[i];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     if (ii)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     else if (sum) ii=i;    return -l;
     b[i]=sum;  }
   }  
   for (i=n;i>=1;i--) {  
     sum=b[i];  /*********** Maximum Likelihood Estimation ***************/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
 }    int i,j, iter;
     double **xi,*delti;
 /************ Frequencies ********************/    double fret;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)    xi=matrix(1,npar,1,npar);
 {  /* Some frequencies */    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double *pp;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   char fileresp[FILENAMELENGTH];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  /**** Computes Hessian and covariance matrix ***/
   if((ficresp=fopen(fileresp,"w"))==NULL) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     printf("Problem with prevalence resultfile: %s\n", fileresp);  {
     exit(0);    double  **a,**y,*x,pd;
   }    double **hess;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int i, j,jk;
   j1=0;    int *indx;
   
   j=cptcoveff;    double hessii(double p[], double delta, int theta, double delti[]);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double hessij(double p[], double delti[], int i, int j);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
   for(k1=1; k1<=j;k1++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;    hess=matrix(1,npar,1,npar);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
          scanf("%d", i);*/    printf("\nCalculation of the hessian matrix. Wait...\n");
         for (i=-1; i<=nlstate+ndeath; i++)      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
          for (jk=-1; jk<=nlstate+ndeath; jk++)      for (i=1;i<=npar;i++){
            for(m=agemin; m <= agemax+3; m++)      printf("%d",i);fflush(stdout);
              freq[i][jk][m]=0;      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
         dateintsum=0;      /*printf(" %f ",p[i]);*/
         k2cpt=0;      /*printf(" %lf ",hess[i][i]);*/
        for (i=1; i<=imx; i++) {    }
          bool=1;    
          if  (cptcovn>0) {    for (i=1;i<=npar;i++) {
            for (z1=1; z1<=cptcoveff; z1++)      for (j=1;j<=npar;j++)  {
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        if (j>i) { 
                bool=0;          printf(".%d%d",i,j);fflush(stdout);
          }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
          if (bool==1) {          hess[i][j]=hessij(p,delti,i,j);
            for(m=firstpass; m<=lastpass; m++){          hess[j][i]=hess[i][j];    
              k2=anint[m][i]+(mint[m][i]/12.);          /*printf(" %lf ",hess[i][j]);*/
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        }
                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];    printf("\n");
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    fprintf(ficlog,"\n");
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                  dateintsum=dateintsum+k2;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                  k2cpt++;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                }    
     a=matrix(1,npar,1,npar);
              }    y=matrix(1,npar,1,npar);
            }    x=vector(1,npar);
          }    indx=ivector(1,npar);
        }    for (i=1;i<=npar;i++)
         if  (cptcovn>0) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
          fprintf(ficresp, "\n#********** Variable ");    ludcmp(a,npar,indx,&pd);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
        fprintf(ficresp, "**********\n#");    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
        for(i=1; i<=nlstate;i++)      x[j]=1;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      lubksb(a,npar,indx,x);
        fprintf(ficresp, "\n");      for (i=1;i<=npar;i++){ 
                matcov[i][j]=x[i];
   for(i=(int)agemin; i <= (int)agemax+3; i++){      }
     if(i==(int)agemax+3)    }
       printf("Total");  
     else    printf("\n#Hessian matrix#\n");
       printf("Age %d", i);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++) { 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (j=1;j<=npar;j++) { 
         pp[jk] += freq[jk][m][i];        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
     for(jk=1; jk <=nlstate ; jk++){      }
       for(m=-1, pos=0; m <=0 ; m++)      printf("\n");
         pos += freq[jk][m][i];      fprintf(ficlog,"\n");
       if(pp[jk]>=1.e-10)    }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
       else    /* Recompute Inverse */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    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 ; jk++){  
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /*  printf("\n#Hessian matrix recomputed#\n");
         pp[jk] += freq[jk][m][i];  
      }    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
     for(jk=1,pos=0; jk <=nlstate ; jk++)      x[j]=1;
       pos += pp[jk];      lubksb(a,npar,indx,x);
     for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++){ 
       if(pos>=1.e-5)        y[i][j]=x[i];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        printf("%.3e ",y[i][j]);
       else        fprintf(ficlog,"%.3e ",y[i][j]);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
       if( i <= (int) agemax){      printf("\n");
         if(pos>=1.e-5){      fprintf(ficlog,"\n");
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    }
           probs[i][jk][j1]= pp[jk]/pos;    */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
         }    free_matrix(a,1,npar,1,npar);
       else    free_matrix(y,1,npar,1,npar);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    free_vector(x,1,npar);
       }    free_ivector(indx,1,npar);
     }    free_matrix(hess,1,npar,1,npar);
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  }
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /*************** hessian matrix ****************/
     printf("\n");  double hessii( double x[], double delta, int theta, double delti[])
     }  {
     }    int i;
  }    int l=1, lmax=20;
   dateintmean=dateintsum/k2cpt;    double k1,k2;
      double p2[NPARMAX+1];
   fclose(ficresp);    double res;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   free_vector(pp,1,nlstate);    double fx;
     int k=0,kmax=10;
   /* End of Freq */    double l1;
 }  
     fx=func(x);
 /************ Prevalence ********************/    for (i=1;i<=npar;i++) p2[i]=x[i];
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    for(l=0 ; l <=lmax; l++){
 {  /* Some frequencies */      l1=pow(10,l);
        delts=delt;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      for(k=1 ; k <kmax; k=k+1){
   double ***freq; /* Frequencies */        delt = delta*(l1*k);
   double *pp;        p2[theta]=x[theta] +delt;
   double pos, k2;        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
   pp=vector(1,nlstate);        k2=func(p2)-fx;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        
   j1=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);
   j=cptcoveff;        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);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  for(k1=1; k1<=j;k1++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(i1=1; i1<=ncodemax[k1];i1++){          k=kmax;
       j1++;        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for (i=-1; i<=nlstate+ndeath; i++)            k=kmax; l=lmax*10.;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          }
           for(m=agemin; m <= agemax+3; m++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             freq[i][jk][m]=0;          delts=delt;
              }
       for (i=1; i<=imx; i++) {      }
         bool=1;    }
         if  (cptcovn>0) {    delti[theta]=delts;
           for (z1=1; z1<=cptcoveff; z1++)    return res; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    
               bool=0;  }
         }  
         if (bool==1) {  double hessij( double x[], double delti[], int thetai,int thetaj)
           for(m=firstpass; m<=lastpass; m++){  {
             k2=anint[m][i]+(mint[m][i]/12.);    int i;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    int l=1, l1, lmax=20;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double k1,k2,k3,k4,res,fx;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double p2[NPARMAX+1];
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    int k;
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];    
             }    fx=func(x);
           }    for (k=1; k<=2; k++) {
         }      for (i=1;i<=npar;i++) p2[i]=x[i];
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
            p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(i=(int)agemin; i <= (int)agemax+3; i++){      k1=func(p2)-fx;
           for(jk=1; jk <=nlstate ; jk++){    
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      p2[thetai]=x[thetai]+delti[thetai]/k;
               pp[jk] += freq[jk][m][i];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           }      k2=func(p2)-fx;
           for(jk=1; jk <=nlstate ; jk++){    
             for(m=-1, pos=0; m <=0 ; m++)      p2[thetai]=x[thetai]-delti[thetai]/k;
             pos += freq[jk][m][i];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k3=func(p2)-fx;
            
          for(jk=1; jk <=nlstate ; jk++){      p2[thetai]=x[thetai]-delti[thetai]/k;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
              pp[jk] += freq[jk][m][i];      k4=func(p2)-fx;
          }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
            #ifdef DEBUG
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      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(jk=1; jk <=nlstate ; jk++){            #endif
            if( i <= (int) agemax){    }
              if(pos>=1.e-5){    return res;
                probs[i][jk][j1]= pp[jk]/pos;  }
              }  
            }  /************** Inverse of matrix **************/
          }  void ludcmp(double **a, int n, int *indx, double *d) 
            { 
         }    int i,imax,j,k; 
     }    double big,dum,sum,temp; 
   }    double *vv; 
     
      vv=vector(1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    *d=1.0; 
   free_vector(pp,1,nlstate);    for (i=1;i<=n;i++) { 
        big=0.0; 
 }  /* End of Freq */      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
 /************* Waves Concatenation ***************/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    } 
 {    for (j=1;j<=n;j++) { 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for (i=1;i<j;i++) { 
      Death is a valid wave (if date is known).        sum=a[i][j]; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        a[i][j]=sum; 
      and mw[mi+1][i]. dh depends on stepm.      } 
      */      big=0.0; 
       for (i=j;i<=n;i++) { 
   int i, mi, m;        sum=a[i][j]; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (k=1;k<j;k++) 
      double sum=0., jmean=0.;*/          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   int j, k=0,jk, ju, jl;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double sum=0.;          big=dum; 
   jmin=1e+5;          imax=i; 
   jmax=-1;        } 
   jmean=0.;      } 
   for(i=1; i<=imx; i++){      if (j != imax) { 
     mi=0;        for (k=1;k<=n;k++) { 
     m=firstpass;          dum=a[imax][k]; 
     while(s[m][i] <= nlstate){          a[imax][k]=a[j][k]; 
       if(s[m][i]>=1)          a[j][k]=dum; 
         mw[++mi][i]=m;        } 
       if(m >=lastpass)        *d = -(*d); 
         break;        vv[imax]=vv[j]; 
       else      } 
         m++;      indx[j]=imax; 
     }/* end while */      if (a[j][j] == 0.0) a[j][j]=TINY; 
     if (s[m][i] > nlstate){      if (j != n) { 
       mi++;     /* Death is another wave */        dum=1.0/(a[j][j]); 
       /* if(mi==0)  never been interviewed correctly before death */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          /* Only death is a correct wave */      } 
       mw[mi][i]=m;    } 
     }    free_vector(vv,1,n);  /* Doesn't work */
   ;
     wav[i]=mi;  } 
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  void lubksb(double **a, int n, int *indx, double b[]) 
   }  { 
     int i,ii=0,ip,j; 
   for(i=1; i<=imx; i++){    double sum; 
     for(mi=1; mi<wav[i];mi++){   
       if (stepm <=0)    for (i=1;i<=n;i++) { 
         dh[mi][i]=1;      ip=indx[i]; 
       else{      sum=b[ip]; 
         if (s[mw[mi+1][i]][i] > nlstate) {      b[ip]=b[i]; 
           if (agedc[i] < 2*AGESUP) {      if (ii) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           if(j==0) j=1;  /* Survives at least one month after exam */      else if (sum) ii=i; 
           k=k+1;      b[i]=sum; 
           if (j >= jmax) jmax=j;    } 
           if (j <= jmin) jmin=j;    for (i=n;i>=1;i--) { 
           sum=sum+j;      sum=b[i]; 
           /* if (j<10) printf("j=%d num=%d ",j,i); */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           }      b[i]=sum/a[i][i]; 
         }    } 
         else{  } 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  /************ Frequencies ********************/
           if (j >= jmax) jmax=j;  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
           else if (j <= jmin)jmin=j;  {  /* Some frequencies */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    
           sum=sum+j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         }    int first;
         jk= j/stepm;    double ***freq; /* Frequencies */
         jl= j -jk*stepm;    double *pp, **prop;
         ju= j -(jk+1)*stepm;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         if(jl <= -ju)    FILE *ficresp;
           dh[mi][i]=jk;    char fileresp[FILENAMELENGTH];
         else    
           dh[mi][i]=jk+1;    pp=vector(1,nlstate);
         if(dh[mi][i]==0)    prop=matrix(1,nlstate,agemin,agemax+3);
           dh[mi][i]=1; /* At least one step */    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }    strcpy(fileresp,"p");
     }    strcat(fileresp,fileres);
   }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   jmean=sum/k;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
  }      exit(0);
 /*********** Tricode ****************************/    }
 void tricode(int *Tvar, int **nbcode, int imx)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 {    j1=0;
   int Ndum[20],ij=1, k, j, i;    
   int cptcode=0;    j=cptcoveff;
   cptcoveff=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
   for (k=0; k<19; k++) Ndum[k]=0;    first=1;
   for (k=1; k<=7; k++) ncodemax[k]=0;  
     for(k1=1; k1<=j;k1++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for(i1=1; i1<=ncodemax[k1];i1++){
     for (i=1; i<=imx; i++) {        j1++;
       ij=(int)(covar[Tvar[j]][i]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       Ndum[ij]++;          scanf("%d", i);*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for (i=-1; i<=nlstate+ndeath; i++)  
       if (ij > cptcode) cptcode=ij;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     }            for(m=agemin; m <= agemax+3; m++)
               freq[i][jk][m]=0;
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;      for (i=1; i<=nlstate; i++)  
     }        for(m=agemin; m <= agemax+3; m++)
     ij=1;          prop[i][m]=0;
         
         dateintsum=0;
     for (i=1; i<=ncodemax[j]; i++) {        k2cpt=0;
       for (k=0; k<=19; k++) {        for (i=1; i<=imx; i++) {
         if (Ndum[k] != 0) {          bool=1;
           nbcode[Tvar[j]][ij]=k;          if  (cptcovn>0) {
           ij++;            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         if (ij > ncodemax[j]) break;                bool=0;
       }            }
     }          if (bool==1){
   }              for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
  for (k=0; k<19; k++) Ndum[k]=0;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
  for (i=1; i<=ncovmodel-2; i++) {                if(agev[m][i]==1) agev[m][i]=agemax+2;
       ij=Tvar[i];                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       Ndum[ij]++;                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];
  ij=1;                }
  for (i=1; i<=10; i++) {                
    if((Ndum[i]!=0) && (i<=ncov)){                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
      Tvaraff[ij]=i;                  dateintsum=dateintsum+k2;
      ij++;                  k2cpt++;
    }                }
  }              }
              }
     cptcoveff=ij-1;          }
 }        }
          
 /*********** Health Expectancies ****************/        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        if  (cptcovn>0) {
 {          fprintf(ficresp, "\n#********** Variable "); 
   /* Health expectancies */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int i, j, nhstepm, hstepm, h;          fprintf(ficresp, "**********\n#");
   double age, agelim,hf;        }
   double ***p3mat;        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficresp, "\n");
   fprintf(ficreseij,"# Age");        
   for(i=1; i<=nlstate;i++)        for(i=(int)agemin; i <= (int)agemax+3; i++){
     for(j=1; j<=nlstate;j++)          if(i==(int)agemax+3){
       fprintf(ficreseij," %1d-%1d",i,j);            fprintf(ficlog,"Total");
   fprintf(ficreseij,"\n");          }else{
             if(first==1){
   hstepm=1*YEARM; /*  Every j years of age (in month) */              first=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              printf("See log file for details...\n");
             }
   agelim=AGESUP;            fprintf(ficlog,"Age %d", i);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     /* nhstepm age range expressed in number of stepm */          for(jk=1; jk <=nlstate ; jk++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     /* Typically if 20 years = 20*12/6=40 stepm */              pp[jk] += freq[jk][m][i]; 
     if (stepm >= YEARM) hstepm=1;          }
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          for(jk=1; jk <=nlstate ; jk++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(m=-1, pos=0; m <=0 ; m++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              pos += freq[jk][m][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            if(pp[jk]>=1.e-10){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(j=1; j<=nlstate;j++)            }else{
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){              if(first==1)
           eij[i][j][(int)age] +=p3mat[i][j][h];                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                }
     hf=1;          }
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );          for(jk=1; jk <=nlstate ; jk++){
     for(i=1; i<=nlstate;i++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(j=1; j<=nlstate;j++){              pp[jk] += freq[jk][m][i];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          }       
       }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     fprintf(ficreseij,"\n");            pos += pp[jk];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            posprop += prop[jk][i];
   }          }
 }          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
 /************ Variance ******************/              if(first==1)
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /* Variance of health expectancies */            }else{
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              if(first==1)
   double **newm;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double **dnewm,**doldm;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int i, j, nhstepm, hstepm, h;            }
   int k, cptcode;            if( i <= (int) agemax){
   double *xp;              if(pos>=1.e-5){
   double **gp, **gm;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double ***gradg, ***trgradg;                probs[i][jk][j1]= pp[jk]/pos;
   double ***p3mat;                /*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 age,agelim;              }
   int theta;              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
    fprintf(ficresvij,"# Covariances of life expectancies\n");            }
   fprintf(ficresvij,"# Age");          }
   for(i=1; i<=nlstate;i++)          
     for(j=1; j<=nlstate;j++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for(m=-1; m <=nlstate+ndeath; m++)
   fprintf(ficresvij,"\n");              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   xp=vector(1,npar);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   dnewm=matrix(1,nlstate,1,npar);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   doldm=matrix(1,nlstate,1,nlstate);              }
            if(i <= (int) agemax)
   hstepm=1*YEARM; /* Every year of age */            fprintf(ficresp,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          if(first==1)
   agelim = AGESUP;            printf("Others in log...\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          fprintf(ficlog,"\n");
     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 */    }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    dateintmean=dateintsum/k2cpt; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);   
     gp=matrix(0,nhstepm,1,nlstate);    fclose(ficresp);
     gm=matrix(0,nhstepm,1,nlstate);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
     for(theta=1; theta <=npar; theta++){    free_matrix(prop,1,nlstate,(int) agemin,(int) agemax+3);
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* End of Freq */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /************ Prevalence ********************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  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)
   {  
       if (popbased==1) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         for(i=1; i<=nlstate;i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
           prlim[i][i]=probs[(int)age][i][ij];       We still use firstpass and lastpass as another selection.
       }    */
         
       for(j=1; j<= nlstate; j++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         for(h=0; h<=nhstepm; h++){    double ***freq; /* Frequencies */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double *pp, **prop;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double pos,posprop; 
         }    double  y2; /* in fractional years */
       }  
        pp=vector(1,nlstate);
       for(i=1; i<=npar; i++) /* Computes gradient */    prop=matrix(1,nlstate,agemin,agemax+3); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      j1=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
     j=cptcoveff;
       if (popbased==1) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];    for(k1=1; k1<=j;k1++){
       }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
       for(j=1; j<= nlstate; j++){        
         for(h=0; h<=nhstepm; h++){        for (i=1; i<=nlstate; i++)  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(m=agemin; m <= agemax+3; m++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            prop[i][m]=0;
         }       
       }        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
       for(j=1; j<= nlstate; j++)          if  (cptcovn>0) {
         for(h=0; h<=nhstepm; h++){            for (z1=1; z1<=cptcoveff; z1++) 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         }                bool=0;
     } /* End theta */          } 
           if (bool==1) { 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for(h=0; h<=nhstepm; h++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(j=1; j<=nlstate;j++)                if(agev[m][i]==0) agev[m][i]=agemax+1;
         for(theta=1; theta <=npar; theta++)                if(agev[m][i]==1) agev[m][i]=agemax+2;
           trgradg[h][j][theta]=gradg[h][theta][j];                if (s[m][i]>0 && s[m][i]<=nlstate) {
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1;i<=nlstate;i++)                  prop[s[m][i]][(int)(agemax+3)] += weight[i];
       for(j=1;j<=nlstate;j++)                }
         vareij[i][j][(int)age] =0.;              }
     for(h=0;h<=nhstepm;h++){            } /* end selection of waves */
       for(k=0;k<=nhstepm;k++){          }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
         for(i=1;i<=nlstate;i++)          
           for(j=1;j<=nlstate;j++)          for(jk=1,posprop=0; jk <=nlstate ; jk++) {
             vareij[i][j][(int)age] += doldm[i][j];            posprop += prop[jk][i];
       }          }
     }          
     h=1;          for(jk=1; jk <=nlstate ; jk++){    
     if (stepm >= YEARM) h=stepm/YEARM;            if( i <= (int) agemax){
     fprintf(ficresvij,"%.0f ",age );              if(posprop>=1.e-5){
     for(i=1; i<=nlstate;i++)               probs[i][jk][j1]= prop[jk][i]/posprop;
       for(j=1; j<=nlstate;j++){              }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            }
       }          }/* end jk */
     fprintf(ficresvij,"\n");        }/* end i */
     free_matrix(gp,0,nhstepm,1,nlstate);      } /* end i1 */
     free_matrix(gm,0,nhstepm,1,nlstate);    } /* end k1 */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   } /* End age */    free_vector(pp,1,nlstate);
      free_matrix(prop,1,nlstate,(int) agemin,(int) agemax+3);
   free_vector(xp,1,npar);  }  /* End of Freq */
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /************* Waves Concatenation ***************/
   
 }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
 /************ Variance of prevlim ******************/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)       Death is a valid wave (if date is known).
 {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   /* Variance of prevalence limit */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       and mw[mi+1][i]. dh depends on stepm.
   double **newm;       */
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;    int i, mi, m;
   int k, cptcode;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double *xp;       double sum=0., jmean=0.;*/
   double *gp, *gm;    int first;
   double **gradg, **trgradg;    int j, k=0,jk, ju, jl;
   double age,agelim;    double sum=0.;
   int theta;    first=0;
        jmin=1e+5;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    jmax=-1;
   fprintf(ficresvpl,"# Age");    jmean=0.;
   for(i=1; i<=nlstate;i++)    for(i=1; i<=imx; i++){
       fprintf(ficresvpl," %1d-%1d",i,i);      mi=0;
   fprintf(ficresvpl,"\n");      m=firstpass;
       while(s[m][i] <= nlstate){
   xp=vector(1,npar);        if(s[m][i]>=1)
   dnewm=matrix(1,nlstate,1,npar);          mw[++mi][i]=m;
   doldm=matrix(1,nlstate,1,nlstate);        if(m >=lastpass)
            break;
   hstepm=1*YEARM; /* Every year of age */        else
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          m++;
   agelim = AGESUP;      }/* end while */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      if (s[m][i] > nlstate){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        mi++;     /* Death is another wave */
     if (stepm >= YEARM) hstepm=1;        /* if(mi==0)  never been interviewed correctly before death */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */           /* Only death is a correct wave */
     gradg=matrix(1,npar,1,nlstate);        mw[mi][i]=m;
     gp=vector(1,nlstate);      }
     gm=vector(1,nlstate);  
       wav[i]=mi;
     for(theta=1; theta <=npar; theta++){      if(mi==0){
       for(i=1; i<=npar; i++){ /* Computes gradient */        if(first==0){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
       }          first=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)        if(first==1){
         gp[i] = prlim[i][i];          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
            }
       for(i=1; i<=npar; i++) /* Computes gradient */      } /* end mi==0 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for(i=1; i<=imx; i++){
         gm[i] = prlim[i][i];      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
       for(i=1;i<=nlstate;i++)          dh[mi][i]=1;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        else{
     } /* End theta */          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
     trgradg =matrix(1,nlstate,1,npar);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */
     for(j=1; j<=nlstate;j++)            k=k+1;
       for(theta=1; theta <=npar; theta++)            if (j >= jmax) jmax=j;
         trgradg[j][theta]=gradg[theta][j];            if (j <= jmin) jmin=j;
             sum=sum+j;
     for(i=1;i<=nlstate;i++)            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       varpl[i][(int)age] =0.;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            /*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]);*/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            }
     for(i=1;i<=nlstate;i++)          }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     fprintf(ficresvpl,"%.0f ",age );            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(i=1; i<=nlstate;i++)            k=k+1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            if (j >= jmax) jmax=j;
     fprintf(ficresvpl,"\n");            else if (j <= jmin)jmin=j;
     free_vector(gp,1,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_vector(gm,1,nlstate);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     free_matrix(gradg,1,npar,1,nlstate);            sum=sum+j;
     free_matrix(trgradg,1,nlstate,1,npar);          }
   } /* End age */          jk= j/stepm;
           jl= j -jk*stepm;
   free_vector(xp,1,npar);          ju= j -(jk+1)*stepm;
   free_matrix(doldm,1,nlstate,1,npar);          if(mle <=1){ 
   free_matrix(dnewm,1,nlstate,1,nlstate);            if(jl==0){
               dh[mi][i]=jk;
 }              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
 /************ Variance of one-step probabilities  ******************/                    * at the price of an extra matrix product in likelihood */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)              dh[mi][i]=jk+1;
 {              bh[mi][i]=ju;
   int i, j;            }
   int k=0, cptcode;          }else{
   double **dnewm,**doldm;            if(jl <= -ju){
   double *xp;              dh[mi][i]=jk;
   double *gp, *gm;              bh[mi][i]=jl;       /* bias is positive if real duration
   double **gradg, **trgradg;                                   * is higher than the multiple of stepm and negative otherwise.
   double age,agelim, cov[NCOVMAX];                                   */
   int theta;            }
   char fileresprob[FILENAMELENGTH];            else{
               dh[mi][i]=jk+1;
   strcpy(fileresprob,"prob");              bh[mi][i]=ju;
   strcat(fileresprob,fileres);            }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            if(dh[mi][i]==0){
     printf("Problem with resultfile: %s\n", fileresprob);              dh[mi][i]=1; /* At least one step */
   }              bh[mi][i]=ju; /* At least one step */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
              }
           }
   xp=vector(1,npar);        } /* end if mle */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      } /* end wave */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    }
      jmean=sum/k;
   cov[1]=1;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   for (age=bage; age<=fage; age ++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     cov[2]=age;   }
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  /*********** Tricode ****************************/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  void tricode(int *Tvar, int **nbcode, int imx)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {
        
     for(theta=1; theta <=npar; theta++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
       for(i=1; i<=npar; i++)    int cptcode=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    cptcoveff=0; 
         
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    for (k=0; k<maxncov; k++) Ndum[k]=0;
        for (k=1; k<=7; k++) ncodemax[k]=0;
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         for(j=1; j<=(nlstate+ndeath);j++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
            k=k+1;                                 modality*/ 
           gp[k]=pmmij[i][j];        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         }        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 
       for(i=1; i<=npar; i++)                                         Tvar[j]. If V=sex and male is 0 and 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                                         female is 1, then  cptcode=1.*/
          }
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=0; i<=cptcode; i++) {
       k=0;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       for(i=1; i<=(nlstate+ndeath); i++){      }
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;      ij=1; 
           gm[k]=pmmij[i][j];      for (i=1; i<=ncodemax[j]; i++) {
         }        for (k=0; k<= maxncov; k++) {
       }          if (Ndum[k] != 0) {
                  nbcode[Tvar[j]][ij]=k; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            /* 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; */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              
     }            ij++;
           }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          if (ij > ncodemax[j]) break; 
       for(theta=1; theta <=npar; theta++)        }  
       trgradg[j][theta]=gradg[theta][j];      } 
      }  
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
      pmij(pmmij,cov,ncovmodel,x,nlstate);   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      k=0;     ij=Tvar[i];
      for(i=1; i<=(nlstate+ndeath); i++){     Ndum[ij]++;
        for(j=1; j<=(nlstate+ndeath);j++){   }
          k=k+1;  
          gm[k]=pmmij[i][j];   ij=1;
         }   for (i=1; i<= maxncov; i++) {
      }     if((Ndum[i]!=0) && (i<=ncovcol)){
             Tvaraff[ij]=i; /*For printing */
      /*printf("\n%d ",(int)age);       ij++;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){     }
           }
    
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));   cptcoveff=ij-1; /*Number of simple covariates*/
      }*/  }
   
   fprintf(ficresprob,"\n%d ",(int)age);  /*********** Health Expectancies ****************/
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  {
   }    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double age, agelim, hf;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double ***p3mat,***varhe;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double **dnewm,**doldm;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double *xp;
 }    double **gp, **gm;
  free_vector(xp,1,npar);    double ***gradg, ***trgradg;
 fclose(ficresprob);    int theta;
  exit(0);  
 }    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     xp=vector(1,npar);
 /***********************************************/    dnewm=matrix(1,nlstate*2,1,npar);
 /**************** Main Program *****************/    doldm=matrix(1,nlstate*2,1,nlstate*2);
 /***********************************************/    
     fprintf(ficreseij,"# Health expectancies\n");
 /*int main(int argc, char *argv[])*/    fprintf(ficreseij,"# Age");
 int main()    for(i=1; i<=nlstate;i++)
 {      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(ficreseij,"\n");
   double agedeb, agefin,hf;  
   double agemin=1.e20, agemax=-1.e20;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   double fret;    }
   double **xi,tmp,delta;    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   double dum; /* Dummy variable */     * This is mainly to measure the difference between two models: for example
   double ***p3mat;     * if stepm=24 months pijx are given only every 2 years and by summing them
   int *indx;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   char line[MAXLINE], linepar[MAXLINE];     * progression in between and thus overestimating or underestimating according
   char title[MAXLINE];     * to the curvature of the survival function. If, for the same date, we 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];     * to compare the new estimate of Life expectancy with the same linear 
   char filerest[FILENAMELENGTH];     * hypothesis. A more precise result, taking into account a more precise
   char fileregp[FILENAMELENGTH];     * curvature will be obtained if estepm is as small as stepm. */
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    /* For example we decided to compute the life expectancy with the smallest unit */
   int firstobs=1, lastobs=10;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int sdeb, sfin; /* Status at beginning and end */       nhstepm is the number of hstepm from age to agelim 
   int c,  h , cpt,l;       nstepm is the number of stepm from age to agelin. 
   int ju,jl, mi;       Look at hpijx to understand the reason of that which relies in memory size
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       and note for a fixed period like estepm months */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int mobilav=0,popforecast=0;       survival function given by stepm (the optimization length). Unfortunately it
   int hstepm, nhstepm;       means that if the survival funtion is printed only each two years of age and if
   int *popage;/*boolprev=0 if date and zero if wave*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;       results. So we changed our mind and took the option of the best precision.
     */
   double bage, fage, age, agelim, agebase;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double ftolpl=FTOL;  
   double **prlim;    agelim=AGESUP;
   double *severity;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double ***param; /* Matrix of parameters */      /* nhstepm age range expressed in number of stepm */
   double  *p;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   double **matcov; /* Matrix of covariance */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double ***delti3; /* Scale */      /* if (stepm >= YEARM) hstepm=1;*/
   double *delti; /* Scale */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double ***eij, ***vareij;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double **varpl; /* Variances of prevalence limits by age */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   double *epj, vepp;      gp=matrix(0,nhstepm,1,nlstate*2);
   double kk1, kk2;      gm=matrix(0,nhstepm,1,nlstate*2);
   double *popeffectif,*popcount;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   double yp,yp1,yp2;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";   
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
   char z[1]="c", occ;      /* Computing Variances of health expectancies */
 #include <sys/time.h>  
 #include <time.h>       for(theta=1; theta <=npar; theta++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* long total_usecs;        }
   struct timeval start_time, end_time;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        cptj=0;
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   printf("\nIMACH, Version 0.7");            cptj=cptj+1;
   printf("\nEnter the parameter file name: ");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 #ifdef windows            }
   scanf("%s",pathtot);          }
   getcwd(pathcd, size);        }
   /*cygwin_split_path(pathtot,path,optionfile);       
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       
   /* cutv(path,optionfile,pathtot,'\\');*/        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 split(pathtot, path,optionfile);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   chdir(path);        
   replace(pathc,path);        cptj=0;
 #endif        for(j=1; j<= nlstate; j++){
 #ifdef unix          for(i=1;i<=nlstate;i++){
   scanf("%s",optionfile);            cptj=cptj+1;
 #endif            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 /*-------- arguments in the command line --------*/            }
           }
   strcpy(fileres,"r");        }
   strcat(fileres, optionfile);        for(j=1; j<= nlstate*2; j++)
           for(h=0; h<=nhstepm-1; h++){
   /*---------arguments file --------*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       } 
     printf("Problem with optionfile %s\n",optionfile);     
     goto end;  /* End theta */
   }  
        trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   strcpy(filereso,"o");  
   strcat(filereso,fileres);       for(h=0; h<=nhstepm-1; h++)
   if((ficparo=fopen(filereso,"w"))==NULL) {        for(j=1; j<=nlstate*2;j++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
        
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){       for(i=1;i<=nlstate*2;i++)
     ungetc(c,ficpar);        for(j=1;j<=nlstate*2;j++)
     fgets(line, MAXLINE, ficpar);          varhe[i][j][(int)age] =0.;
     puts(line);  
     fputs(line,ficparo);       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   ungetc(c,ficpar);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
   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);          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   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);          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   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);          for(i=1;i<=nlstate*2;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){            for(j=1;j<=nlstate*2;j++)
     ungetc(c,ficpar);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      }
     fputs(line,ficparo);      /* Computing expectancies */
   }      for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);        for(j=1; j<=nlstate;j++)
            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   covar=matrix(0,NCOVMAX,1,n);            
   cptcovn=0;  /* 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]);*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
           }
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      fprintf(ficreseij,"%3.0f",age );
        cptj=0;
   /* Read guess parameters */      for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */        for(j=1; j<=nlstate;j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          cptj++;
     ungetc(c,ficpar);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      fprintf(ficreseij,"\n");
     fputs(line,ficparo);     
   }      free_matrix(gm,0,nhstepm,1,nlstate*2);
   ungetc(c,ficpar);      free_matrix(gp,0,nhstepm,1,nlstate*2);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     for(i=1; i <=nlstate; i++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);    printf("\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficlog,"\n");
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    free_vector(xp,1,npar);
         fscanf(ficpar," %lf",&param[i][j][k]);    free_matrix(dnewm,1,nlstate*2,1,npar);
         printf(" %lf",param[i][j][k]);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
         fprintf(ficparo," %lf",param[i][j][k]);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
       }  }
       fscanf(ficpar,"\n");  
       printf("\n");  /************ Variance ******************/
       fprintf(ficparo,"\n");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     }  {
      /* Variance of health expectancies */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   p=param[1][1];    double **dnewm,**doldm;
      double **dnewmp,**doldmp;
   /* Reads comments: lines beginning with '#' */    int i, j, nhstepm, hstepm, h, nstepm ;
   while((c=getc(ficpar))=='#' && c!= EOF){    int k, cptcode;
     ungetc(c,ficpar);    double *xp;
     fgets(line, MAXLINE, ficpar);    double **gp, **gm;  /* for var eij */
     puts(line);    double ***gradg, ***trgradg; /*for var eij */
     fputs(line,ficparo);    double **gradgp, **trgradgp; /* for var p point j */
   }    double *gpp, *gmp; /* for var p point j */
   ungetc(c,ficpar);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double age,agelim, hf;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    double ***mobaverage;
   for(i=1; i <=nlstate; i++){    int theta;
     for(j=1; j <=nlstate+ndeath-1; j++){    char digit[4];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    char digitp[25];
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    char fileresprobmorprev[FILENAMELENGTH];
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    if(popbased==1){
         printf(" %le",delti3[i][j][k]);      if(mobilav!=0)
         fprintf(ficparo," %le",delti3[i][j][k]);        strcpy(digitp,"-populbased-mobilav-");
       }      else strcpy(digitp,"-populbased-nomobil-");
       fscanf(ficpar,"\n");    }
       printf("\n");    else 
       fprintf(ficparo,"\n");      strcpy(digitp,"-stablbased-");
     }  
   }    if (mobilav!=0) {
   delti=delti3[1][1];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   /* Reads comments: lines beginning with '#' */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   while((c=getc(ficpar))=='#' && c!= EOF){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);    }
     puts(line);  
     fputs(line,ficparo);    strcpy(fileresprobmorprev,"prmorprev"); 
   }    sprintf(digit,"%-d",ij);
   ungetc(c,ficpar);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
   matcov=matrix(1,npar,1,npar);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   for(i=1; i <=npar; i++){    strcat(fileresprobmorprev,fileres);
     fscanf(ficpar,"%s",&str);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     printf("%s",str);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     fprintf(ficparo,"%s",str);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     for(j=1; j <=i; j++){    }
       fscanf(ficpar," %le",&matcov[i][j]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       printf(" %.5le",matcov[i][j]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficparo," %.5le",matcov[i][j]);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fscanf(ficpar,"\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
     fprintf(ficparo,"\n");      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   for(i=1; i <=npar; i++)    }  
     for(j=i+1;j<=npar;j++)    fprintf(ficresprobmorprev,"\n");
       matcov[i][j]=matcov[j][i];    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
          printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   printf("\n");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
     }
     /*-------- data file ----------*/    else{
     if((ficres =fopen(fileres,"w"))==NULL) {      fprintf(ficgp,"\n# Routine varevsij");
       printf("Problem with resultfile: %s\n", fileres);goto end;    }
     }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     fprintf(ficres,"#%s\n",version);      printf("Problem with html file: %s\n", optionfilehtm);
          fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     if((fic=fopen(datafile,"r"))==NULL)    {      exit(0);
       printf("Problem with datafile: %s\n", datafile);goto end;    }
     }    else{
       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");
     n= lastobs;      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     severity = vector(1,maxwav);    }
     outcome=imatrix(1,maxwav+1,1,n);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     num=ivector(1,n);  
     moisnais=vector(1,n);    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");
     annais=vector(1,n);    fprintf(ficresvij,"# Age");
     moisdc=vector(1,n);    for(i=1; i<=nlstate;i++)
     andc=vector(1,n);      for(j=1; j<=nlstate;j++)
     agedc=vector(1,n);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     cod=ivector(1,n);    fprintf(ficresvij,"\n");
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    xp=vector(1,npar);
     mint=matrix(1,maxwav,1,n);    dnewm=matrix(1,nlstate,1,npar);
     anint=matrix(1,maxwav,1,n);    doldm=matrix(1,nlstate,1,nlstate);
     s=imatrix(1,maxwav+1,1,n);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     adl=imatrix(1,maxwav+1,1,n);        doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     i=1;    gmp=vector(nlstate+1,nlstate+ndeath);
     while (fgets(line, MAXLINE, fic) != NULL)    {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       if ((i >= firstobs) && (i <=lastobs)) {    
            if(estepm < stepm){
         for (j=maxwav;j>=1;j--){      printf ("Problem %d lower than %d\n",estepm, stepm);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    }
           strcpy(line,stra);    else  hstepm=estepm;   
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* For example we decided to compute the life expectancy with the smallest unit */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         }       nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       Look at hpijx to understand the reason of that which relies in memory size
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);       survival function given by stepm (the optimization length). Unfortunately it
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);       results. So we changed our mind and took the option of the best precision.
         for (j=ncov;j>=1;j--){    */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }    agelim = AGESUP;
         num[i]=atol(stra);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           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;}*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         i=i+1;      gp=matrix(0,nhstepm,1,nlstate);
       }      gm=matrix(0,nhstepm,1,nlstate);
     }  
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/      for(theta=1; theta <=npar; theta++){
   imx=i-1; /* Number of individuals */        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* for (i=1; i<=imx; i++){        }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }        if (popbased==1) {
           if(mobilav ==0){
     for (i=1; i<=imx; i++)            for(i=1; i<=nlstate;i++)
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   /* Calculation of the number of parameter from char model*/            for(i=1; i<=nlstate;i++)
   Tvar=ivector(1,15);              prlim[i][i]=mobaverage[(int)age][i][ij];
   Tprod=ivector(1,15);          }
   Tvaraff=ivector(1,15);        }
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);              for(j=1; j<= nlstate; j++){
              for(h=0; h<=nhstepm; h++){
   if (strlen(model) >1){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     j=nbocc(model,'+');          }
     j1=nbocc(model,'*');        }
     cptcovn=j+1;        /* This for computing probability of death (h=1 means
     cptcovprod=j1;           computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
            */
     strcpy(modelsav,model);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       printf("Error. Non available option model=%s ",model);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       goto end;        }    
     }        /* end probability of death */
      
     for(i=(j+1); i>=1;i--){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       cutv(stra,strb,modelsav,'+');          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       /*scanf("%d",i);*/   
       if (strchr(strb,'*')) {        if (popbased==1) {
         cutv(strd,strc,strb,'*');          if(mobilav ==0){
         if (strcmp(strc,"age")==0) {            for(i=1; i<=nlstate;i++)
           cptcovprod--;              prlim[i][i]=probs[(int)age][i][ij];
           cutv(strb,stre,strd,'V');          }else{ /* mobilav */ 
           Tvar[i]=atoi(stre);            for(i=1; i<=nlstate;i++)
           cptcovage++;              prlim[i][i]=mobaverage[(int)age][i][ij];
             Tage[cptcovage]=i;          }
             /*printf("stre=%s ", stre);*/        }
         }  
         else if (strcmp(strd,"age")==0) {        for(j=1; j<= nlstate; j++){
           cptcovprod--;          for(h=0; h<=nhstepm; h++){
           cutv(strb,stre,strc,'V');            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           Tvar[i]=atoi(stre);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           cptcovage++;          }
           Tage[cptcovage]=i;        }
         }        /* This for computing probability of death (h=1 means
         else {           computed over hstepm matrices product = hstepm*stepm months) 
           cutv(strb,stre,strc,'V');           as a weighted average of prlim.
           Tvar[i]=ncov+k1;        */
           cutv(strb,strc,strd,'V');        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           Tprod[k1]=i;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           Tvard[k1][1]=atoi(strc);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           Tvard[k1][2]=atoi(stre);        }    
           Tvar[cptcovn+k2]=Tvard[k1][1];        /* end probability of death */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)        for(j=1; j<= nlstate; j++) /* vareij */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          for(h=0; h<=nhstepm; h++){
           k1++;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           k2=k2+2;          }
         }  
       }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       else {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         /*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,1,npar); /* veij */
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      for(h=0; h<=nhstepm; h++) /* veij */
         scanf("%d",i);*/        for(j=1; j<=nlstate;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]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   printf("cptcovprod=%d ", cptcovprod);        for(theta=1; theta <=npar; theta++)
   scanf("%d ",i);*/          trgradgp[j][theta]=gradgp[theta][j];
     fclose(fic);    
   
     /*  if(mle==1){*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     if (weightopt != 1) { /* Maximisation without weights*/      for(i=1;i<=nlstate;i++)
       for(i=1;i<=n;i++) weight[i]=1.0;        for(j=1;j<=nlstate;j++)
     }          vareij[i][j][(int)age] =0.;
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
    for (i=1; i<=imx; i++)          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      for(m=2; (m<= maxwav); m++)          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          for(i=1;i<=nlstate;i++)
          anint[m][i]=9999;            for(j=1;j<=nlstate;j++)
          s[m][i]=-1;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        }        }
          }
     for (i=1; i<=imx; i++)  {    
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      /* pptj */
       for(m=1; (m<= maxwav); m++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         if(s[m][i] >0){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           if (s[m][i] == nlstate+1) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
             if(agedc[i]>0)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
               if(moisdc[i]!=99 && andc[i]!=9999)          varppt[j][i]=doldmp[j][i];
               agev[m][i]=agedc[i];      /* end ppptj */
             else {      /*  x centered again */
               if (andc[i]!=9999){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               agev[m][i]=-1;   
               }      if (popbased==1) {
             }        if(mobilav ==0){
           }          for(i=1; i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */            prlim[i][i]=probs[(int)age][i][ij];
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        }else{ /* mobilav */ 
             if(mint[m][i]==99 || anint[m][i]==9999)          for(i=1; i<=nlstate;i++)
               agev[m][i]=1;            prlim[i][i]=mobaverage[(int)age][i][ij];
             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);*/               
             }      /* This for computing probability of death (h=1 means
             else if(agev[m][i] >agemax){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
               agemax=agev[m][i];         as a weighted average of prlim.
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      */
             }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
             /*agev[m][i]=anint[m][i]-annais[i];*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
             /*   agev[m][i] = age[i]+2*m;*/          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           }      }    
           else { /* =9 */      /* end probability of death */
             agev[m][i]=1;  
             s[m][i]=-1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         else /*= 0 Unknown */        for(i=1; i<=nlstate;i++){
           agev[m][i]=1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       }        }
          } 
     }      fprintf(ficresprobmorprev,"\n");
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){      fprintf(ficresvij,"%.0f ",age );
         if (s[m][i] > (nlstate+ndeath)) {      for(i=1; i<=nlstate;i++)
           printf("Error: Wrong value in nlstate or ndeath\n");          for(j=1; j<=nlstate;j++){
           goto end;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }        }
       }      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     free_vector(severity,1,maxwav);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_imatrix(outcome,1,maxwav+1,1,n);    } /* End age */
     free_vector(moisnais,1,n);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(annais,1,n);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     /* free_matrix(mint,1,maxwav,1,n);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        free_matrix(anint,1,maxwav,1,n);*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     free_vector(moisdc,1,n);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     free_vector(andc,1,n);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     wav=ivector(1,imx);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     /* Concatenates waves */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       Tcode=ivector(1,100);  */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    free_vector(xp,1,npar);
          free_matrix(doldm,1,nlstate,1,nlstate);
    codtab=imatrix(1,100,1,10);    free_matrix(dnewm,1,nlstate,1,npar);
    h=0;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    m=pow(2,cptcoveff);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    for(k=1;k<=cptcoveff; k++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1; i <=(m/pow(2,k));i++){    fclose(ficresprobmorprev);
        for(j=1; j <= ncodemax[k]; j++){    fclose(ficgp);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    fclose(fichtm);
            h++;  }  
            if (h>m) h=1;codtab[h][k]=j;  
          }  /************ 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)
      }  {
    }    /* Variance of prevalence limit */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    /* Calculates basic frequencies. Computes observed prevalence at single age    double **newm;
        and prints on file fileres'p'. */    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
        int k, cptcode;
        double *xp;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *gp, *gm;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **gradg, **trgradg;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double age,agelim;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int theta;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     
          fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficresvpl,"# Age");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    for(i=1; i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     /*--------- results files --------------*/    
     fprintf(ficres,"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);    hstepm=1*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
    jk=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    fprintf(ficres,"# Parameters\n");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    printf("# Parameters\n");      if (stepm >= YEARM) hstepm=1;
    for(i=1,jk=1; i <=nlstate; i++){      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      for(k=1; k <=(nlstate+ndeath); k++){      gradg=matrix(1,npar,1,nlstate);
        if (k != i)      gp=vector(1,nlstate);
          {      gm=vector(1,nlstate);
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);      for(theta=1; theta <=npar; theta++){
            for(j=1; j <=ncovmodel; j++){        for(i=1; i<=npar; i++){ /* Computes gradient */
              printf("%f ",p[jk]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              fprintf(ficres,"%f ",p[jk]);        }
              jk++;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            }        for(i=1;i<=nlstate;i++)
            printf("\n");          gp[i] = prlim[i][i];
            fprintf(ficres,"\n");      
          }        for(i=1; i<=npar; i++) /* Computes gradient */
      }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  if(mle==1){        for(i=1;i<=nlstate;i++)
     /* Computing hessian and covariance matrix */          gm[i] = prlim[i][i];
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);        for(i=1;i<=nlstate;i++)
  }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fprintf(ficres,"# Scales\n");      } /* End theta */
     printf("# Scales\n");  
      for(i=1,jk=1; i <=nlstate; i++){      trgradg =matrix(1,nlstate,1,npar);
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {      for(j=1; j<=nlstate;j++)
           fprintf(ficres,"%1d%1d",i,j);        for(theta=1; theta <=npar; theta++)
           printf("%1d%1d",i,j);          trgradg[j][theta]=gradg[theta][j];
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);      for(i=1;i<=nlstate;i++)
             fprintf(ficres," %.5e",delti[jk]);        varpl[i][(int)age] =0.;
             jk++;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           printf("\n");      for(i=1;i<=nlstate;i++)
           fprintf(ficres,"\n");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         }  
       }      fprintf(ficresvpl,"%.0f ",age );
      }      for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     k=1;      fprintf(ficresvpl,"\n");
     fprintf(ficres,"# Covariance\n");      free_vector(gp,1,nlstate);
     printf("# Covariance\n");      free_vector(gm,1,nlstate);
     for(i=1;i<=npar;i++){      free_matrix(gradg,1,npar,1,nlstate);
       /*  if (k>nlstate) k=1;      free_matrix(trgradg,1,nlstate,1,npar);
       i1=(i-1)/(ncovmodel*nlstate)+1;    } /* End age */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    free_vector(xp,1,npar);
       fprintf(ficres,"%3d",i);    free_matrix(doldm,1,nlstate,1,npar);
       printf("%3d",i);    free_matrix(dnewm,1,nlstate,1,nlstate);
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);  }
         printf(" %.5e",matcov[i][j]);  
       }  /************ Variance of one-step probabilities  ******************/
       fprintf(ficres,"\n");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
       printf("\n");  {
       k++;    int i, j=0,  i1, k1, l1, t, tj;
     }    int k2, l2, j1,  z1;
        int k=0,l, cptcode;
     while((c=getc(ficpar))=='#' && c!= EOF){    int first=1, first1;
       ungetc(c,ficpar);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       fgets(line, MAXLINE, ficpar);    double **dnewm,**doldm;
       puts(line);    double *xp;
       fputs(line,ficparo);    double *gp, *gm;
     }    double **gradg, **trgradg;
     ungetc(c,ficpar);    double **mu;
      double age,agelim, cov[NCOVMAX];
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        int theta;
     if (fage <= 2) {    char fileresprob[FILENAMELENGTH];
       bage = agemin;    char fileresprobcov[FILENAMELENGTH];
       fage = agemax;    char fileresprobcor[FILENAMELENGTH];
     }  
     double ***varpij;
     fprintf(ficres,"# agemin agemax for life expectancy.\n");  
     strcpy(fileresprob,"prob"); 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    strcat(fileresprob,fileres);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
     while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    strcpy(fileresprobcov,"probcov"); 
     puts(line);    strcat(fileresprobcov,fileres);
     fputs(line,ficparo);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    strcpy(fileresprobcor,"probcor"); 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    strcat(fileresprobcor,fileres);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
            printf("Problem with resultfile: %s\n", fileresprobcor);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     puts(line);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fputs(line,ficparo);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   }    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   ungetc(c,ficpar);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fscanf(ficpar,"pop_based=%d\n",&popbased);    fprintf(ficresprobcov,"# Age");
    fprintf(ficparo,"pop_based=%d\n",popbased);      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
    fprintf(ficres,"pop_based=%d\n",popbased);      fprintf(ficresprobcov,"# Age");
   
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     fputs(line,ficparo);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   ungetc(c,ficpar);      }  
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);   /* fprintf(ficresprob,"\n");
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    fprintf(ficresprobcov,"\n");
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    fprintf(ficresprobcor,"\n");
    */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  /*------------ gnuplot -------------*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 chdir(pathcd);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     printf("Problem with file graph.gp");goto end;    first=1;
   }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 #ifdef windows      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   fprintf(ficgp,"cd \"%s\" \n",pathc);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 #endif      exit(0);
 m=pow(2,cptcoveff);    }
      else{
  /* 1eme*/      fprintf(ficgp,"\n# Routine varprob");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    }
    for (k1=1; k1<= m ; k1 ++) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
 #ifdef windows      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     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);      exit(0);
 #endif    }
 #ifdef unix    else{
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 #endif      fprintf(fichtm,"\n");
   
 for (i=1; i<= nlstate ; i ++) {      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      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");
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    cov[1]=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    tj=cptcoveff;
 }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    j1=0;
      for (i=1; i<= nlstate ; i ++) {    for(t=1; t<=tj;t++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(i1=1; i1<=ncodemax[t];i1++){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        j1++;
 }          if  (cptcovn>0) {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          fprintf(ficresprob, "\n#********** Variable "); 
 #ifdef unix          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficgp,"\nset ter gif small size 400,300");          fprintf(ficresprob, "**********\n#\n");
 #endif          fprintf(ficresprobcov, "\n#********** Variable "); 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    }          fprintf(ficresprobcov, "**********\n#\n");
   }          
   /*2 eme*/          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (k1=1; k1<= m ; k1 ++) {          fprintf(ficgp, "**********\n#\n");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          
              
     for (i=1; i<= nlstate+1 ; i ++) {          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       k=2*i;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       for (j=1; j<= nlstate+1 ; j ++) {          
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresprobcor, "\n#********** Variable ");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }            fprintf(ficresprobcor, "**********\n#");    
       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 (age=bage; age<=fage; age ++){ 
       for (j=1; j<= nlstate+1 ; j ++) {          cov[2]=age;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for (k=1; k<=cptcovn;k++) {
         else fprintf(ficgp," \%%*lf (\%%*lf)");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
 }            }
       fprintf(ficgp,"\" t\"\" w l 0,");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for (k=1; k<=cptcovprod;k++)
       for (j=1; j<= nlstate+1 ; j ++) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 }            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          gp=vector(1,(nlstate)*(nlstate+ndeath));
       else fprintf(ficgp,"\" t\"\" w l 0,");          gm=vector(1,(nlstate)*(nlstate+ndeath));
     }      
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
                xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*3eme*/            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for (k1=1; k1<= m ; k1 ++) {            
     for (cpt=1; cpt<= nlstate ; cpt ++) {            k=0;
       k=2+nlstate*(cpt-1);            for(i=1; i<= (nlstate); i++){
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);              for(j=1; j<=(nlstate+ndeath);j++){
       for (i=1; i< nlstate ; i ++) {                k=k+1;
         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);                gp[k]=pmmij[i][j];
       }              }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            }
     }            
   }            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:0);
   /* CV preval stat */      
   for (k1=1; k1<= m ; k1 ++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     for (cpt=1; cpt<nlstate ; cpt ++) {            k=0;
       k=3;            for(i=1; i<=(nlstate); i++){
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              for(j=1; j<=(nlstate+ndeath);j++){
       for (i=1; i< nlstate ; i ++)                k=k+1;
         fprintf(ficgp,"+$%d",k+i+1);                gm[k]=pmmij[i][j];
       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/($%d",fileres,k1,l+cpt+1,l+1);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       for (i=1; i< nlstate ; i ++) {              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);  
       }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              trgradg[j][theta]=gradg[theta][j];
     }          
   }            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);
   /* proba elementaires */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
    for(i=1,jk=1; i <=nlstate; i++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     for(k=1; k <=(nlstate+ndeath); k++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       if (k != i) {          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for(j=1; j <=ncovmodel; j++){  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          pmij(pmmij,cov,ncovmodel,x,nlstate);
           /*fprintf(ficgp,"%s",alph[1]);*/          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          k=0;
           jk++;          for(i=1; i<=(nlstate); i++){
           fprintf(ficgp,"\n");            for(j=1; j<=(nlstate+ndeath);j++){
         }              k=k+1;
       }              mu[k][(int) age]=pmmij[i][j];
     }            }
     }          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   for(jk=1; jk <=m; jk++) {            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              varpij[i][j][(int)age] = doldm[i][j];
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {          /*printf("\n%d ",(int)age);
      k3=i;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      for(k=1; k<=(nlstate+ndeath); k++) {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        if (k != k2){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            }*/
 ij=1;  
         for(j=3; j <=ncovmodel; j++) {          fprintf(ficresprob,"\n%d ",(int)age);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(ficresprobcov,"\n%d ",(int)age);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          fprintf(ficresprobcor,"\n%d ",(int)age);
             ij++;  
           }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           else            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           fprintf(ficgp,")/(1");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                  }
         for(k1=1; k1 <=nlstate; k1++){            i=0;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          for (k=1; k<=(nlstate);k++){
 ij=1;            for (l=1; l<=(nlstate+ndeath);l++){ 
           for(j=3; j <=ncovmodel; j++){              i=i++;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             ij++;              for (j=1; j<=i;j++){
           }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           else                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              }
           }            }
           fprintf(ficgp,")");          }/* end of loop for state */
         }        } /* end of loop for age */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        /* Confidence intervalle of pij  */
         i=i+ncovmodel;        /*
        }          fprintf(ficgp,"\nset noparametric;unset label");
      }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
    }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          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);
   }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
              fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   fclose(ficgp);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   /* end gnuplot */        */
      
 chdir(path);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
            first1=1;
     free_ivector(wav,1,imx);        for (k2=1; k2<=(nlstate);k2++){
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              if(l2==k2) continue;
     free_ivector(num,1,n);            j=(k2-1)*(nlstate+ndeath)+l2;
     free_vector(agedc,1,n);            for (k1=1; k1<=(nlstate);k1++){
     /*free_matrix(covar,1,NCOVMAX,1,n);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     fclose(ficparo);                if(l1==k1) continue;
     fclose(ficres);                i=(k1-1)*(nlstate+ndeath)+l1;
     /*  }*/                if(i<=j) continue;
                    for (age=bage; age<=fage; age ++){ 
    /*________fin mle=1_________*/                  if ((int)age %5==0){
                        v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     /* No more information from the sample is required now */                    mu1=mu[i][(int) age]/stepm*YEARM ;
   /* Reads comments: lines beginning with '#' */                    mu2=mu[j][(int) age]/stepm*YEARM;
   while((c=getc(ficpar))=='#' && c!= EOF){                    c12=cv12/sqrt(v1*v2);
     ungetc(c,ficpar);                    /* Computing eigen value of matrix of covariance */
     fgets(line, MAXLINE, ficpar);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     puts(line);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fputs(line,ficparo);                    /* Eigen vectors */
   }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   ungetc(c,ficpar);                    /*v21=sqrt(1.-v11*v11); *//* error */
                      v21=(lc1-v1)/cv12*v11;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                    v12=-v21;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);                    v22=v11;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                    tnalp=v21/v11;
 /*--------- index.htm --------*/                    if(first1==1){
                       first1=0;
   strcpy(optionfilehtm,optionfile);                      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);
   strcat(optionfilehtm,".htm");                    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     printf("Problem with %s \n",optionfilehtm);goto end;                    /*printf(fignu*/
   }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">                    if(first==1){
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>                      first=0;
 Total number of observations=%d <br>                      fprintf(ficgp,"\nset parametric;unset label");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>                      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);
 <hr  size=\"2\" color=\"#EC5E5E\">                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 <li>Outputs files<br><br>\n                      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);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                    }else{
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>                      first=0;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                      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(fichtm," <li>Graphs</li><p>");                      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",\
  m=cptcoveff;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
  j1=0;                  } /* age mod 5 */
  for(k1=1; k1<=m;k1++){                } /* end loop age */
    for(i1=1; i1<=ncodemax[k1];i1++){                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
        j1++;                first=1;
        if (cptcovn > 0) {              } /*l12 */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            } /* k12 */
          for (cpt=1; cpt<=cptcoveff;cpt++)          } /*l1 */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        }/* k1 */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      } /* loop covariates */
        }    }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        for(cpt=1; cpt<nlstate;cpt++){    free_vector(xp,1,npar);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    fclose(ficresprob);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    fclose(ficresprobcov);
        }    fclose(ficresprobcor);
     for(cpt=1; cpt<=nlstate;cpt++) {    fclose(ficgp);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    fclose(fichtm);
 interval) in state (%d): v%s%d%d.gif <br>  }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {  /******************* Printing html file ***********/
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                    int lastpass, int stepm, int weightopt, char model[],\
      }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                    int popforecast, int estepm ,\
 health expectancies in states (1) and (2): e%s%d.gif<br>                    double jprev1, double mprev1,double anprev1, \
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                    double jprev2, double mprev2,double anprev2){
 fprintf(fichtm,"\n</body>");    int jj1, k1, i1, cpt;
    }    /*char optionfilehtm[FILENAMELENGTH];*/
  }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
 fclose(fichtm);      printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   /*--------------- Prevalence limit --------------*/    }
    
   strcpy(filerespl,"pl");     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   strcat(filerespl,fileres);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   - 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): 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   fprintf(ficrespl,"#Prevalence limit\n");    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   fprintf(ficrespl,"\n");  
     m=cptcoveff;
   prlim=matrix(1,nlstate,1,nlstate);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   jj1=0;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for(k1=1; k1<=m;k1++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for(i1=1; i1<=ncodemax[k1];i1++){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       jj1++;
   k=0;       if (cptcovn > 0) {
   agebase=agemin;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   agelim=agemax;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   ftolpl=1.e-10;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   i1=cptcoveff;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   if (cptcovn < 1){i1=1;}       }
        /* Pij */
   for(cptcov=1;cptcov<=i1;cptcov++){       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>
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
         k=k+1;       /* Quasi-incidences */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
         fprintf(ficrespl,"\n#******");  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
         for(j=1;j<=cptcoveff;j++)         /* Stable prevalence in each health state */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         for(cpt=1; cpt<nlstate;cpt++){
         fprintf(ficrespl,"******\n");           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 (age=agebase; age<=agelim; age++){         }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficrespl,"%.0f",age );          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
           for(i=1; i<=nlstate;i++)  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           fprintf(ficrespl," %.5f", prlim[i][i]);       }
           fprintf(ficrespl,"\n");       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 */
   fclose(ficrespl);   }/* End k1 */
    fprintf(fichtm,"</ul>");
   /*------------- h Pij x at various ages ------------*/  
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   if((ficrespij=fopen(filerespij,"w"))==NULL) {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   - 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
   printf("Computing pij: result on file '%s' \n", filerespij);   - 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 
   stepsize=(int) (stepm+YEARM-1)/YEARM;   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
   /*if (stepm<=24) stepsize=2;*/   - 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);
   
   agelim=AGESUP;   if(popforecast==1) fprintf(fichtm,"\n
   hstepm=stepsize*YEARM; /* Every year of age */   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
            <br>",fileres,fileres,fileres,fileres);
   k=0;   else 
   for(cptcov=1;cptcov<=i1;cptcov++){     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");   m=cptcoveff;
         for(j=1;j<=cptcoveff;j++)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");   jj1=0;
           for(k1=1; k1<=m;k1++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     for(i1=1; i1<=ncodemax[k1];i1++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       jj1++;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       if (cptcovn > 0) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           oldm=oldms;savm=savms;         for (cpt=1; cpt<=cptcoveff;cpt++) 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(ficrespij,"# Age");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           for(i=1; i<=nlstate;i++)       }
             for(j=1; j<=nlstate+ndeath;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
               fprintf(ficrespij," %1d-%1d",i,j);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
           fprintf(ficrespij,"\n");  interval) in state (%d): v%s%d%d.png <br>
           for (h=0; h<=nhstepm; h++){  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       }
             for(i=1; i<=nlstate;i++)     } /* end i1 */
               for(j=1; j<=nlstate+ndeath;j++)   }/* End k1 */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   fprintf(fichtm,"</ul>");
             fprintf(ficrespij,"\n");  fclose(fichtm);
           }  }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");  /******************* 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;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
   fclose(ficrespij);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   if(stepm == 1) {  
   /*---------- Forecasting ------------------*/    /*#ifdef windows */
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   /*printf("calage= %f", calagedate);*/  m=pow(2,cptcoveff);
      
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   strcpy(fileresf,"f");       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   strcat(fileresf,fileres);       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);
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing forecasting: result on file '%s' \n", fileresf);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
   free_matrix(mint,1,maxwav,1,n);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
   free_matrix(anint,1,maxwav,1,n);       for (i=1; i<= nlstate ; i ++) {
   free_matrix(agev,1,maxwav,1,imx);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* Mobile average */         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
   if (mobilav==1) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)       }  
       for (i=1; i<=nlstate;i++)       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)     }
           mobaverage[(int)agedeb][i][cptcod]=0.;    }
        /*2 eme*/
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    
       for (i=1; i<=nlstate;i++){    for (k1=1; k1<= m ; k1 ++) { 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
           for (cpt=0;cpt<=4;cpt++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      
           }      for (i=1; i<= nlstate+1 ; i ++) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        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)");
         }   
   stepsize=(int) (stepm+YEARM-1)/YEARM;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   if (stepm<=12) stepsize=1;        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);
   agelim=AGESUP;        for (j=1; j<= nlstate+1 ; j ++) {
   /*hstepm=stepsize*YEARM; *//* Every year of age */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   hstepm=1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        }   
   yp1=modf(dateintmean,&yp);        fprintf(ficgp,"\" t\"\" w l 0,");
   anprojmean=yp;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   yp2=modf((yp1*12),&yp);        for (j=1; j<= nlstate+1 ; j ++) {
   mprojmean=yp;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   yp1=modf((yp2*30.5),&yp);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   jprojmean=yp;        }   
   if(jprojmean==0) jprojmean=1;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   if(mprojmean==0) jprojmean=1;        else fprintf(ficgp,"\" t\"\" w l 0,");
       }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    }
     
   if (popforecast==1) {    /*3eme*/
     if((ficpop=fopen(popfile,"r"))==NULL)    {    
       printf("Problem with population file : %s\n",popfile);goto end;    for (k1=1; k1<= m ; k1 ++) { 
     }      for (cpt=1; cpt<= nlstate ; cpt ++) {
     popage=ivector(0,AGESUP);        k=2+nlstate*(2*cpt-2);
     popeffectif=vector(0,AGESUP);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     popcount=vector(0,AGESUP);        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);
     i=1;            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          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);
         i=i+1;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     imx=i;          
            */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[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+2*i,cpt,i+1);
           
   for(cptcov=1;cptcov<=i1;cptcov++){        } 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }
       k=k+1;    }
       fprintf(ficresf,"\n#******");    
       for(j=1;j<=cptcoveff;j++) {    /* CV preval stat */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<nlstate ; cpt ++) {
       fprintf(ficresf,"******\n");        k=3;
       fprintf(ficresf,"# StartingAge FinalAge");        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
       if (popforecast==1)  fprintf(ficresf," [Population]");        
            for (i=1; i< nlstate ; i ++)
       for (cpt=0; cpt<4;cpt++) {          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficresf,"\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          
         l=3+(nlstate+ndeath)*cpt;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for (i=1; i< nlstate ; i ++) {
         nhstepm = nhstepm/hstepm;          l=3+(nlstate+ndeath)*cpt;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/          fprintf(ficgp,"+$%d",l+i+1);
         }
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
         oldm=oldms;savm=savms;      } 
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }  
            
         for (h=0; h<=nhstepm; h++){    /* proba elementaires */
           if (h==(int) (calagedate+YEARM*cpt)) {    for(i=1,jk=1; i <=nlstate; i++){
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);      for(k=1; k <=(nlstate+ndeath); k++){
           }        if (k != i) {
           for(j=1; j<=nlstate+ndeath;j++) {          for(j=1; j <=ncovmodel; j++){
             kk1=0.;kk2=0;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             for(i=1; i<=nlstate;i++) {                    jk++; 
               if (mobilav==1)            fprintf(ficgp,"\n");
                 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];      }
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/     }
               }  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];       for(jk=1; jk <=m; jk++) {
             }         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
                   if (ng==2)
             if (h==(int)(calagedate+12*cpt)){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
               fprintf(ficresf," %.3f", kk1);         else
                         fprintf(ficgp,"\nset title \"Probability\"\n");
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);         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;
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           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
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   if (popforecast==1) {               ij=1;
     free_ivector(popage,0,AGESUP);               for(j=3; j <=ncovmodel; j++) {
     free_vector(popeffectif,0,AGESUP);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     free_vector(popcount,0,AGESUP);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   }                   ij++;
   free_imatrix(s,1,maxwav+1,1,n);                 }
   free_vector(weight,1,n);                 else
   fclose(ficresf);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   }/* End forecasting */               }
   else{               fprintf(ficgp,")/(1");
     erreur=108;               
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);               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;
   /*---------- Health expectancies and variances ------------*/                 for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   strcpy(filerest,"t");                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   strcat(filerest,fileres);                     ij++;
   if((ficrest=fopen(filerest,"w"))==NULL) {                   }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                   else
   }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                 }
                  fprintf(ficgp,")");
                }
   strcpy(filerese,"e");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   strcat(filerese,fileres);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   if((ficreseij=fopen(filerese,"w"))==NULL) {               i=i+ncovmodel;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);             }
   }           } /* end k */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);         } /* end k2 */
        } /* end jk */
  strcpy(fileresv,"v");     } /* end ng */
   strcat(fileresv,fileres);     fclose(ficgp); 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  }  /* end gnuplot */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    int i, cpt, cptcod;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int modcovmax =1;
       k=k+1;    int mobilavrange, mob;
       fprintf(ficrest,"\n#****** ");    double age;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       fprintf(ficrest,"******\n");                             a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      if(mobilav==1) mobilavrange=5; /* default */
       fprintf(ficreseij,"******\n");      else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
       fprintf(ficresvij,"\n#****** ");        for (i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)          for (cptcod=1;cptcod<=modcovmax;cptcod++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       fprintf(ficresvij,"******\n");      /* 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
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);         we use a 5 terms etc. until the borders are no more concerned. 
       oldm=oldms;savm=savms;      */ 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        for (mob=3;mob <=mobilavrange;mob=mob+2){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       oldm=oldms;savm=savms;          for (i=1; i<=nlstate;i++){
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                    mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                for (cpt=1;cpt<=(mob-1)/2;cpt++){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       fprintf(ficrest,"\n");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                        }
       hf=1;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
       if (stepm >= YEARM) hf=stepm/YEARM;            }
       epj=vector(1,nlstate+1);          }
       for(age=bage; age <=fage ;age++){        }/* end age */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }/* end mob */
         if (popbased==1) {    }else return -1;
           for(i=1; i<=nlstate;i++)    return 0;
             prlim[i][i]=probs[(int)age][i][k];  }/* End movingaverage */
         }  
          
         fprintf(ficrest," %.0f",age);  /************** Forecasting ******************/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  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){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /* proj1, year, month, day of starting projection 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       agemin, agemax range of age
           }       dateprev1 dateprev2 range of dates during which prevalence is computed
           epj[nlstate+1] +=epj[j];       anproj2 year of en of projection (same day and month as proj1).
         }    */
         for(i=1, vepp=0.;i <=nlstate;i++)    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
           for(j=1;j <=nlstate;j++)    int *popage;
             vepp += vareij[i][j][(int)age];    double agec; /* generic age */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
         for(j=1;j <=nlstate;j++){    double *popeffectif,*popcount;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    double ***p3mat;
         }    double ***mobaverage;
         fprintf(ficrest,"\n");    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) {
  fclose(ficreseij);      printf("Problem with forecast resultfile: %s\n", fileresf);
  fclose(ficresvij);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   fclose(ficrest);    }
   fclose(ficpar);    printf("Computing forecasting: result on file '%s' \n", fileresf);
   free_vector(epj,1,nlstate+1);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   /*  scanf("%d ",i); */  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   /*------- Variance limit prevalence------*/    
     if (mobilav!=0) {
 strcpy(fileresvpl,"vpl");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(fileresvpl,fileres);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     exit(0);      }
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
  k=0;    if (stepm<=12) stepsize=1;
  for(cptcov=1;cptcov<=i1;cptcov++){    
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    hstepm=1;
      k=k+1;    hstepm=hstepm/stepm; 
      fprintf(ficresvpl,"\n#****** ");    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
      for(j=1;j<=cptcoveff;j++)                                 fractional in yp1 */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    anprojmean=yp;
      fprintf(ficresvpl,"******\n");    yp2=modf((yp1*12),&yp);
          mprojmean=yp;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    yp1=modf((yp2*30.5),&yp);
      oldm=oldms;savm=savms;    jprojmean=yp;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if(jprojmean==0) jprojmean=1;
    }    if(mprojmean==0) jprojmean=1;
  }  
     i1=cptcoveff;
   fclose(ficresvpl);    if (cptcovn < 1){i1=1;}
     
   /*---------- End : free ----------------*/    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    
      fprintf(ficresf,"#****** Routine prevforecast **\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          k=k+1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficresf,"\n#******");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1;j<=cptcoveff;j++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          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]]);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
          fprintf(ficresf,"******\n");
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   free_vector(delti,1,npar);        for(j=1; j<=nlstate+ndeath;j++){ 
            for(i=1; i<=nlstate;i++)              
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
   if(erreur >0)        }
     printf("End of Imach with error %d\n",erreur);        for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { 
   else   printf("End of Imach\n");          fprintf(ficresf,"\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
    
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   /*printf("Total time was %d uSec.\n", total_usecs);*/            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   /*------ End -----------*/            nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
  end:            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
 #ifdef windows          
  chdir(pathcd);            for (h=0; h<=nhstepm; h++){
 #endif              if (h==(int) (YEARM*yearp)) {
                  fprintf(ficresf,"\n");
  system("..\\gp37mgw\\wgnuplot graph.plt");                for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 #ifdef windows                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   while (z[0] != 'q') {              } 
     chdir(pathcd);              for(j=1; j<=nlstate+ndeath;j++) {
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                ppij=0.;
     scanf("%s",z);                for(i=1; i<=nlstate;i++) {
     if (z[0] == 'c') system("./imach");                  if (mobilav==1) 
     else if (z[0] == 'e') {                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
       chdir(path);                  else {
       system(optionfilehtm);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
     }                  }
     else if (z[0] == 'q') exit(0);                  if (h==(int)(YEARM*yearp))
   }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
 #endif                }
 }                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.1.21  
changed lines
  Added in v.1.73


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