Diff for /imach/src/imach.c between versions 1.15 and 1.54

version 1.15, 2002/02/20 17:08:52 version 1.54, 2002/07/24 09:07:45
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 or quarter trimester,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is model 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 unix
 #define MAXN 20000  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define YEARM 12. /* Number of months per year */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define AGESUP 130  
 #define AGEBASE 40  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int nvar;  #define NINTERVMAX 8
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int npar=NPARMAX;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int nlstate=2; /* Number of live states */  #define NCOVMAX 8 /* Maximum number of covariates */
 int ndeath=1; /* Number of dead states */  #define MAXN 20000
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #define YEARM 12. /* Number of months per year */
 int popbased=0;  #define AGESUP 130
   #define AGEBASE 40
 int *wav; /* Number of waves for this individuual 0 is possible */  #ifdef windows
 int maxwav; /* Maxim number of waves */  #define DIRSEPARATOR '\\'
 int jmin, jmax; /* min, max spacing between 2 waves */  #define ODIRSEPARATOR '/'
 int mle, weightopt;  #else
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define DIRSEPARATOR '/'
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define ODIRSEPARATOR '\\'
 double jmean; /* Mean space between 2 waves */  #endif
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  int erreur; /* Error number */
 FILE *ficgp, *fichtm,*ficresprob;  int nvar;
 FILE *ficreseij;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   char filerese[FILENAMELENGTH];  int npar=NPARMAX;
  FILE  *ficresvij;  int nlstate=2; /* Number of live states */
   char fileresv[FILENAMELENGTH];  int ndeath=1; /* Number of dead states */
  FILE  *ficresvpl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   char fileresvpl[FILENAMELENGTH];  int popbased=0;
   
 #define NR_END 1  int *wav; /* Number of waves for this individuual 0 is possible */
 #define FREE_ARG char*  int maxwav; /* Maxim number of waves */
 #define FTOL 1.0e-10  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 #define NRANSI  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define ITMAX 200  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double jmean; /* Mean space between 2 waves */
 #define TOL 2.0e-4  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define CGOLD 0.3819660  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define ZEPS 1.0e-10  FILE *ficlog;
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define GOLD 1.618034  FILE *fichtm; /* Html File */
 #define GLIMIT 100.0  FILE *ficreseij;
 #define TINY 1.0e-20  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 static double maxarg1,maxarg2;  char fileresv[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvpl;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 static double sqrarg;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char filelog[FILENAMELENGTH]; /* Log file */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 int imx;  char popfile[FILENAMELENGTH];
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 int m,nb;  #define NR_END 1
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define FREE_ARG char*
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define FTOL 1.0e-10
 double **pmmij, ***probs, ***mobaverage;  
   #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, ***mobaverage;
       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 *s;                             /* 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++) {     s= strrchr( path, DIRSEPARATOR );            /* find last / */
     (s[i] = t[i]);     if ( s == 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 */
         s++;                              /* after this, the filename */
 void cutv(char *u,char *v, char*t, char occ)        l2 = strlen( s );                 /* length of filename */
 {        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,lg,j,p=0;        strcpy( name, s );                /* 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';     s = strrchr( name, '.' );            /* find last / */
      s++;
    for(j=0; j<= lg; j++) {     strcpy(ext,s);                       /* save extension */
     if (j>=(p+1))(v[j-p-1] = t[j]);     l1= strlen( name);
   }     l2= strlen( s)+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(1);
    }
   /* 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 'nhstepm*hstepm*stepm' month 
       for(d=0; d<dh[mi][i]; d++){       duration (i.e. until
         newm=savm;       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         for (kk=1; kk<=cptcovage;kk++) {       (typically every 2 years instead of every month which is too big).
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       Model is determined by parameters x and covariates have to be 
         }       included manually here. 
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;    int i, j, d, h, k;
         oldm=newm;    double **out, cov[NCOVMAX];
            double **newm;
          
       } /* end mult */    /* Hstepm could be zero and should return the unit matrix */
          for (i=1;i<=nlstate+ndeath;i++)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      for (j=1;j<=nlstate+ndeath;j++){
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        oldm[i][j]=(i==j ? 1.0 : 0.0);
       ipmx +=1;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     } /* end of wave */    for(h=1; h <=nhstepm; h++){
   } /* end of individual */      for(d=1; d <=hstepm; d++){
         newm=savm;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        /* Covariates have to be included here again */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        cov[1]=1.;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   return -l;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 }        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 /*********** Maximum Likelihood Estimation ***************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int i,j, iter;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double **xi,*delti;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double fret;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   xi=matrix(1,npar,1,npar);        savm=oldm;
   for (i=1;i<=npar;i++)        oldm=newm;
     for (j=1;j<=npar;j++)      }
       xi[i][j]=(i==j ? 1.0 : 0.0);      for(i=1; i<=nlstate+ndeath; i++)
   printf("Powell\n");        for(j=1;j<=nlstate+ndeath;j++) {
   powell(p,xi,npar,ftol,&iter,&fret,func);          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#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));           */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        }
     } /* end h */
 }    return po;
   }
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  /*************** log-likelihood *************/
   double  **a,**y,*x,pd;  double func( double *x)
   double **hess;  {
   int i, j,jk;    int i, ii, j, k, mi, d, kk;
   int *indx;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   double hessii(double p[], double delta, int theta, double delti[]);    double sw; /* Sum of weights */
   double hessij(double p[], double delti[], int i, int j);    double lli; /* Individual log likelihood */
   void lubksb(double **a, int npar, int *indx, double b[]) ;    long ipmx;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /*extern weight */
     /* We are differentiating ll according to initial status */
   hess=matrix(1,npar,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   printf("\nCalculation of the hessian matrix. Wait...\n");      printf(" %d\n",s[4][i]);
   for (i=1;i<=npar;i++){    */
     printf("%d",i);fflush(stdout);    cov[1]=1.;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
     /*printf(" %lf ",hess[i][i]);*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=npar;i++) {        for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=npar;j++)  {          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (j>i) {        for(d=0; d<dh[mi][i]; d++){
         printf(".%d%d",i,j);fflush(stdout);          newm=savm;
         hess[i][j]=hessij(p,delti,i,j);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         hess[j][i]=hess[i][j];              for (kk=1; kk<=cptcovage;kk++) {
         /*printf(" %lf ",hess[i][j]);*/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }          }
     }          
   }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   printf("\n");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          oldm=newm;
            
   a=matrix(1,npar,1,npar);          
   y=matrix(1,npar,1,npar);        } /* end mult */
   x=vector(1,npar);        
   indx=ivector(1,npar);        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   for (i=1;i<=npar;i++)        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        ipmx +=1;
   ludcmp(a,npar,indx,&pd);        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (j=1;j<=npar;j++) {      } /* end of wave */
     for (i=1;i<=npar;i++) x[i]=0;    } /* end of individual */
     x[j]=1;  
     lubksb(a,npar,indx,x);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for (i=1;i<=npar;i++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       matcov[i][j]=x[i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }  }
   
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /*********** Maximum Likelihood Estimation ***************/
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     }  {
     printf("\n");    int i,j, iter;
   }    double **xi,*delti;
     double fret;
   /* Recompute Inverse */    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      for (j=1;j<=npar;j++)
   ludcmp(a,npar,indx,&pd);        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /*  printf("\n#Hessian matrix recomputed#\n");    powell(p,xi,npar,ftol,&iter,&fret,func);
   
   for (j=1;j<=npar;j++) {     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for (i=1;i<=npar;i++) x[i]=0;    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     x[j]=1;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  }
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  /**** Computes Hessian and covariance matrix ***/
     }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     printf("\n");  {
   }    double  **a,**y,*x,pd;
   */    double **hess;
     int i, j,jk;
   free_matrix(a,1,npar,1,npar);    int *indx;
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);    double hessii(double p[], double delta, int theta, double delti[]);
   free_ivector(indx,1,npar);    double hessij(double p[], double delti[], int i, int j);
   free_matrix(hess,1,npar,1,npar);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   
 }    hess=matrix(1,npar,1,npar);
   
 /*************** hessian matrix ****************/    printf("\nCalculation of the hessian matrix. Wait...\n");
 double hessii( double x[], double delta, int theta, double delti[])    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 {    for (i=1;i<=npar;i++){
   int i;      printf("%d",i);fflush(stdout);
   int l=1, lmax=20;      fprintf(ficlog,"%d",i);fflush(ficlog);
   double k1,k2;      hess[i][i]=hessii(p,ftolhess,i,delti);
   double p2[NPARMAX+1];      /*printf(" %f ",p[i]);*/
   double res;      /*printf(" %lf ",hess[i][i]);*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    }
   double fx;    
   int k=0,kmax=10;    for (i=1;i<=npar;i++) {
   double l1;      for (j=1;j<=npar;j++)  {
         if (j>i) { 
   fx=func(x);          printf(".%d%d",i,j);fflush(stdout);
   for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for(l=0 ; l <=lmax; l++){          hess[i][j]=hessij(p,delti,i,j);
     l1=pow(10,l);          hess[j][i]=hess[i][j];    
     delts=delt;          /*printf(" %lf ",hess[i][j]);*/
     for(k=1 ; k <kmax; k=k+1){        }
       delt = delta*(l1*k);      }
       p2[theta]=x[theta] +delt;    }
       k1=func(p2)-fx;    printf("\n");
       p2[theta]=x[theta]-delt;    fprintf(ficlog,"\n");
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
          
 #ifdef DEBUG    a=matrix(1,npar,1,npar);
       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);    y=matrix(1,npar,1,npar);
 #endif    x=vector(1,npar);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    indx=ivector(1,npar);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (i=1;i<=npar;i++)
         k=kmax;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      x[j]=1;
         delts=delt;      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
     }        matcov[i][j]=x[i];
   }      }
   delti[theta]=delts;    }
   return res;  
      printf("\n#Hessian matrix#\n");
 }    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)      for (j=1;j<=npar;j++) { 
 {        printf("%.3e ",hess[i][j]);
   int i;        fprintf(ficlog,"%.3e ",hess[i][j]);
   int l=1, l1, lmax=20;      }
   double k1,k2,k3,k4,res,fx;      printf("\n");
   double p2[NPARMAX+1];      fprintf(ficlog,"\n");
   int k;    }
   
   fx=func(x);    /* Recompute Inverse */
   for (k=1; k<=2; k++) {    for (i=1;i<=npar;i++)
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     p2[thetai]=x[thetai]+delti[thetai]/k;    ludcmp(a,npar,indx,&pd);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    /*  printf("\n#Hessian matrix recomputed#\n");
    
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (j=1;j<=npar;j++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for (i=1;i<=npar;i++) x[i]=0;
     k2=func(p2)-fx;      x[j]=1;
        lubksb(a,npar,indx,x);
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=npar;i++){ 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        y[i][j]=x[i];
     k3=func(p2)-fx;        printf("%.3e ",y[i][j]);
          fprintf(ficlog,"%.3e ",y[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      printf("\n");
     k4=func(p2)-fx;      fprintf(ficlog,"\n");
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    }
 #ifdef DEBUG    */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
   return res;    free_vector(x,1,npar);
 }    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  /*************** hessian matrix ****************/
   double *vv;  double hessii( double x[], double delta, int theta, double delti[])
    {
   vv=vector(1,n);    int i;
   *d=1.0;    int l=1, lmax=20;
   for (i=1;i<=n;i++) {    double k1,k2;
     big=0.0;    double p2[NPARMAX+1];
     for (j=1;j<=n;j++)    double res;
       if ((temp=fabs(a[i][j])) > big) big=temp;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    double fx;
     vv[i]=1.0/big;    int k=0,kmax=10;
   }    double l1;
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {    fx=func(x);
       sum=a[i][j];    for (i=1;i<=npar;i++) p2[i]=x[i];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    for(l=0 ; l <=lmax; l++){
       a[i][j]=sum;      l1=pow(10,l);
     }      delts=delt;
     big=0.0;      for(k=1 ; k <kmax; k=k+1){
     for (i=j;i<=n;i++) {        delt = delta*(l1*k);
       sum=a[i][j];        p2[theta]=x[theta] +delt;
       for (k=1;k<j;k++)        k1=func(p2)-fx;
         sum -= a[i][k]*a[k][j];        p2[theta]=x[theta]-delt;
       a[i][j]=sum;        k2=func(p2)-fx;
       if ( (dum=vv[i]*fabs(sum)) >= big) {        /*res= (k1-2.0*fx+k2)/delt/delt; */
         big=dum;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         imax=i;        
       }  #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);
     if (j != imax) {        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       for (k=1;k<=n;k++) {  #endif
         dum=a[imax][k];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         a[imax][k]=a[j][k];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         a[j][k]=dum;          k=kmax;
       }        }
       *d = -(*d);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       vv[imax]=vv[j];          k=kmax; l=lmax*10.;
     }        }
     indx[j]=imax;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     if (a[j][j] == 0.0) a[j][j]=TINY;          delts=delt;
     if (j != n) {        }
       dum=1.0/(a[j][j]);      }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    }
     }    delti[theta]=delts;
   }    return res; 
   free_vector(vv,1,n);  /* Doesn't work */    
 ;  }
 }  
   double hessij( double x[], double delti[], int thetai,int thetaj)
 void lubksb(double **a, int n, int *indx, double b[])  {
 {    int i;
   int i,ii=0,ip,j;    int l=1, l1, lmax=20;
   double sum;    double k1,k2,k3,k4,res,fx;
      double p2[NPARMAX+1];
   for (i=1;i<=n;i++) {    int k;
     ip=indx[i];  
     sum=b[ip];    fx=func(x);
     b[ip]=b[i];    for (k=1; k<=2; k++) {
     if (ii)      for (i=1;i<=npar;i++) p2[i]=x[i];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      p2[thetai]=x[thetai]+delti[thetai]/k;
     else if (sum) ii=i;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     b[i]=sum;      k1=func(p2)-fx;
   }    
   for (i=n;i>=1;i--) {      p2[thetai]=x[thetai]+delti[thetai]/k;
     sum=b[i];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      k2=func(p2)-fx;
     b[i]=sum/a[i][i];    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
 /************ Frequencies ********************/    
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)      p2[thetai]=x[thetai]-delti[thetai]/k;
 {  /* Some frequencies */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   double ***freq; /* Frequencies */  #ifdef DEBUG
   double *pp;      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);
   double pos;      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);
   FILE *ficresp;  #endif
   char fileresp[FILENAMELENGTH];    }
     return res;
   pp=vector(1,nlstate);  }
  probs= ma3x(1,130 ,1,8, 1,8);  
   strcpy(fileresp,"p");  /************** Inverse of matrix **************/
   strcat(fileresp,fileres);  void ludcmp(double **a, int n, int *indx, double *d) 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    int i,imax,j,k; 
     exit(0);    double big,dum,sum,temp; 
   }    double *vv; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);   
   j1=0;    vv=vector(1,n); 
     *d=1.0; 
   j=cptcoveff;    for (i=1;i<=n;i++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      big=0.0; 
       for (j=1;j<=n;j++) 
   for(k1=1; k1<=j;k1++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
    for(i1=1; i1<=ncodemax[k1];i1++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        j1++;      vv[i]=1.0/big; 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    } 
          scanf("%d", i);*/    for (j=1;j<=n;j++) { 
         for (i=-1; i<=nlstate+ndeath; i++)        for (i=1;i<j;i++) { 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          sum=a[i][j]; 
            for(m=agemin; m <= agemax+3; m++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
              freq[i][jk][m]=0;        a[i][j]=sum; 
              } 
        for (i=1; i<=imx; i++) {      big=0.0; 
          bool=1;      for (i=j;i<=n;i++) { 
          if  (cptcovn>0) {        sum=a[i][j]; 
            for (z1=1; z1<=cptcoveff; z1++)        for (k=1;k<j;k++) 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          sum -= a[i][k]*a[k][j]; 
                bool=0;        a[i][j]=sum; 
          }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           if (bool==1) {          big=dum; 
            for(m=fprev1; m<=lprev1; m++){          imax=i; 
              if(agev[m][i]==0) agev[m][i]=agemax+1;        } 
              if(agev[m][i]==1) agev[m][i]=agemax+2;      } 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if (j != imax) { 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for (k=1;k<=n;k++) { 
            }          dum=a[imax][k]; 
          }          a[imax][k]=a[j][k]; 
        }          a[j][k]=dum; 
         if  (cptcovn>0) {        } 
          fprintf(ficresp, "\n#********** Variable ");        *d = -(*d); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        vv[imax]=vv[j]; 
        fprintf(ficresp, "**********\n#");      } 
         }      indx[j]=imax; 
        for(i=1; i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      if (j != n) { 
        fprintf(ficresp, "\n");        dum=1.0/(a[j][j]); 
                for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for(i=(int)agemin; i <= (int)agemax+3; i++){      } 
     if(i==(int)agemax+3)    } 
       printf("Total");    free_vector(vv,1,n);  /* Doesn't work */
     else  ;
       printf("Age %d", i);  } 
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  void lubksb(double **a, int n, int *indx, double b[]) 
         pp[jk] += freq[jk][m][i];  { 
     }    int i,ii=0,ip,j; 
     for(jk=1; jk <=nlstate ; jk++){    double sum; 
       for(m=-1, pos=0; m <=0 ; m++)   
         pos += freq[jk][m][i];    for (i=1;i<=n;i++) { 
       if(pp[jk]>=1.e-10)      ip=indx[i]; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      sum=b[ip]; 
       else      b[ip]=b[i]; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      if (ii) 
     }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
      for(jk=1; jk <=nlstate ; jk++){      b[i]=sum; 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
         pp[jk] += freq[jk][m][i];    for (i=n;i>=1;i--) { 
      }      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)      b[i]=sum/a[i][i]; 
       pos += pp[jk];    } 
     for(jk=1; jk <=nlstate ; jk++){  } 
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /************ Frequencies ********************/
       else  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  {  /* Some frequencies */
       if( i <= (int) agemax){    
         if(pos>=1.e-5){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    int first;
           probs[i][jk][j1]= pp[jk]/pos;    double ***freq; /* Frequencies */
           /*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 *pp;
         }    double pos, k2, dateintsum=0,k2cpt=0;
       else    FILE *ficresp;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    char fileresp[FILENAMELENGTH];
       }    
     }    pp=vector(1,nlstate);
     for(jk=-1; jk <=nlstate+ndeath; jk++)    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(m=-1; m <=nlstate+ndeath; m++)    strcpy(fileresp,"p");
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    strcat(fileresp,fileres);
     if(i <= (int) agemax)    if((ficresp=fopen(fileresp,"w"))==NULL) {
       fprintf(ficresp,"\n");      printf("Problem with prevalence resultfile: %s\n", fileresp);
     printf("\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
     }    }
  }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
      j1=0;
   fclose(ficresp);    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    j=cptcoveff;
   free_vector(pp,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
 }  /* End of Freq */    first=1;
   
 /************ Prevalence ********************/    for(k1=1; k1<=j;k1++){
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)      for(i1=1; i1<=ncodemax[k1];i1++){
 {  /* Some frequencies */        j1++;
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          scanf("%d", i);*/
   double ***freq; /* Frequencies */        for (i=-1; i<=nlstate+ndeath; i++)  
   double *pp;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   double pos;            for(m=agemin; m <= agemax+3; m++)
               freq[i][jk][m]=0;
   pp=vector(1,nlstate);        
   probs= ma3x(1,130 ,1,8, 1,8);        dateintsum=0;
          k2cpt=0;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for (i=1; i<=imx; i++) {
   j1=0;          bool=1;
            if  (cptcovn>0) {
   j=cptcoveff;            for (z1=1; z1<=cptcoveff; z1++) 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
  for(k1=1; k1<=j;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){          if (bool==1) {
       j1++;            for(m=firstpass; m<=lastpass; m++){
                k2=anint[m][i]+(mint[m][i]/12.);
       for (i=-1; i<=nlstate+ndeath; i++)                if ((k2>=dateprev1) && (k2<=dateprev2)) {
         for (jk=-1; jk<=nlstate+ndeath; jk++)                  if(agev[m][i]==0) agev[m][i]=agemax+1;
           for(m=agemin; m <= agemax+3; m++)                if(agev[m][i]==1) agev[m][i]=agemax+2;
           freq[i][jk][m]=0;                if (m<lastpass) {
                        freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for (i=1; i<=imx; i++) {                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
         bool=1;                }
         if  (cptcovn>0) {                
           for (z1=1; z1<=cptcoveff; z1++)                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])                  dateintsum=dateintsum+k2;
               bool=0;                  k2cpt++;
               }                }
         if (bool==1) {              }
           for(m=fprev1; m<=lprev1; m++){            }
             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];         
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
           }  
         }        if  (cptcovn>0) {
       }          fprintf(ficresp, "\n#********** Variable "); 
        for(i=(int)agemin; i <= (int)agemax+3; i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(jk=1; jk <=nlstate ; jk++){          fprintf(ficresp, "**********\n#");
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
             pp[jk] += freq[jk][m][i];        for(i=1; i<=nlstate;i++) 
         }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficresp, "\n");
           for(m=-1, pos=0; m <=0 ; m++)        
             pos += freq[jk][m][i];        for(i=(int)agemin; i <= (int)agemax+3; i++){
         }          if(i==(int)agemax+3){
                    fprintf(ficlog,"Total");
          for(jk=1; jk <=nlstate ; jk++){          }else{
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            if(first==1){
              pp[jk] += freq[jk][m][i];              first=0;
          }              printf("See log file for details...\n");
                      }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            fprintf(ficlog,"Age %d", i);
           }
          for(jk=1; jk <=nlstate ; jk++){                    for(jk=1; jk <=nlstate ; jk++){
            if( i <= (int) agemax){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
              if(pos>=1.e-5){              pp[jk] += freq[jk][m][i]; 
                probs[i][jk][j1]= pp[jk]/pos;          }
              }          for(jk=1; jk <=nlstate ; jk++){
            }            for(m=-1, pos=0; m <=0 ; m++)
          }              pos += freq[jk][m][i];
                      if(pp[jk]>=1.e-10){
          }              if(first==1){
     }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              if(first==1)
   free_vector(pp,1,nlstate);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }  /* End of Freq */            }
 /************* Waves Concatenation ***************/          }
   
 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(jk=1; jk <=nlstate ; jk++){
 {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              pp[jk] += freq[jk][m][i];
      Death is a valid wave (if date is known).          }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for(jk=1,pos=0; jk <=nlstate ; jk++)
      and mw[mi+1][i]. dh depends on stepm.            pos += pp[jk];
      */          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   int i, mi, m;              if(first==1)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      double sum=0., jmean=0.;*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   int j, k=0,jk, ju, jl;              if(first==1)
   double sum=0.;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   jmin=1e+5;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   jmax=-1;            }
   jmean=0.;            if( i <= (int) agemax){
   for(i=1; i<=imx; i++){              if(pos>=1.e-5){
     mi=0;                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
     m=firstpass;                probs[i][jk][j1]= pp[jk]/pos;
     while(s[m][i] <= nlstate){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       if(s[m][i]>=1)              }
         mw[++mi][i]=m;              else
       if(m >=lastpass)                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
         break;            }
       else          }
         m++;          
     }/* end while */          for(jk=-1; jk <=nlstate+ndeath; jk++)
     if (s[m][i] > nlstate){            for(m=-1; m <=nlstate+ndeath; m++)
       mi++;     /* Death is another wave */              if(freq[jk][m][i] !=0 ) {
       /* if(mi==0)  never been interviewed correctly before death */              if(first==1)
          /* Only death is a correct wave */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       mw[mi][i]=m;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
           if(i <= (int) agemax)
     wav[i]=mi;            fprintf(ficresp,"\n");
     if(mi==0)          if(first==1)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            printf("Others in log...\n");
   }          fprintf(ficlog,"\n");
         }
   for(i=1; i<=imx; i++){      }
     for(mi=1; mi<wav[i];mi++){    }
       if (stepm <=0)    dateintmean=dateintsum/k2cpt; 
         dh[mi][i]=1;   
       else{    fclose(ficresp);
         if (s[mw[mi+1][i]][i] > nlstate) {    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
           if (agedc[i] < 2*AGESUP) {    free_vector(pp,1,nlstate);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    
           if(j==0) j=1;  /* Survives at least one month after exam */    /* End of Freq */
           k=k+1;  }
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;  /************ Prevalence ********************/
           sum=sum+j;  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
           /* if (j<10) printf("j=%d num=%d ",j,i); */  {  /* Some frequencies */
           }   
         }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         else{    double ***freq; /* Frequencies */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double *pp;
           k=k+1;    double pos, k2;
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;    pp=vector(1,nlstate);
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    
           sum=sum+j;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         }    j1=0;
         jk= j/stepm;    
         jl= j -jk*stepm;    j=cptcoveff;
         ju= j -(jk+1)*stepm;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         if(jl <= -ju)    
           dh[mi][i]=jk;    for(k1=1; k1<=j;k1++){
         else      for(i1=1; i1<=ncodemax[k1];i1++){
           dh[mi][i]=jk+1;        j1++;
         if(dh[mi][i]==0)        
           dh[mi][i]=1; /* At least one step */        for (i=-1; i<=nlstate+ndeath; i++)  
       }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     }            for(m=agemin; m <= agemax+3; m++)
   }              freq[i][jk][m]=0;
   jmean=sum/k;       
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for (i=1; i<=imx; i++) {
  }          bool=1;
 /*********** Tricode ****************************/          if  (cptcovn>0) {
 void tricode(int *Tvar, int **nbcode, int imx)            for (z1=1; z1<=cptcoveff; z1++) 
 {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   int Ndum[20],ij=1, k, j, i;                bool=0;
   int cptcode=0;          } 
   cptcoveff=0;          if (bool==1) { 
              for(m=firstpass; m<=lastpass; m++){
   for (k=0; k<19; k++) Ndum[k]=0;              k2=anint[m][i]+(mint[m][i]/12.);
   for (k=1; k<=7; k++) ncodemax[k]=0;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {                if(agev[m][i]==1) agev[m][i]=agemax+2;
     for (i=1; i<=imx; i++) {                if (m<lastpass) {
       ij=(int)(covar[Tvar[j]][i]);                  if (calagedate>0) 
       Ndum[ij]++;                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/                  else
       if (ij > cptcode) cptcode=ij;                    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]; 
                 }
     for (i=0; i<=cptcode; i++) {              }
       if(Ndum[i]!=0) ncodemax[j]++;            }
     }          }
     ij=1;        }
         for(i=(int)agemin; i <= (int)agemax+3; i++){ 
           for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=ncodemax[j]; i++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for (k=0; k<=19; k++) {              pp[jk] += freq[jk][m][i]; 
         if (Ndum[k] != 0) {          }
           nbcode[Tvar[j]][ij]=k;          for(jk=1; jk <=nlstate ; jk++){
           ij++;            for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
         if (ij > ncodemax[j]) break;          }
       }            
     }          for(jk=1; jk <=nlstate ; jk++){
   }              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
  for (k=0; k<19; k++) Ndum[k]=0;          }
           
  for (i=1; i<=ncovmodel-2; i++) {          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
       ij=Tvar[i];          
       Ndum[ij]++;          for(jk=1; jk <=nlstate ; jk++){    
     }            if( i <= (int) agemax){
               if(pos>=1.e-5){
  ij=1;                probs[i][jk][j1]= pp[jk]/pos;
  for (i=1; i<=10; i++) {              }
    if((Ndum[i]!=0) && (i<=ncov)){            }
      Tvaraff[ij]=i;          }/* end jk */
      ij++;        }/* end i */
    }      } /* end i1 */
  }    } /* end k1 */
    
     cptcoveff=ij-1;    
 }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
 /*********** Health Expectancies ****************/    
   }  /* End of Freq */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  
 {  /************* Waves Concatenation ***************/
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   double age, agelim,hf;  {
   double ***p3mat;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
   fprintf(ficreseij,"# Health expectancies\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   fprintf(ficreseij,"# Age");       dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
   for(i=1; i<=nlstate;i++)       and mw[mi+1][i]. dh depends on stepm.
     for(j=1; j<=nlstate;j++)       */
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   hstepm=1*YEARM; /*  Every j years of age (in month) */       double sum=0., jmean=0.;*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int first;
     int j, k=0,jk, ju, jl;
   agelim=AGESUP;    double sum=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    first=0;
     /* nhstepm age range expressed in number of stepm */    jmin=1e+5;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    jmax=-1;
     /* Typically if 20 years = 20*12/6=40 stepm */    jmean=0.;
     if (stepm >= YEARM) hstepm=1;    for(i=1; i<=imx; i++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      mi=0;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      m=firstpass;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      while(s[m][i] <= nlstate){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        if(s[m][i]>=1)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            mw[++mi][i]=m;
         if(m >=lastpass)
           break;
     for(i=1; i<=nlstate;i++)        else
       for(j=1; j<=nlstate;j++)          m++;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      }/* end while */
           eij[i][j][(int)age] +=p3mat[i][j][h];      if (s[m][i] > nlstate){
         }        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     hf=1;           /* Only death is a correct wave */
     if (stepm >= YEARM) hf=stepm/YEARM;        mw[mi][i]=m;
     fprintf(ficreseij,"%.0f",age );      }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){      wav[i]=mi;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      if(mi==0){
       }        if(first==0){
     fprintf(ficreseij,"\n");          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          first=1;
   }        }
 }        if(first==1){
           fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
 /************ Variance ******************/        }
 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)      } /* end mi==0 */
 {    }
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for(i=1; i<=imx; i++){
   double **newm;      for(mi=1; mi<wav[i];mi++){
   double **dnewm,**doldm;        if (stepm <=0)
   int i, j, nhstepm, hstepm, h;          dh[mi][i]=1;
   int k, cptcode;        else{
   double *xp;          if (s[mw[mi+1][i]][i] > nlstate) {
   double **gp, **gm;            if (agedc[i] < 2*AGESUP) {
   double ***gradg, ***trgradg;            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   double ***p3mat;            if(j==0) j=1;  /* Survives at least one month after exam */
   double age,agelim;            k=k+1;
   int theta;            if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
    fprintf(ficresvij,"# Covariances of life expectancies\n");            sum=sum+j;
   fprintf(ficresvij,"# Age");            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          else{
   fprintf(ficresvij,"\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             k=k+1;
   xp=vector(1,npar);            if (j >= jmax) jmax=j;
   dnewm=matrix(1,nlstate,1,npar);            else if (j <= jmin)jmin=j;
   doldm=matrix(1,nlstate,1,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
              sum=sum+j;
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          jk= j/stepm;
   agelim = AGESUP;          jl= j -jk*stepm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ju= j -(jk+1)*stepm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          if(jl <= -ju)
     if (stepm >= YEARM) hstepm=1;            dh[mi][i]=jk;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          else
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            dh[mi][i]=jk+1;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          if(dh[mi][i]==0)
     gp=matrix(0,nhstepm,1,nlstate);            dh[mi][i]=1; /* At least one step */
     gm=matrix(0,nhstepm,1,nlstate);        }
       }
     for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){ /* Computes gradient */    jmean=sum/k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       }    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   /*********** Tricode ****************************/
       if (popbased==1) {  void tricode(int *Tvar, int **nbcode, int imx)
         for(i=1; i<=nlstate;i++)  {
           prlim[i][i]=probs[(int)age][i][ij];    int Ndum[20],ij=1, k, j, i;
       }    int cptcode=0;
          cptcoveff=0; 
       for(j=1; j<= nlstate; j++){   
         for(h=0; h<=nhstepm; h++){    for (k=0; k<19; k++) Ndum[k]=0;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (k=1; k<=7; k++) ncodemax[k]=0;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       }      for (i=1; i<=imx; i++) {
            ij=(int)(covar[Tvar[j]][i]);
       for(i=1; i<=npar; i++) /* Computes gradient */        Ndum[ij]++; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          if (ij > cptcode) cptcode=ij; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }
   
       if (popbased==1) {      for (i=0; i<=cptcode; i++) {
         for(i=1; i<=nlstate;i++)        if(Ndum[i]!=0) ncodemax[j]++;
           prlim[i][i]=probs[(int)age][i][ij];      }
       }      ij=1; 
   
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){      for (i=1; i<=ncodemax[j]; i++) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for (k=0; k<=19; k++) {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          if (Ndum[k] != 0) {
         }            nbcode[Tvar[j]][ij]=k; 
       }            
             ij++;
       for(j=1; j<= nlstate; j++)          }
         for(h=0; h<=nhstepm; h++){          if (ij > ncodemax[j]) break; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        }  
         }      } 
     } /* End theta */    }  
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);   for (k=0; k<19; k++) Ndum[k]=0;
   
     for(h=0; h<=nhstepm; h++)   for (i=1; i<=ncovmodel-2; i++) {
       for(j=1; j<=nlstate;j++)     ij=Tvar[i];
         for(theta=1; theta <=npar; theta++)     Ndum[ij]++; 
           trgradg[h][j][theta]=gradg[h][theta][j];   }
   
     for(i=1;i<=nlstate;i++)   ij=1;
       for(j=1;j<=nlstate;j++)   for (i=1; i<=10; i++) {
         vareij[i][j][(int)age] =0.;     if((Ndum[i]!=0) && (i<=ncovcol)){
     for(h=0;h<=nhstepm;h++){       Tvaraff[ij]=i; 
       for(k=0;k<=nhstepm;k++){       ij++;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);     }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);   }
         for(i=1;i<=nlstate;i++)   
           for(j=1;j<=nlstate;j++)   cptcoveff=ij-1;
             vareij[i][j][(int)age] += doldm[i][j];  }
       }  
     }  /*********** Health Expectancies ****************/
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++){    /* Health expectancies */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       }    double age, agelim, hf;
     fprintf(ficresvij,"\n");    double ***p3mat,***varhe;
     free_matrix(gp,0,nhstepm,1,nlstate);    double **dnewm,**doldm;
     free_matrix(gm,0,nhstepm,1,nlstate);    double *xp;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double **gp, **gm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double ***gradg, ***trgradg;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
   } /* End age */  
      varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   free_vector(xp,1,npar);    xp=vector(1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    dnewm=matrix(1,nlstate*2,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    doldm=matrix(1,nlstate*2,1,nlstate*2);
     
 }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
 /************ Variance of prevlim ******************/    for(i=1; i<=nlstate;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)      for(j=1; j<=nlstate;j++)
 {        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   /* Variance of prevalence limit */    fprintf(ficreseij,"\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    if(estepm < stepm){
   double **dnewm,**doldm;      printf ("Problem %d lower than %d\n",estepm, stepm);
   int i, j, nhstepm, hstepm;    }
   int k, cptcode;    else  hstepm=estepm;   
   double *xp;    /* We compute the life expectancy from trapezoids spaced every estepm months
   double *gp, *gm;     * This is mainly to measure the difference between two models: for example
   double **gradg, **trgradg;     * if stepm=24 months pijx are given only every 2 years and by summing them
   double age,agelim;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   int theta;     * progression inbetween and thus overestimating or underestimating according
         * to the curvature of the survival function. If, for the same date, we 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   fprintf(ficresvpl,"# Age");     * to compare the new estimate of Life expectancy with the same linear 
   for(i=1; i<=nlstate;i++)     * hypothesis. A more precise result, taking into account a more precise
       fprintf(ficresvpl," %1d-%1d",i,i);     * curvature will be obtained if estepm is as small as stepm. */
   fprintf(ficresvpl,"\n");  
     /* For example we decided to compute the life expectancy with the smallest unit */
   xp=vector(1,npar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   dnewm=matrix(1,nlstate,1,npar);       nhstepm is the number of hstepm from age to agelim 
   doldm=matrix(1,nlstate,1,nlstate);       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   hstepm=1*YEARM; /* Every year of age */       and note for a fixed period like estepm months */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   agelim = AGESUP;       survival function given by stepm (the optimization length). Unfortunately it
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       means that if the survival funtion is printed only each two years of age and if
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     if (stepm >= YEARM) hstepm=1;       results. So we changed our mind and took the option of the best precision.
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    */
     gradg=matrix(1,npar,1,nlstate);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for(theta=1; theta <=npar; theta++){      /* nhstepm age range expressed in number of stepm */
       for(i=1; i<=npar; i++){ /* Computes gradient */      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }      /* if (stepm >= YEARM) hstepm=1;*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(i=1;i<=nlstate;i++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         gp[i] = prlim[i][i];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
          gp=matrix(0,nhstepm,1,nlstate*2);
       for(i=1; i<=npar; i++) /* Computes gradient */      gm=matrix(0,nhstepm,1,nlstate*2);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       for(i=1;i<=nlstate;i++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         gm[i] = prlim[i][i];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     } /* End theta */  
       /* Computing Variances of health expectancies */
     trgradg =matrix(1,nlstate,1,npar);  
        for(theta=1; theta <=npar; theta++){
     for(j=1; j<=nlstate;j++)        for(i=1; i<=npar; i++){ 
       for(theta=1; theta <=npar; theta++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         trgradg[j][theta]=gradg[theta][j];        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(i=1;i<=nlstate;i++)    
       varpl[i][(int)age] =0.;        cptj=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        for(j=1; j<= nlstate; j++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          for(i=1; i<=nlstate; i++){
     for(i=1;i<=nlstate;i++)            cptj=cptj+1;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fprintf(ficresvpl,"%.0f ",age );            }
     for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        }
     fprintf(ficresvpl,"\n");       
     free_vector(gp,1,nlstate);       
     free_vector(gm,1,nlstate);        for(i=1; i<=npar; i++) 
     free_matrix(gradg,1,npar,1,nlstate);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_matrix(trgradg,1,nlstate,1,npar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   } /* End age */        
         cptj=0;
   free_vector(xp,1,npar);        for(j=1; j<= nlstate; j++){
   free_matrix(doldm,1,nlstate,1,npar);          for(i=1;i<=nlstate;i++){
   free_matrix(dnewm,1,nlstate,1,nlstate);            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
 /************ Variance of one-step probabilities  ******************/          }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        }
 {        for(j=1; j<= nlstate*2; j++)
   int i, j;          for(h=0; h<=nhstepm-1; h++){
   int k=0, cptcode;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   double **dnewm,**doldm;          }
   double *xp;       } 
   double *gp, *gm;     
   double **gradg, **trgradg;  /* End theta */
   double age,agelim, cov[NCOVMAX];  
   int theta;       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   char fileresprob[FILENAMELENGTH];  
        for(h=0; h<=nhstepm-1; h++)
   strcpy(fileresprob,"prob");        for(j=1; j<=nlstate*2;j++)
   strcat(fileresprob,fileres);          for(theta=1; theta <=npar; theta++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
     printf("Problem with resultfile: %s\n", fileresprob);       
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);       for(i=1;i<=nlstate*2;i++)
          for(j=1;j<=nlstate*2;j++)
           varhe[i][j][(int)age] =0.;
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       printf("%d|",(int)age);fflush(stdout);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
   cov[1]=1;        for(k=0;k<=nhstepm-1;k++){
   for (age=bage; age<=fage; age ++){          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
     cov[2]=age;          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     gradg=matrix(1,npar,1,9);          for(i=1;i<=nlstate*2;i++)
     trgradg=matrix(1,9,1,npar);            for(j=1;j<=nlstate*2;j++)
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
          }
     for(theta=1; theta <=npar; theta++){      /* Computing expectancies */
       for(i=1; i<=npar; i++)      for(i=1; i<=nlstate;i++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(j=1; j<=nlstate;j++)
                for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                
       k=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]);*/
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;  
           gp[k]=pmmij[i][j];      fprintf(ficreseij,"%3.0f",age );
         }      cptj=0;
       }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
       for(i=1; i<=npar; i++)          cptj++;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
            }
       fprintf(ficreseij,"\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);     
       k=0;      free_matrix(gm,0,nhstepm,1,nlstate*2);
       for(i=1; i<=(nlstate+ndeath); i++){      free_matrix(gp,0,nhstepm,1,nlstate*2);
         for(j=1; j<=(nlstate+ndeath);j++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
           k=k+1;      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
           gm[k]=pmmij[i][j];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    }
       }    printf("\n");
          fprintf(ficlog,"\n");
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_vector(xp,1,npar);
     }    free_matrix(dnewm,1,nlstate*2,1,npar);
     free_matrix(doldm,1,nlstate*2,1,nlstate*2);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
       for(theta=1; theta <=npar; theta++)  }
       trgradg[j][theta]=gradg[theta][j];  
    /************ Variance ******************/
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  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)
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  {
     /* Variance of health expectancies */
      pmij(pmmij,cov,ncovmodel,x,nlstate);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
      k=0;    double **dnewm,**doldm;
      for(i=1; i<=(nlstate+ndeath); i++){    double **dnewmp,**doldmp;
        for(j=1; j<=(nlstate+ndeath);j++){    int i, j, nhstepm, hstepm, h, nstepm ;
          k=k+1;    int k, cptcode;
          gm[k]=pmmij[i][j];    double *xp;
         }    double **gp, **gm;  /* for var eij */
      }    double ***gradg, ***trgradg; /*for var eij */
          double **gradgp, **trgradgp; /* for var p point j */
      /*printf("\n%d ",(int)age);    double *gpp, *gmp; /* for var p point j */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
            double ***p3mat;
     double age,agelim, hf;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double ***mobaverage;
      }*/    int theta;
     char digit[4];
   fprintf(ficresprob,"\n%d ",(int)age);    char digitp[16];
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    char fileresprobmorprev[FILENAMELENGTH];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    if(popbased==1)
   }      strcpy(digitp,"-populbased-");
     else
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      strcpy(digitp,"-stablbased-");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    if(mobilav!=0)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      strcat(digitp,"mobilav-");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    else
 }      strcat(digitp,"nomobil-");
  free_vector(xp,1,npar);    if (mobilav!=0) {
 fclose(ficresprob);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  exit(0);      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);
 /***********************************************/      }
 /**************** Main Program *****************/    }
 /***********************************************/  
     strcpy(fileresprobmorprev,"prmorprev"); 
 /*int main(int argc, char *argv[])*/    sprintf(digit,"%-d",ij);
 int main()    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    strcat(fileresprobmorprev,fileres);
   double agedeb, agefin,hf;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   double agemin=1.e20, agemax=-1.e20;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   double fret;    }
   double **xi,tmp,delta;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double dum; /* Dummy variable */    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
   double ***p3mat;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   int *indx;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   char line[MAXLINE], linepar[MAXLINE];      fprintf(ficresprobmorprev," p.%-d SE",j);
   char title[MAXLINE];      for(i=1; i<=nlstate;i++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    }  
   char filerest[FILENAMELENGTH];    fprintf(ficresprobmorprev,"\n");
   char fileregp[FILENAMELENGTH];    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   int firstobs=1, lastobs=10;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   int sdeb, sfin; /* Status at beginning and end */      exit(0);
   int c,  h , cpt,l;    }
   int ju,jl, mi;    else{
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      fprintf(ficgp,"\n# Routine varevsij");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    }
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   int hstepm, nhstepm;      printf("Problem with html file: %s\n", optionfilehtm);
       fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   double bage, fage, age, agelim, agebase;      exit(0);
   double ftolpl=FTOL;    }
   double **prlim;    else{
   double *severity;      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   double ***param; /* Matrix of parameters */      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
   double  *p;    }
   double **matcov; /* Matrix of covariance */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double ***delti3; /* Scale */  
   double *delti; /* Scale */    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");
   double ***eij, ***vareij;    fprintf(ficresvij,"# Age");
   double **varpl; /* Variances of prevalence limits by age */    for(i=1; i<=nlstate;i++)
   double *epj, vepp;      for(j=1; j<=nlstate;j++)
   double kk1;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   char z[1]="c", occ;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 #include <sys/time.h>    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   /* long total_usecs;    gpp=vector(nlstate+1,nlstate+ndeath);
   struct timeval start_time, end_time;    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   printf("\nIMACH, Version 0.64b");    }
   printf("\nEnter the parameter file name: ");    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
 #ifdef windows    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   scanf("%s",pathtot);       nhstepm is the number of hstepm from age to agelim 
   getcwd(pathcd, size);       nstepm is the number of stepm from age to agelin. 
   /*cygwin_split_path(pathtot,path,optionfile);       Look at hpijx to understand the reason of that which relies in memory size
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       and note for a fixed period like k years */
   /* cutv(path,optionfile,pathtot,'\\');*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
 split(pathtot, path,optionfile);       means that if the survival funtion is printed only each two years of age and if
   chdir(path);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   replace(pathc,path);       results. So we changed our mind and took the option of the best precision.
 #endif    */
 #ifdef unix    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   scanf("%s",optionfile);    agelim = AGESUP;
 #endif    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 /*-------- arguments in the command line --------*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(fileres,"r");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   strcat(fileres, optionfile);      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   /*---------arguments file --------*/  
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      for(theta=1; theta <=npar; theta++){
     printf("Problem with optionfile %s\n",optionfile);        for(i=1; i<=npar; i++){ /* Computes gradient */
     goto end;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcpy(filereso,"o");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {        if (popbased==1) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   /* Reads comments: lines beginning with '#' */          }else{ /* mobilav */ 
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=mobaverage[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }
     puts(line);        }
     fputs(line,ficparo);    
   }        for(j=1; j<= nlstate; j++){
   ungetc(c,ficpar);          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);        }
 while((c=getc(ficpar))=='#' && c!= EOF){        /* This for computing forces of mortality (h=1)as a weighted average */
     ungetc(c,ficpar);        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);          for(i=1; i<= nlstate; i++)
     puts(line);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fputs(line,ficparo);        }    
   }        /* end force of mortality */
   ungetc(c,ficpar);  
          for(i=1; i<=npar; i++) /* Computes gradient */
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
  while((c=getc(ficpar))=='#' && c!= EOF){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fgets(line, MAXLINE, ficpar);   
     puts(line);        if (popbased==1) {
     fputs(line,ficparo);          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   covar=matrix(0,NCOVMAX,1,n);          }
   cptcovn=0;        }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
         for(j=1; j<= nlstate; j++){
   ncovmodel=2+cptcovn;          for(h=0; h<=nhstepm; h++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   /* Read guess parameters */          }
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        /* This for computing force of mortality (h=1)as a weighted average */
     ungetc(c,ficpar);        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);          for(i=1; i<= nlstate; i++)
     puts(line);            gmp[j] += prlim[i][i]*p3mat[i][j][1];
     fputs(line,ficparo);        }    
   }        /* end force of mortality */
   ungetc(c,ficpar);  
          for(j=1; j<= nlstate; j++) /* vareij */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for(h=0; h<=nhstepm; h++){
     for(i=1; i <=nlstate; i++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(j=1; j <=nlstate+ndeath-1; j++){          }
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       fprintf(ficparo,"%1d%1d",i1,j1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       printf("%1d%1d",i,j);        }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);      } /* End theta */
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       }  
       fscanf(ficpar,"\n");      for(h=0; h<=nhstepm; h++) /* veij */
       printf("\n");        for(j=1; j<=nlstate;j++)
       fprintf(ficparo,"\n");          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
   p=param[1][1];          trgradgp[j][theta]=gradgp[theta][j];
    
   /* Reads comments: lines beginning with '#' */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);        for(j=1;j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);          vareij[i][j][(int)age] =0.;
     puts(line);  
     fputs(line,ficparo);      for(h=0;h<=nhstepm;h++){
   }        for(k=0;k<=nhstepm;k++){
   ungetc(c,ficpar);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for(i=1;i<=nlstate;i++)
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            for(j=1;j<=nlstate;j++)
   for(i=1; i <=nlstate; i++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     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);      /* pptj */
       for(k=1; k<=ncovmodel;k++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         printf(" %le",delti3[i][j][k]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         fprintf(ficparo," %le",delti3[i][j][k]);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       }          varppt[j][i]=doldmp[j][i];
       fscanf(ficpar,"\n");      /* end ppptj */
       printf("\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficparo,"\n");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     }   
   }      if (popbased==1) {
   delti=delti3[1][1];        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */            prlim[i][i]=probs[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){        }else{ /* mobilav */ 
     ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);            prlim[i][i]=mobaverage[(int)age][i][ij];
     puts(line);        }
     fputs(line,ficparo);      }
   }      
   ungetc(c,ficpar);      /* This for computing force of mortality (h=1)as a weighted average */
        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   matcov=matrix(1,npar,1,npar);        for(i=1; i<= nlstate; i++)
   for(i=1; i <=npar; i++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     fscanf(ficpar,"%s",&str);      }    
     printf("%s",str);      /* end force of mortality */
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fscanf(ficpar," %le",&matcov[i][j]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf(" %.5le",matcov[i][j]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       fprintf(ficparo," %.5le",matcov[i][j]);        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fscanf(ficpar,"\n");        }
     printf("\n");      } 
     fprintf(ficparo,"\n");      fprintf(ficresprobmorprev,"\n");
   }  
   for(i=1; i <=npar; i++)      fprintf(ficresvij,"%.0f ",age );
     for(j=i+1;j<=npar;j++)      for(i=1; i<=nlstate;i++)
       matcov[i][j]=matcov[j][i];        for(j=1; j<=nlstate;j++){
              fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   printf("\n");        }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
     /*-------- data file ----------*/      free_matrix(gm,0,nhstepm,1,nlstate);
     if((ficres =fopen(fileres,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       printf("Problem with resultfile: %s\n", fileres);goto end;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"#%s\n",version);    } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
     if((fic=fopen(datafile,"r"))==NULL)    {    free_vector(gmp,nlstate+1,nlstate+ndeath);
       printf("Problem with datafile: %s\n", datafile);goto end;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     n= lastobs;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     severity = vector(1,maxwav);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     outcome=imatrix(1,maxwav+1,1,n);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
     num=ivector(1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
     moisnais=vector(1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
     annais=vector(1,n);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     moisdc=vector(1,n);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
     andc=vector(1,n);    /*  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);
     agedc=vector(1,n);  */
     cod=ivector(1,n);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_vector(xp,1,npar);
     mint=matrix(1,maxwav,1,n);    free_matrix(doldm,1,nlstate,1,nlstate);
     anint=matrix(1,maxwav,1,n);    free_matrix(dnewm,1,nlstate,1,npar);
     s=imatrix(1,maxwav+1,1,n);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     adl=imatrix(1,maxwav+1,1,n);        free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     tab=ivector(1,NCOVMAX);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ncodemax=ivector(1,8);    free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     i=1;    fclose(ficgp);
     while (fgets(line, MAXLINE, fic) != NULL)    {    fclose(fichtm);
       if ((i >= firstobs) && (i <=lastobs)) {  
          }
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  /************ Variance of prevlim ******************/
           strcpy(line,stra);  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)
           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);    /* Variance of prevalence limit */
         }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
            double **newm;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double **dnewm,**doldm;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    int i, j, nhstepm, hstepm;
     int k, cptcode;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    double *xp;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double *gp, *gm;
     double **gradg, **trgradg;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    double age,agelim;
         for (j=ncov;j>=1;j--){    int theta;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);     
         }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         num[i]=atol(stra);    fprintf(ficresvpl,"# Age");
            for(i=1; i<=nlstate;i++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        fprintf(ficresvpl," %1d-%1d",i,i);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    fprintf(ficresvpl,"\n");
   
         i=i+1;    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     /* printf("ii=%d", ij);    
        scanf("%d",i);*/    hstepm=1*YEARM; /* Every year of age */
   imx=i-1; /* Number of individuals */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   /* for (i=1; i<=imx; i++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      if (stepm >= YEARM) hstepm=1;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     }      gradg=matrix(1,npar,1,nlstate);
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);      for(theta=1; theta <=npar; theta++){
   Tprod=ivector(1,15);        for(i=1; i<=npar; i++){ /* Computes gradient */
   Tvaraff=ivector(1,15);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   Tvard=imatrix(1,15,1,2);        }
   Tage=ivector(1,15);              prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            for(i=1;i<=nlstate;i++)
   if (strlen(model) >1){          gp[i] = prlim[i][i];
     j=0, j1=0, k1=1, k2=1;      
     j=nbocc(model,'+');        for(i=1; i<=npar; i++) /* Computes gradient */
     j1=nbocc(model,'*');          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     cptcovn=j+1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     cptcovprod=j1;        for(i=1;i<=nlstate;i++)
              gm[i] = prlim[i][i];
      
     strcpy(modelsav,model);        for(i=1;i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       printf("Error. Non available option model=%s ",model);      } /* End theta */
       goto end;  
     }      trgradg =matrix(1,nlstate,1,npar);
      
     for(i=(j+1); i>=1;i--){      for(j=1; j<=nlstate;j++)
       cutv(stra,strb,modelsav,'+');        for(theta=1; theta <=npar; theta++)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          trgradg[j][theta]=gradg[theta][j];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/      for(i=1;i<=nlstate;i++)
       if (strchr(strb,'*')) {        varpl[i][(int)age] =0.;
         cutv(strd,strc,strb,'*');      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         if (strcmp(strc,"age")==0) {      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           cptcovprod--;      for(i=1;i<=nlstate;i++)
           cutv(strb,stre,strd,'V');        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           Tvar[i]=atoi(stre);  
           cptcovage++;      fprintf(ficresvpl,"%.0f ",age );
             Tage[cptcovage]=i;      for(i=1; i<=nlstate;i++)
             /*printf("stre=%s ", stre);*/        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         }      fprintf(ficresvpl,"\n");
         else if (strcmp(strd,"age")==0) {      free_vector(gp,1,nlstate);
           cptcovprod--;      free_vector(gm,1,nlstate);
           cutv(strb,stre,strc,'V');      free_matrix(gradg,1,npar,1,nlstate);
           Tvar[i]=atoi(stre);      free_matrix(trgradg,1,nlstate,1,npar);
           cptcovage++;    } /* End age */
           Tage[cptcovage]=i;  
         }    free_vector(xp,1,npar);
         else {    free_matrix(doldm,1,nlstate,1,npar);
           cutv(strb,stre,strc,'V');    free_matrix(dnewm,1,nlstate,1,nlstate);
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');  }
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);  /************ Variance of one-step probabilities  ******************/
           Tvard[k1][2]=atoi(stre);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           Tvar[cptcovn+k2]=Tvard[k1][1];  {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int i, j=0,  i1, k1, l1, t, tj;
           for (k=1; k<=lastobs;k++)    int k2, l2, j1,  z1;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int k=0,l, cptcode;
           k1++;    int first=1, first1;
           k2=k2+2;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         }    double **dnewm,**doldm;
       }    double *xp;
       else {    double *gp, *gm;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double **gradg, **trgradg;
        /*  scanf("%d",i);*/    double **mu;
       cutv(strd,strc,strb,'V');    double age,agelim, cov[NCOVMAX];
       Tvar[i]=atoi(strc);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       }    int theta;
       strcpy(modelsav,stra);      char fileresprob[FILENAMELENGTH];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    char fileresprobcov[FILENAMELENGTH];
         scanf("%d",i);*/    char fileresprobcor[FILENAMELENGTH];
     }  
 }    double ***varpij;
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    strcpy(fileresprob,"prob"); 
   printf("cptcovprod=%d ", cptcovprod);    strcat(fileresprob,fileres);
   scanf("%d ",i);*/    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     fclose(fic);      printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     /*  if(mle==1){*/    }
     if (weightopt != 1) { /* Maximisation without weights*/    strcpy(fileresprobcov,"probcov"); 
       for(i=1;i<=n;i++) weight[i]=1.0;    strcat(fileresprobcov,fileres);
     }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     /*-calculation of age at interview from date of interview and age at death -*/      printf("Problem with resultfile: %s\n", fileresprobcov);
     agev=matrix(1,maxwav,1,imx);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
    for (i=1; i<=imx; i++)    strcpy(fileresprobcor,"probcor"); 
      for(m=2; (m<= maxwav); m++)    strcat(fileresprobcor,fileres);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
          anint[m][i]=9999;      printf("Problem with resultfile: %s\n", fileresprobcor);
          s[m][i]=-1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
        }    }
        printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       for(m=1; (m<= maxwav); m++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         if(s[m][i] >0){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           if (s[m][i] == nlstate+1) {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
             if(agedc[i]>0)    
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
               agev[m][i]=agedc[i];    fprintf(ficresprob,"# Age");
             else {    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
               if (andc[i]!=9999){    fprintf(ficresprobcov,"# Age");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
               agev[m][i]=-1;    fprintf(ficresprobcov,"# Age");
               }  
             }  
           }    for(i=1; i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */      for(j=1; j<=(nlstate+ndeath);j++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
             if(mint[m][i]==99 || anint[m][i]==9999)        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               agev[m][i]=1;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             else if(agev[m][i] <agemin){      }  
               agemin=agev[m][i];    fprintf(ficresprob,"\n");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    fprintf(ficresprobcov,"\n");
             }    fprintf(ficresprobcor,"\n");
             else if(agev[m][i] >agemax){    xp=vector(1,npar);
               agemax=agev[m][i];    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
             /*agev[m][i]=anint[m][i]-annais[i];*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
             /*   agev[m][i] = age[i]+2*m;*/    first=1;
           }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           else { /* =9 */      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
             agev[m][i]=1;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
             s[m][i]=-1;      exit(0);
           }    }
         }    else{
         else /*= 0 Unknown */      fprintf(ficgp,"\n# Routine varprob");
           agev[m][i]=1;    }
       }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
          printf("Problem with html file: %s\n", optionfilehtm);
     }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     for (i=1; i<=imx; i++)  {      exit(0);
       for(m=1; (m<= maxwav); m++){    }
         if (s[m][i] > (nlstate+ndeath)) {    else{
           printf("Error: Wrong value in nlstate or ndeath\n");        fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           goto end;      fprintf(fichtm,"\n");
         }  
       }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     }      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(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");
 printf("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);    cov[1]=1;
     free_vector(annais,1,n);    tj=cptcoveff;
     free_matrix(mint,1,maxwav,1,n);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     free_matrix(anint,1,maxwav,1,n);    j1=0;
     free_vector(moisdc,1,n);    for(t=1; t<=tj;t++){
     free_vector(andc,1,n);      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
            
     wav=ivector(1,imx);        if  (cptcovn>0) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficresprob, "\n#********** Variable "); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprob, "**********\n#");
     /* Concatenates waves */          fprintf(ficresprobcov, "\n#********** Variable "); 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#");
           
       Tcode=ivector(1,100);          fprintf(ficgp, "\n#********** Variable "); 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       ncodemax[1]=1;          fprintf(ficgp, "**********\n#");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          
                
    codtab=imatrix(1,100,1,10);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    h=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    m=pow(2,cptcoveff);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
            
    for(k=1;k<=cptcoveff; k++){          fprintf(ficresprobcor, "\n#********** Variable ");    
      for(i=1; i <=(m/pow(2,k));i++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        for(j=1; j <= ncodemax[k]; j++){          fprintf(ficgp, "**********\n#");    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        }
            h++;        
            if (h>m) h=1;codtab[h][k]=j;        for (age=bage; age<=fage; age ++){ 
          }          cov[2]=age;
        }          for (k=1; k<=cptcovn;k++) {
      }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
    }          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
    /*for(i=1; i <=m ;i++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      for(k=1; k <=cptcovn; k++){          
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
      }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      printf("\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
    }          gm=vector(1,(nlstate)*(nlstate+ndeath));
    scanf("%d",i);*/      
              for(theta=1; theta <=npar; theta++){
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(i=1; i<=npar; i++)
        and prints on file fileres'p'. */              xp[i] = x[i] + (i==theta ?delti[theta]:0);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1; i<= (nlstate); i++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for(j=1; j<=(nlstate+ndeath);j++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                k=k+1;
                      gp[k]=pmmij[i][j];
     /* 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) */            
             for(i=1; i<=npar; i++)
     if(mle==1){              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                k=0;
     /*--------- results files --------------*/            for(i=1; i<=(nlstate); i++){
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);              for(j=1; j<=(nlstate+ndeath);j++){
                    k=k+1;
    jk=1;                gm[k]=pmmij[i][j];
    fprintf(ficres,"# Parameters\n");              }
    printf("# Parameters\n");            }
    for(i=1,jk=1; i <=nlstate; i++){       
      for(k=1; k <=(nlstate+ndeath); k++){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
        if (k != i)              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
          {          }
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            for(j=1; j <=ncovmodel; j++){            for(theta=1; theta <=npar; theta++)
              printf("%f ",p[jk]);              trgradg[j][theta]=gradg[theta][j];
              fprintf(ficres,"%f ",p[jk]);          
              jk++;          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);
            printf("\n");          
            fprintf(ficres,"\n");          pmij(pmmij,cov,ncovmodel,x,nlstate);
          }          
      }          k=0;
    }          for(i=1; i<=(nlstate); i++){
  if(mle==1){            for(j=1; j<=(nlstate+ndeath);j++){
     /* Computing hessian and covariance matrix */              k=k+1;
     ftolhess=ftol; /* Usually correct */              mu[k][(int) age]=pmmij[i][j];
     hesscov(matcov, p, npar, delti, ftolhess, func);            }
  }          }
     fprintf(ficres,"# Scales\n");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     printf("# Scales\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
      for(i=1,jk=1; i <=nlstate; i++){              varpij[i][j][(int)age] = doldm[i][j];
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {          /*printf("\n%d ",(int)age);
           fprintf(ficres,"%1d%1d",i,j);       for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           printf("%1d%1d",i,j);         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           for(k=1; k<=ncovmodel;k++){         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             printf(" %.5e",delti[jk]);       }*/
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;          fprintf(ficresprob,"\n%d ",(int)age);
           }          fprintf(ficresprobcov,"\n%d ",(int)age);
           printf("\n");          fprintf(ficresprobcor,"\n%d ",(int)age);
           fprintf(ficres,"\n");  
         }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     k=1;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     fprintf(ficres,"# Covariance\n");          }
     printf("# Covariance\n");          i=0;
     for(i=1;i<=npar;i++){          for (k=1; k<=(nlstate);k++){
       /*  if (k>nlstate) k=1;            for (l=1; l<=(nlstate+ndeath);l++){ 
       i1=(i-1)/(ncovmodel*nlstate)+1;              i=i++;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       printf("%s%d%d",alph[k],i1,tab[i]);*/              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       fprintf(ficres,"%3d",i);              for (j=1; j<=i;j++){
       printf("%3d",i);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       for(j=1; j<=i;j++){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         fprintf(ficres," %.5e",matcov[i][j]);              }
         printf(" %.5e",matcov[i][j]);            }
       }          }/* end of loop for state */
       fprintf(ficres,"\n");        } /* end of loop for age */
       printf("\n");  
       k++;        /* Confidence intervalle of pij  */
     }        /*
            fprintf(ficgp,"\nset noparametric;unset label");
     while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       ungetc(c,ficpar);        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fgets(line, MAXLINE, ficpar);        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);
       puts(line);        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       fputs(line,ficparo);        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     }        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     ungetc(c,ficpar);        */
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
            first1=1;
     if (fage <= 2) {        for (k2=1; k2<=(nlstate);k2++){
       bage = agemin;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       fage = agemax;            if(l2==k2) continue;
     }            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                    if(i<=j) continue;
 /*------------ gnuplot -------------*/                for (age=bage; age<=fage; age ++){ 
 chdir(pathcd);                  if ((int)age %5==0){
   if((ficgp=fopen("graph.plt","w"))==NULL) {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("Problem with file graph.gp");goto end;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
 #ifdef windows                    mu1=mu[i][(int) age]/stepm*YEARM ;
   fprintf(ficgp,"cd \"%s\" \n",pathc);                    mu2=mu[j][(int) age]/stepm*YEARM;
 #endif                    c12=cv12/sqrt(v1*v2);
 m=pow(2,cptcoveff);                    /* Computing eigen value of matrix of covariance */
                      lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  /* 1eme*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   for (cpt=1; cpt<= nlstate ; cpt ++) {                    /* Eigen vectors */
    for (k1=1; k1<= m ; k1 ++) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
 #ifdef windows                    v21=(lc1-v1)/cv12*v11;
     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);                    v12=-v21;
 #endif                    v22=v11;
 #ifdef unix                    tnalp=v21/v11;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                    if(first1==1){
 #endif                      first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
 for (i=1; i<= nlstate ; i ++) {                    }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                    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);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                    /*printf(fignu*/
 }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     for (i=1; i<= nlstate ; i ++) {                    if(first==1){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                      first=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                      fprintf(ficgp,"\nset parametric;unset label");
 }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
      for (i=1; i<= nlstate ; i ++) {                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
 }                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 #ifdef unix                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 fprintf(ficgp,"\nset ter gif small size 400,300");                      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",\
 #endif                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
    }                    }else{
   }                      first=0;
   /*2 eme*/                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   for (k1=1; k1<= m ; k1 ++) {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                  mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     for (i=1; i<= nlstate+1 ; i ++) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       k=2*i;                    }/* if first */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                  } /* age mod 5 */
       for (j=1; j<= nlstate+1 ; j ++) {                } /* end loop age */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                first=1;
 }                } /*l12 */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            } /* k12 */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          } /*l1 */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        }/* k1 */
       for (j=1; j<= nlstate+1 ; j ++) {      } /* loop covariates */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         else fprintf(ficgp," \%%*lf (\%%*lf)");      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 }        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficgp,"\" t\"\" w l 0,");      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       for (j=1; j<= nlstate+1 ; j ++) {      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(xp,1,npar);
 }      fclose(ficresprob);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fclose(ficresprobcov);
       else fprintf(ficgp,"\" t\"\" w l 0,");    fclose(ficresprobcor);
     }    fclose(ficgp);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    fclose(fichtm);
   }  }
    
   /*3eme*/  
   /******************* Printing html file ***********/
   for (k1=1; k1<= m ; k1 ++) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     for (cpt=1; cpt<= nlstate ; cpt ++) {                    int lastpass, int stepm, int weightopt, char model[],\
       k=2+nlstate*(cpt-1);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       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);                    int popforecast, int estepm ,\
       for (i=1; i< nlstate ; i ++) {                    double jprev1, double mprev1,double anprev1, \
         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);                    double jprev2, double mprev2,double anprev2){
       }    int jj1, k1, i1, cpt;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /*char optionfilehtm[FILENAMELENGTH];*/
     }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   }      printf("Problem with %s \n",optionfilehtm), exit(0);
        fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   /* CV preval stat */    }
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
       k=3;   - 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
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       for (i=1; i< nlstate ; i ++)   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
         fprintf(ficgp,"+$%d",k+i+1);   - Life expectancies by age and initial health status (estepm=%2d months): 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
          jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;   m=cptcoveff;
         fprintf(ficgp,"+$%d",l+i+1);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);     jj1=0;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   for(k1=1; k1<=m;k1++){
     }     for(i1=1; i1<=ncodemax[k1];i1++){
   }         jj1++;
        if (cptcovn > 0) {
   /* proba elementaires */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    for(i=1,jk=1; i <=nlstate; i++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
     for(k=1; k <=(nlstate+ndeath); k++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       if (k != i) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1; j <=ncovmodel; j++){       }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/       /* Pij */
           /*fprintf(ficgp,"%s",alph[1]);*/       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>
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           jk++;       /* Quasi-incidences */
           fprintf(ficgp,"\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
         }  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
       }         /* Stable prevalence in each health state */
     }         for(cpt=1; cpt<nlstate;cpt++){
     }           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   for(jk=1; jk <=m; jk++) {         }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);       for(cpt=1; cpt<=nlstate;cpt++) {
    i=1;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
    for(k2=1; k2<=nlstate; k2++) {  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
      k3=i;       }
      for(k=1; k<=(nlstate+ndeath); k++) {       fprintf(fichtm,"\n<br>- Total life expectancy by age and
        if (k != k2){  health expectancies in states (1) and (2): e%s%d.png<br>
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
 ij=1;     } /* end i1 */
         for(j=3; j <=ncovmodel; j++) {   }/* End k1 */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {   fprintf(fichtm,"</ul>");
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  
           }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
           else   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   - 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
           fprintf(ficgp,")/(1");   - 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 
         for(k1=1; k1 <=nlstate; k1++){     - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);   - 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);
 ij=1;  
           for(j=3; j <=ncovmodel; j++){   if(popforecast==1) fprintf(fichtm,"\n
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
             ij++;          <br>",fileres,fileres,fileres,fileres);
           }   else 
           else     fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           }  
           fprintf(ficgp,")");   m=cptcoveff;
         }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");   jj1=0;
         i=i+ncovmodel;   for(k1=1; k1<=m;k1++){
        }     for(i1=1; i1<=ncodemax[k1];i1++){
      }       jj1++;
    }       if (cptcovn > 0) {
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   }         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fclose(ficgp);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           }
 chdir(path);       for(cpt=1; cpt<=nlstate;cpt++) {
             fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     free_ivector(wav,1,imx);  interval) in state (%d): v%s%d%d.png <br>
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         }
     free_ivector(num,1,n);     } /* end i1 */
     free_vector(agedc,1,n);   }/* End k1 */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/   fprintf(fichtm,"</ul>");
     fclose(ficparo);  fclose(fichtm);
     fclose(ficres);  }
     /*  }*/  
      /******************* Gnuplot file **************/
    /*________fin mle=1_________*/  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;
     /* No more information from the sample is required now */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   /* Reads comments: lines beginning with '#' */      printf("Problem with file %s",optionfilegnuplot);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /*#ifdef windows */
     fputs(line,ficparo);      fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   ungetc(c,ficpar);  m=pow(2,cptcoveff);
      
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);   /* 1eme*/
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     for (k1=1; k1<= m ; k1 ++) {
 /*--------- index.htm --------*/       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");       for (i=1; i<= nlstate ; i ++) {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("Problem with %s \n",optionfilehtm);goto end;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">       for (i=1; i<= nlstate ; i ++) {
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 Total number of observations=%d <br>         else fprintf(ficgp," \%%*lf (\%%*lf)");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>       } 
 <hr  size=\"2\" color=\"#EC5E5E\">       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
 <li>Outputs files<br><br>\n       for (i=1; i<= nlstate ; i ++) {
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>         else fprintf(ficgp," \%%*lf (\%%*lf)");
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>       }  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>     }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    /*2 eme*/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    for (k1=1; k1<= m ; k1 ++) { 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
 <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(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
  fprintf(fichtm," <li>Graphs</li><p>");      for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
  m=cptcoveff;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  j1=0;          else fprintf(ficgp," \%%*lf (\%%*lf)");
  for(k1=1; k1<=m;k1++){        }   
    for(i1=1; i1<=ncodemax[k1];i1++){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        j1++;        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
        if (cptcovn > 0) {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for (j=1; j<= nlstate+1 ; j ++) {
          for (cpt=1; cpt<=cptcoveff;cpt++)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }   
        }        fprintf(ficgp,"\" t\"\" w l 0,");
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            for (j=1; j<= nlstate+1 ; j ++) {
        for(cpt=1; cpt<nlstate;cpt++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          else fprintf(ficgp," \%%*lf (\%%*lf)");
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        }   
        }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     for(cpt=1; cpt<=nlstate;cpt++) {        else fprintf(ficgp,"\" t\"\" w l 0,");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      }
 interval) in state (%d): v%s%d%d.gif <br>    }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      
      }    /*3eme*/
      for(cpt=1; cpt<=nlstate;cpt++) {    
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    for (k1=1; k1<= m ; k1 ++) { 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      for (cpt=1; cpt<= nlstate ; cpt ++) {
      }        k=2+nlstate*(2*cpt-2);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 health expectancies in states (1) and (2): e%s%d.gif<br>        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 fprintf(fichtm,"\n</body>");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
  }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 fclose(fichtm);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   /*--------------- Prevalence limit --------------*/          
          */
   strcpy(filerespl,"pl");        for (i=1; i< nlstate ; i ++) {
   strcat(filerespl,fileres);          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);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        } 
   }      }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    }
   fprintf(ficrespl,"#Prevalence limit\n");    
   fprintf(ficrespl,"#Age ");    /* CV preval stat */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for (k1=1; k1<= m ; k1 ++) { 
   fprintf(ficrespl,"\n");      for (cpt=1; cpt<nlstate ; cpt ++) {
          k=3;
   prlim=matrix(1,nlstate,1,nlstate);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i< nlstate ; i ++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"+$%d",k+i+1);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   k=0;        
   agebase=agemin;        l=3+(nlstate+ndeath)*cpt;
   agelim=agemax;        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   ftolpl=1.e-10;        for (i=1; i< nlstate ; i ++) {
   i1=cptcoveff;          l=3+(nlstate+ndeath)*cpt;
   if (cptcovn < 1){i1=1;}          fprintf(ficgp,"+$%d",l+i+1);
         }
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     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#******");    /* proba elementaires */
         for(j=1;j<=cptcoveff;j++)    for(i=1,jk=1; i <=nlstate; i++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(k=1; k <=(nlstate+ndeath); k++){
         fprintf(ficrespl,"******\n");        if (k != i) {
                  for(j=1; j <=ncovmodel; j++){
         for (age=agebase; age<=agelim; age++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            jk++; 
           fprintf(ficrespl,"%.0f",age );            fprintf(ficgp,"\n");
           for(i=1; i<=nlstate;i++)          }
           fprintf(ficrespl," %.5f", prlim[i][i]);        }
           fprintf(ficrespl,"\n");      }
         }     }
       }  
     }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   fclose(ficrespl);       for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   /*------------- h Pij x at various ages ------------*/         if (ng==2)
             fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);         else
   if((ficrespij=fopen(filerespij,"w"))==NULL) {           fprintf(ficgp,"\nset title \"Probability\"\n");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   }         i=1;
   printf("Computing pij: result on file '%s' \n", filerespij);         for(k2=1; k2<=nlstate; k2++) {
             k3=i;
   stepsize=(int) (stepm+YEARM-1)/YEARM;           for(k=1; k<=(nlstate+ndeath); k++) {
   /*if (stepm<=24) stepsize=2;*/             if (k != k2){
                if(ng==2)
   agelim=AGESUP;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   hstepm=stepsize*YEARM; /* Every year of age */               else
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   k=0;               for(j=3; j <=ncovmodel; j++) {
   for(cptcov=1;cptcov<=i1;cptcov++){                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       k=k+1;                   ij++;
         fprintf(ficrespij,"\n#****** ");                 }
         for(j=1;j<=cptcoveff;j++)                 else
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         fprintf(ficrespij,"******\n");               }
                       fprintf(ficgp,")/(1");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */               
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */               for(k1=1; k1 <=nlstate; k1++){   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                 ij=1;
           oldm=oldms;savm=savms;                 for(j=3; j <=ncovmodel; j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                     if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           fprintf(ficrespij,"# Age");                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           for(i=1; i<=nlstate;i++)                     ij++;
             for(j=1; j<=nlstate+ndeath;j++)                   }
               fprintf(ficrespij," %1d-%1d",i,j);                   else
           fprintf(ficrespij,"\n");                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
           for (h=0; h<=nhstepm; h++){                 }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                 fprintf(ficgp,")");
             for(i=1; i<=nlstate;i++)               }
               for(j=1; j<=nlstate+ndeath;j++)               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
             fprintf(ficrespij,"\n");               i=i+ncovmodel;
           }             }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           } /* end k */
           fprintf(ficrespij,"\n");         } /* end k2 */
         }       } /* end jk */
     }     } /* end ng */
   }     fclose(ficgp); 
   }  /* end gnuplot */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
   
   fclose(ficrespij);  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   /*---------- Forecasting ------------------*/  
     int i, cpt, cptcod;
   strcpy(fileresf,"f");    int mobilavrange, mob;
   strcat(fileresf,fileres);    double age;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      if(mobilav==1) mobilavrange=5; /* default */
   }      else mobilavrange=mobilav;
   printf("Computing forecasting: result on file '%s' \n", fileresf);      for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);          for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
  free_matrix(agev,1,maxwav,1,imx);      /* We keep the original values on the extreme ages bage, fage and for 
   /* Mobile average */         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
   if (mobilav==1) {        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (i=1; i<=nlstate;i++){
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)            for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       for (i=1; i<=nlstate;i++)              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                for (cpt=1;cpt<=(mob-1)/2;cpt++){
           mobaverage[(int)agedeb][i][cptcod]=0.;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                      mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     for (agedeb=bage+4; agedeb<=fage; agedeb++){                }
       for (i=1; i<=nlstate;i++){              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }/* end age */
           }      }/* end mob */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    }else return -1;
         }    return 0;
       }  }/* End movingaverage */
     }    
   }  
   /************** Forecasting ******************/
   stepsize=(int) (stepm+YEARM-1)/YEARM;  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
   if (stepm<=12) stepsize=1;    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   agelim=AGESUP;    int *popage;
   hstepm=stepsize*YEARM; /* Every year of age */    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    double *popeffectif,*popcount;
     double ***p3mat;
    k=0;    char fileresf[FILENAMELENGTH];
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   agelim=AGESUP;
       k=k+1;  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
       fprintf(ficresf,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++) {    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   
       }   
       fprintf(ficresf,"******\n");    strcpy(fileresf,"f"); 
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");    strcat(fileresf,fileres);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       for (agedeb=fage; agedeb>=bage; agedeb--){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);    }
        if (mobilav==1) {    printf("Computing forecasting: result on file '%s' \n", fileresf);
         for(j=1; j<=nlstate;j++)    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
           fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);  
         }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         else {  
           for(j=1; j<=nlstate;j++)    if (mobilav!=0) {
           fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }        if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       for (cpt=1; cpt<=nforecast;cpt++)        }
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    }
          
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    stepsize=(int) (stepm+YEARM-1)/YEARM;
         nhstepm = nhstepm/hstepm;    if (stepm<=12) stepsize=1;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    
     agelim=AGESUP;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
         oldm=oldms;savm=savms;    hstepm=1;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      hstepm=hstepm/stepm; 
                    yp1=modf(dateintmean,&yp);
         for (h=0; h<=nhstepm; h++){    anprojmean=yp;
            yp2=modf((yp1*12),&yp);
          if (h*hstepm/YEARM*stepm==cpt)    mprojmean=yp;
             fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);    yp1=modf((yp2*30.5),&yp);
              jprojmean=yp;
              if(jprojmean==0) jprojmean=1;
           for(j=1; j<=nlstate+ndeath;j++) {    if(mprojmean==0) jprojmean=1;
             kk1=0.;    
             for(i=1; i<=nlstate;i++) {            fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
               if (mobilav==1)    
               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    for(cptcov=1;cptcov<=i2;cptcov++){
               else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
             }            k=k+1;
           if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);        fprintf(ficresf,"\n#******");
           }        for(j=1;j<=cptcoveff;j++) {
         }          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
       }        fprintf(ficresf,"******\n");
     }        fprintf(ficresf,"# StartingAge FinalAge");
   }        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        
   free_imatrix(s,1,maxwav+1,1,n);        
   free_vector(weight,1,n);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
   fclose(ficresf);          fprintf(ficresf,"\n");
   /*---------- Health expectancies and variances ------------*/          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   
   strcpy(filerest,"t");          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   strcat(filerest,fileres);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   if((ficrest=fopen(filerest,"w"))==NULL) {            nhstepm = nhstepm/hstepm; 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
   strcpy(filerese,"e");            for (h=0; h<=nhstepm; h++){
   strcat(filerese,fileres);              if (h==(int) (calagedate+YEARM*cpt)) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              } 
   }              for(j=1; j<=nlstate+ndeath;j++) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
  strcpy(fileresv,"v");                  if (mobilav==1) 
   strcat(fileresv,fileres);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                  else {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   }                  }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                  
                 }
   k=0;                if (h==(int)(calagedate+12*cpt)){
   for(cptcov=1;cptcov<=i1;cptcov++){                  fprintf(ficresf," %.3f", kk1);
     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]]);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficrest,"******\n");          }
         }
       fprintf(ficreseij,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);         
       fprintf(ficreseij,"******\n");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
       fprintf(ficresvij,"\n#****** ");    fclose(ficresf);
       for(j=1;j<=cptcoveff;j++)  }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /************** Forecasting ******************/
       fprintf(ficresvij,"******\n");  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){
     
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       oldm=oldms;savm=savms;    int *popage;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *popeffectif,*popcount;
       oldm=oldms;savm=savms;    double ***p3mat,***tabpop,***tabpopprev;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    char filerespop[FILENAMELENGTH];
        
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficrest,"\n");    agelim=AGESUP;
            calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
       hf=1;    
       if (stepm >= YEARM) hf=stepm/YEARM;    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
       epj=vector(1,nlstate+1);    
       for(age=bage; age <=fage ;age++){    
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    strcpy(filerespop,"pop"); 
         if (popbased==1) {    strcat(filerespop,fileres);
           for(i=1; i<=nlstate;i++)    if((ficrespop=fopen(filerespop,"w"))==NULL) {
             prlim[i][i]=probs[(int)age][i][k];      printf("Problem with forecast resultfile: %s\n", filerespop);
         }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
            }
         fprintf(ficrest," %.0f",age);    printf("Computing forecasting: result on file '%s' \n", filerespop);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           }  
           epj[nlstate+1] +=epj[j];    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(i=1, vepp=0.;i <=nlstate;i++)      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           for(j=1;j <=nlstate;j++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             vepp += vareij[i][j][(int)age];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      }
         for(j=1;j <=nlstate;j++){    }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }    stepsize=(int) (stepm+YEARM-1)/YEARM;
         fprintf(ficrest,"\n");    if (stepm<=12) stepsize=1;
       }    
     }    agelim=AGESUP;
   }    
            hstepm=1;
            hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
  fclose(ficreseij);      if((ficpop=fopen(popfile,"r"))==NULL) {
  fclose(ficresvij);        printf("Problem with population file : %s\n",popfile);exit(0);
   fclose(ficrest);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
   fclose(ficpar);      } 
   free_vector(epj,1,nlstate+1);      popage=ivector(0,AGESUP);
   /*  scanf("%d ",i); */      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
   /*------- Variance limit prevalence------*/        
       i=1;   
 strcpy(fileresvpl,"vpl");      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   strcat(fileresvpl,fileres);     
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      imx=i;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     exit(0);    }
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    for(cptcov=1;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
  k=0;        k=k+1;
  for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficrespop,"\n#******");
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1;j<=cptcoveff;j++) {
      k=k+1;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      fprintf(ficresvpl,"\n#****** ");        }
      for(j=1;j<=cptcoveff;j++)        fprintf(ficrespop,"******\n");
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficrespop,"# Age");
      fprintf(ficresvpl,"******\n");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
              if (popforecast==1)  fprintf(ficrespop," [Population]");
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        
      oldm=oldms;savm=savms;        for (cpt=0; cpt<=0;cpt++) { 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
    }          
  }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fclose(ficresvpl);            nhstepm = nhstepm/hstepm; 
             
   /*---------- End : free ----------------*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for (h=0; h<=nhstepm; h++){
                if (h==(int) (calagedate+YEARM*cpt)) {
                  fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);              } 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);              for(j=1; j<=nlstate+ndeath;j++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                kk1=0.;kk2=0;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                for(i=1; i<=nlstate;i++) {              
                    if (mobilav==1) 
   free_matrix(matcov,1,npar,1,npar);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   free_vector(delti,1,npar);                  else {
                      kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                  }
                 }
   printf("End of Imach\n");                if (h==(int)(calagedate+12*cpt)){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                      /*fprintf(ficrespop," %.3f", kk1);
   /* 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);*/                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   /*printf("Total time was %d uSec.\n", total_usecs);*/                }
   /*------ End -----------*/              }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
  end:                  for(j=1; j<=nlstate;j++){
 #ifdef windows                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
  chdir(pathcd);                  }
 #endif                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
                }
  system("..\\gp37mgw\\wgnuplot graph.plt");  
               if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
 #ifdef windows                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   while (z[0] != 'q') {            }
     chdir(pathcd);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          }
     scanf("%s",z);        }
     if (z[0] == 'c') system("./imach");   
     else if (z[0] == 'e') {    /******/
       chdir(path);  
       system(optionfilehtm);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     }          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     else if (z[0] == 'q') exit(0);          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 #endif            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) (calagedate+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)(calagedate+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 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,**adl,*tab; 
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
     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; 
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn;
     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;
   
     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);
       adl=imatrix(1,maxwav+1,1,n);    
       tab=ivector(1,NCOVMAX);
       ncodemax=ivector(1,8);
   
       i=1;
       while (fgets(line, MAXLINE, fic) != NULL)    {
         if ((i >= firstobs) && (i <=lastobs)) {
           
           for (j=maxwav;j>=1;j--){
             cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
             strcpy(line,stra);
             cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
             cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           }
           
           cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
           cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
           cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
           for (j=ncovcol;j>=1;j--){
             cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           } 
           num[i]=atol(stra);
           
           /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
             printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
           i=i+1;
         }
       } 
       /* printf("ii=%d", ij);
          scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+');
       j1=nbocc(model,'*');
       cptcovn=j+1;
       cptcovprod=j1;
       
       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;
       }
       
       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 analyze 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 */
     
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
     scanf("%d ",i);*/
       fclose(fic);
   
       /*  if(mle==1){*/
       if (weightopt != 1) { /* Maximisation without weights*/
         for(i=1;i<=n;i++) weight[i]=1.0;
       }
       /*-calculation of age at interview from date of interview and age at death -*/
       agev=matrix(1,maxwav,1,imx);
   
       for (i=1; i<=imx; i++) {
         for(m=2; (m<= maxwav); m++) {
          if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
            anint[m][i]=9999;
            s[m][i]=-1;
          }
        if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
         }
       }
   
       for (i=1; i<=imx; i++)  {
         agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
         for(m=1; (m<= maxwav); m++){
           if(s[m][i] >0){
             if (s[m][i] >= nlstate+1) {
               if(agedc[i]>0)
                 if(moisdc[i]!=99 && andc[i]!=9999)
                   agev[m][i]=agedc[i];
               /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
                 if (andc[i]!=9999){
                 printf("Warning negative age at death: %d line:%d\n",num[i],i);
                 fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                 agev[m][i]=-1;
                 }
               }
             }
             else if(s[m][i] !=9){ /* Should no more exist */
               agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
               if(mint[m][i]==99 || anint[m][i]==9999)
                 agev[m][i]=1;
               else if(agev[m][i] <agemin){ 
                 agemin=agev[m][i];
                 /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
               }
               else if(agev[m][i] >agemax){
                 agemax=agev[m][i];
                /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
               }
               /*agev[m][i]=anint[m][i]-annais[i];*/
               /*   agev[m][i] = age[i]+2*m;*/
             }
             else { /* =9 */
               agev[m][i]=1;
               s[m][i]=-1;
             }
           }
           else /*= 0 Unknown */
             agev[m][i]=1;
         }
       
       }
       for (i=1; i<=imx; i++)  {
         for(m=1; (m<= maxwav); m++){
           if (s[m][i] > (nlstate+ndeath)) {
             printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);   
             fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);   
             goto end;
           }
         }
       }
   
   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
       free_vector(severity,1,maxwav);
       free_imatrix(outcome,1,maxwav+1,1,n);
       free_vector(moisnais,1,n);
       free_vector(annais,1,n);
       /* free_matrix(mint,1,maxwav,1,n);
          free_matrix(anint,1,maxwav,1,n);*/
       free_vector(moisdc,1,n);
       free_vector(andc,1,n);
   
      
       wav=ivector(1,imx);
       dh=imatrix(1,lastpass-firstpass+1,1,imx);
       mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
       /* Concatenates waves */
         concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
   
         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);
      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){
       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");
          }
        }
      }
      
      k=1;
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      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;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);
      
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        puts(line);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
    
   
      dateprev1=anprev1+mprev1/12.+jprev1/365.;
      dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
   fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,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,Tvar,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(mw,1,lastpass-firstpass+1,1,imx);   
    free_ivector(num,1,n);
    free_vector(agedc,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);
     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 */
     k=0;
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1;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(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*/
   
     k=0;
     for(cptcov=1;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Age");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
              for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
                }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     calagedate=-1;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     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);
       }
     }
   
     k=0;
     for(cptcov=1;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_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
       free_vector(weight,1,n);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     free_vector(epj,1,nlstate+1);
     
     /*------- 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);
   
     k=0;
     for(cptcov=1;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);
       }
    }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     
     free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     
     
     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(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);
   
     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.1.15  
changed lines
  Added in v.1.54


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