Diff for /imach/src/imach.c between versions 1.6 and 1.56

version 1.6, 2001/05/02 17:47:10 version 1.56, 2002/07/24 17:28:25
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 windows
 #define MAXN 20000  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define YEARM 12. /* Number of months per year */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define AGESUP 130  
 #define AGEBASE 40  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int nvar;  #define NINTERVMAX 8
 static int cptcov;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int cptcovn, cptcovage=0;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int npar=NPARMAX;  #define NCOVMAX 8 /* Maximum number of covariates */
 int nlstate=2; /* Number of live states */  #define MAXN 20000
 int ndeath=1; /* Number of dead states */  #define YEARM 12. /* Number of months per year */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #define AGESUP 130
   #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 mle, weightopt;  #define ODIRSEPARATOR '/'
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #else
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define DIRSEPARATOR '/'
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define ODIRSEPARATOR '\\'
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #endif
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;  char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
 FILE *ficreseij;  int erreur; /* Error number */
   char filerese[FILENAMELENGTH];  int nvar;
  FILE  *ficresvij;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   char fileresv[FILENAMELENGTH];  int npar=NPARMAX;
  FILE  *ficresvpl;  int nlstate=2; /* Number of live states */
   char fileresvpl[FILENAMELENGTH];  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define NR_END 1  int popbased=0;
 #define FREE_ARG char*  
 #define FTOL 1.0e-10  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 #define NRANSI  int jmin, jmax; /* min, max spacing between 2 waves */
 #define ITMAX 200  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define TOL 2.0e-4  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double jmean; /* Mean space between 2 waves */
 #define CGOLD 0.3819660  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define ZEPS 1.0e-10  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 #define GOLD 1.618034  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define GLIMIT 100.0  FILE *ficresprobmorprev;
 #define TINY 1.0e-20  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 static double maxarg1,maxarg2;  char filerese[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvij;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char fileresvpl[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 static double sqrarg;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 int imx;  char filerest[FILENAMELENGTH];
 int stepm;  char fileregp[FILENAMELENGTH];
 /* Stepm, step in month: minimum step interpolation*/  char popfile[FILENAMELENGTH];
   
 int m,nb;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define NR_END 1
 double **pmmij;  #define FREE_ARG char*
   #define FTOL 1.0e-10
 double *weight;  
 int **s; /* Status */  #define NRANSI 
 double *agedc, **covar, idx;  #define ITMAX 200 
 int **nbcode, *Tcode, *Tvar, **codtab;  
   #define TOL 2.0e-4 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 static  int split( char *path, char *dirc, char *name )  
 {  #define GOLD 1.618034 
    char *s;                             /* pointer */  #define GLIMIT 100.0 
    int  l1, l2;                         /* length counters */  #define TINY 1.0e-20 
   
    l1 = strlen( path );                 /* length of path */  static double maxarg1,maxarg2;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    s = strrchr( path, '\\' );           /* find last / */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    if ( s == NULL ) {                   /* no directory, so use current */    
 #if     defined(__bsd__)                /* get current working directory */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       extern char       *getwd( );  #define rint(a) floor(a+0.5)
   
       if ( getwd( dirc ) == NULL ) {  static double sqrarg;
 #else  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       extern char       *getcwd( );  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int imx; 
 #endif  int stepm;
          return( GLOCK_ERROR_GETCWD );  /* Stepm, step in month: minimum step interpolation*/
       }  
       strcpy( name, path );             /* we've got it */  int estepm;
    } else {                             /* strip direcotry from path */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  int m,nb;
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       strcpy( name, s );                /* save file name */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double **pmmij, ***probs;
       dirc[l1-l2] = 0;                  /* add zero */  double dateintmean=0;
    }  
    l1 = strlen( dirc );                 /* length of directory */  double *weight;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int **s; /* Status */
    return( 0 );                         /* we're done */  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /******************************************/  double ftolhess; /* Tolerance for computing hessian */
   
 void replace(char *s, char*t)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int i;  {
   int lg=20;     char *s;                             /* pointer */
   i=0;     int  l1, l2;                         /* length counters */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {     l1 = strlen( path );                 /* length of path */
     (s[i] = t[i]);     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (t[i]== '\\') s[i]='/';     s= strrchr( path, DIRSEPARATOR );            /* find last / */
   }     if ( s == NULL ) {                   /* no directory, so use current */
 }       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 int nbocc(char *s, char occ)  #if     defined(__bsd__)                /* get current working directory */
 {        extern char       *getwd( );
   int i,j=0;  
   int lg=20;        if ( getwd( dirc ) == NULL ) {
   i=0;  #else
   lg=strlen(s);        extern char       *getcwd( );
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   }  #endif
   return j;           return( GLOCK_ERROR_GETCWD );
 }        }
         strcpy( name, path );             /* we've got it */
 void cutv(char *u,char *v, char*t, char occ)     } else {                             /* strip direcotry from path */
 {        s++;                              /* after this, the filename */
   int i,lg,j,p=0;        l2 = strlen( s );                 /* length of filename */
   i=0;        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(j=0; j<=strlen(t)-1; j++) {        strcpy( name, s );                /* save file name */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;        strncpy( dirc, path, l1 - l2 );   /* now the directory */
   }        dirc[l1-l2] = 0;                  /* add zero */
      }
   lg=strlen(t);     l1 = strlen( dirc );                 /* length of directory */
   for(j=0; j<p; j++) {  #ifdef windows
     (u[j] = t[j]);     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      u[p]='\0';     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
    for(j=0; j<= lg; j++) {     s = strrchr( name, '.' );            /* find last / */
     if (j>=(p+1))(v[j-p-1] = t[j]);     s++;
   }     strcpy(ext,s);                       /* save extension */
 }     l1= strlen( name);
      l2= strlen( s)+1;
 /********************** nrerror ********************/     strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
 void nrerror(char error_text[])     return( 0 );                         /* we're done */
 {  }
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  /******************************************/
 }  
 /*********************** vector *******************/  void replace(char *s, char*t)
 double *vector(int nl, int nh)  {
 {    int i;
   double *v;    int lg=20;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    i=0;
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ivector *******************************/    int lg=20;
 int *ivector(long nl,long nh)    i=0;
 {    lg=strlen(s);
   int *v;    for(i=0; i<= lg; i++) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    if  (s[i] == occ ) j++;
   if (!v) nrerror("allocation failure in ivector");    }
   return v-nl+NR_END;    return j;
 }  }
   
 /******************free ivector **************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_ivector(int *v, long nl, long nh)  {
 {    /* cuts string t into u and v where u is ended by char occ excluding it
   free((FREE_ARG)(v+nl-NR_END));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************* imatrix *******************************/    i=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<=strlen(t)-1; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* allocate pointers to rows */      (u[j] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");       u[p]='\0';
   m += NR_END;  
   m -= nrl;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
      }
   /* allocate rows and set pointers to them */  }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
    {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   /* return pointer to array of pointers to rows */    exit(1);
   return m;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /****************** free_imatrix *************************/  {
 void free_imatrix(m,nrl,nrh,ncl,nch)    double *v;
       int **m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       long nch,ncl,nrh,nrl;    if (!v) nrerror("allocation failure in vector");
      /* free an int matrix allocated by imatrix() */    return v-nl+NR_END;
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /******************* matrix *******************************/    free((FREE_ARG)(v+nl-NR_END));
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /************************ivector *******************************/
   double **m;  int *ivector(long nl,long nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m -= nrl;    return v-nl+NR_END;
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_ivector(int *v, long nl, long nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /*************************free matrix ************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  { 
 {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int **m; 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /******************* ma3x *******************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m += NR_END; 
 {    m -= nrl; 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    
   double ***m;    
     /* allocate rows and set pointers to them */ 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m += NR_END;    m[nrl] += NR_END; 
   m -= nrl;    m[nrl] -= ncl; 
     
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    /* return pointer to array of pointers to rows */ 
   m[nrl] -= ncl;    return m; 
   } 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /****************** free_imatrix *************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_imatrix(m,nrl,nrh,ncl,nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");        int **m;
   m[nrl][ncl] += NR_END;        long nch,ncl,nrh,nrl; 
   m[nrl][ncl] -= nll;       /* free an int matrix allocated by imatrix() */ 
   for (j=ncl+1; j<=nch; j++)  { 
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   for (i=nrl+1; i<=nrh; i++) {  } 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /******************* matrix *******************************/
       m[i][j]=m[i][j-1]+nlay;  double **matrix(long nrl, long nrh, long ncl, long nch)
   }  {
   return m;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /*************************free ma3x ************************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m -= nrl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /***************** f1dim *************************/    m[nrl] -= ncl;
 extern int ncom;  
 extern double *pcom,*xicom;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 extern double (*nrfunc)(double []);    return m;
    }
 double f1dim(double x)  
 {  /*************************free matrix ************************/
   int j;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double f;  {
   double *xt;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   xt=vector(1,ncom);  }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /******************* ma3x *******************************/
   free_vector(xt,1,ncom);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   return f;  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int iter;    m += NR_END;
   double a,b,d,etemp;    m -= nrl;
   double fu,fv,fw,fx;  
   double ftemp;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double e=0.0;    m[nrl] += NR_END;
      m[nrl] -= ncl;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (iter=1;iter<=ITMAX;iter++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     xm=0.5*(a+b);    m[nrl][ncl] += NR_END;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m[nrl][ncl] -= nll;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (j=ncl+1; j<=nch; j++) 
     printf(".");fflush(stdout);      m[nrl][j]=m[nrl][j-1]+nlay;
 #ifdef DEBUG    
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    for (i=nrl+1; i<=nrh; i++) {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #endif      for (j=ncl+1; j<=nch; j++) 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){        m[i][j]=m[i][j-1]+nlay;
       *xmin=x;    }
       return fx;    return m;
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /*************************free ma3x ************************/
       r=(x-w)*(fx-fv);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       q=2.0*(q-r);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if (q > 0.0) p = -p;    free((FREE_ARG)(m+nrl-NR_END));
       q=fabs(q);  }
       etemp=e;  
       e=d;  /***************** f1dim *************************/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  extern int ncom; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern double *pcom,*xicom;
       else {  extern double (*nrfunc)(double []); 
         d=p/q;   
         u=x+d;  double f1dim(double x) 
         if (u-a < tol2 || b-u < tol2)  { 
           d=SIGN(tol1,xm-x);    int j; 
       }    double f;
     } else {    double *xt; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));   
     }    xt=vector(1,ncom); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     fu=(*f)(u);    f=(*nrfunc)(xt); 
     if (fu <= fx) {    free_vector(xt,1,ncom); 
       if (u >= x) a=x; else b=x;    return f; 
       SHFT(v,w,x,u)  } 
         SHFT(fv,fw,fx,fu)  
         } else {  /*****************brent *************************/
           if (u < x) a=u; else b=u;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
           if (fu <= fw || w == x) {  { 
             v=w;    int iter; 
             w=u;    double a,b,d,etemp;
             fv=fw;    double fu,fv,fw,fx;
             fw=fu;    double ftemp;
           } else if (fu <= fv || v == x || v == w) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             v=u;    double e=0.0; 
             fv=fu;   
           }    a=(ax < cx ? ax : cx); 
         }    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
   nrerror("Too many iterations in brent");    fw=fv=fx=(*f)(x); 
   *xmin=x;    for (iter=1;iter<=ITMAX;iter++) { 
   return fx;      xm=0.5*(a+b); 
 }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 /****************** mnbrak ***********************/      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #ifdef DEBUG
             double (*func)(double))      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double ulim,u,r,q, dum;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double fu;  #endif
        if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   *fa=(*func)(*ax);        *xmin=x; 
   *fb=(*func)(*bx);        return fx; 
   if (*fb > *fa) {      } 
     SHFT(dum,*ax,*bx,dum)      ftemp=fu;
       SHFT(dum,*fb,*fa,dum)      if (fabs(e) > tol1) { 
       }        r=(x-w)*(fx-fv); 
   *cx=(*bx)+GOLD*(*bx-*ax);        q=(x-v)*(fx-fw); 
   *fc=(*func)(*cx);        p=(x-v)*q-(x-w)*r; 
   while (*fb > *fc) {        q=2.0*(q-r); 
     r=(*bx-*ax)*(*fb-*fc);        if (q > 0.0) p = -p; 
     q=(*bx-*cx)*(*fb-*fa);        q=fabs(q); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        etemp=e; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        e=d; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     if ((*bx-u)*(u-*cx) > 0.0) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       fu=(*func)(u);        else { 
     } else if ((*cx-u)*(u-ulim) > 0.0) {          d=p/q; 
       fu=(*func)(u);          u=x+d; 
       if (fu < *fc) {          if (u-a < tol2 || b-u < tol2) 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))            d=SIGN(tol1,xm-x); 
           SHFT(*fb,*fc,fu,(*func)(u))        } 
           }      } else { 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       u=ulim;      } 
       fu=(*func)(u);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     } else {      fu=(*f)(u); 
       u=(*cx)+GOLD*(*cx-*bx);      if (fu <= fx) { 
       fu=(*func)(u);        if (u >= x) a=x; else b=x; 
     }        SHFT(v,w,x,u) 
     SHFT(*ax,*bx,*cx,u)          SHFT(fv,fw,fx,fu) 
       SHFT(*fa,*fb,*fc,fu)          } else { 
       }            if (u < x) a=u; else b=u; 
 }            if (fu <= fw || w == x) { 
               v=w; 
 /*************** linmin ************************/              w=u; 
               fv=fw; 
 int ncom;              fw=fu; 
 double *pcom,*xicom;            } else if (fu <= fv || v == x || v == w) { 
 double (*nrfunc)(double []);              v=u; 
                fv=fu; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))            } 
 {          } 
   double brent(double ax, double bx, double cx,    } 
                double (*f)(double), double tol, double *xmin);    nrerror("Too many iterations in brent"); 
   double f1dim(double x);    *xmin=x; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    return fx; 
               double *fc, double (*func)(double));  } 
   int j;  
   double xx,xmin,bx,ax;  /****************** mnbrak ***********************/
   double fx,fb,fa;  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   ncom=n;              double (*func)(double)) 
   pcom=vector(1,n);  { 
   xicom=vector(1,n);    double ulim,u,r,q, dum;
   nrfunc=func;    double fu; 
   for (j=1;j<=n;j++) {   
     pcom[j]=p[j];    *fa=(*func)(*ax); 
     xicom[j]=xi[j];    *fb=(*func)(*bx); 
   }    if (*fb > *fa) { 
   ax=0.0;      SHFT(dum,*ax,*bx,dum) 
   xx=1.0;        SHFT(dum,*fb,*fa,dum) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *cx=(*bx)+GOLD*(*bx-*ax); 
 #ifdef DEBUG    *fc=(*func)(*cx); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    while (*fb > *fc) { 
 #endif      r=(*bx-*ax)*(*fb-*fc); 
   for (j=1;j<=n;j++) {      q=(*bx-*cx)*(*fb-*fa); 
     xi[j] *= xmin;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     p[j] += xi[j];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   free_vector(xicom,1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
   free_vector(pcom,1,n);        fu=(*func)(u); 
 }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
 /*************** powell ************************/        if (fu < *fc) { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             double (*func)(double []))            SHFT(*fb,*fc,fu,(*func)(u)) 
 {            } 
   void linmin(double p[], double xi[], int n, double *fret,      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
               double (*func)(double []));        u=ulim; 
   int i,ibig,j;        fu=(*func)(u); 
   double del,t,*pt,*ptt,*xit;      } else { 
   double fp,fptt;        u=(*cx)+GOLD*(*cx-*bx); 
   double *xits;        fu=(*func)(u); 
   pt=vector(1,n);      } 
   ptt=vector(1,n);      SHFT(*ax,*bx,*cx,u) 
   xit=vector(1,n);        SHFT(*fa,*fb,*fc,fu) 
   xits=vector(1,n);        } 
   *fret=(*func)(p);  } 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /*************** linmin ************************/
     fp=(*fret);  
     ibig=0;  int ncom; 
     del=0.0;  double *pcom,*xicom;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double (*nrfunc)(double []); 
     for (i=1;i<=n;i++)   
       printf(" %d %.12f",i, p[i]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("\n");  { 
     for (i=1;i<=n;i++) {    double brent(double ax, double bx, double cx, 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];                 double (*f)(double), double tol, double *xmin); 
       fptt=(*fret);    double f1dim(double x); 
 #ifdef DEBUG    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("fret=%lf \n",*fret);                double *fc, double (*func)(double)); 
 #endif    int j; 
       printf("%d",i);fflush(stdout);    double xx,xmin,bx,ax; 
       linmin(p,xit,n,fret,func);    double fx,fb,fa;
       if (fabs(fptt-(*fret)) > del) {   
         del=fabs(fptt-(*fret));    ncom=n; 
         ibig=i;    pcom=vector(1,n); 
       }    xicom=vector(1,n); 
 #ifdef DEBUG    nrfunc=func; 
       printf("%d %.12e",i,(*fret));    for (j=1;j<=n;j++) { 
       for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      xicom[j]=xi[j]; 
         printf(" x(%d)=%.12e",j,xit[j]);    } 
       }    ax=0.0; 
       for(j=1;j<=n;j++)    xx=1.0; 
         printf(" p=%.12e",p[j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       printf("\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 #endif  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #ifdef DEBUG  #endif
       int k[2],l;    for (j=1;j<=n;j++) { 
       k[0]=1;      xi[j] *= xmin; 
       k[1]=-1;      p[j] += xi[j]; 
       printf("Max: %.12e",(*func)(p));    } 
       for (j=1;j<=n;j++)    free_vector(xicom,1,n); 
         printf(" %.12e",p[j]);    free_vector(pcom,1,n); 
       printf("\n");  } 
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /*************** powell ************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);              double (*func)(double [])) 
         }  { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
 #endif    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
     double fp,fptt;
       free_vector(xit,1,n);    double *xits;
       free_vector(xits,1,n);    pt=vector(1,n); 
       free_vector(ptt,1,n);    ptt=vector(1,n); 
       free_vector(pt,1,n);    xit=vector(1,n); 
       return;    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (j=1;j<=n;j++) {    for (*iter=1;;++(*iter)) { 
       ptt[j]=2.0*p[j]-pt[j];      fp=(*fret); 
       xit[j]=p[j]-pt[j];      ibig=0; 
       pt[j]=p[j];      del=0.0; 
     }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     fptt=(*func)(ptt);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     if (fptt < fp) {      for (i=1;i<=n;i++) 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf(" %d %.12f",i, p[i]);
       if (t < 0.0) {      fprintf(ficlog," %d %.12f",i, p[i]);
         linmin(p,xit,n,fret,func);      printf("\n");
         for (j=1;j<=n;j++) {      fprintf(ficlog,"\n");
           xi[j][ibig]=xi[j][n];      for (i=1;i<=n;i++) { 
           xi[j][n]=xit[j];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        printf("fret=%lf \n",*fret);
         for(j=1;j<=n;j++)        fprintf(ficlog,"fret=%lf \n",*fret);
           printf(" %.12e",xit[j]);  #endif
         printf("\n");        printf("%d",i);fflush(stdout);
 #endif        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
 }          ibig=i; 
         } 
 /**** Prevalence limit ****************/  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
      matrix by transitions matrix until convergence is reached */          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   int i, ii,j,k;        }
   double min, max, maxmin, maxmax,sumnew=0.;        for(j=1;j<=n;j++) {
   double **matprod2();          printf(" p=%.12e",p[j]);
   double **out, cov[NCOVMAX], **pmij();          fprintf(ficlog," p=%.12e",p[j]);
   double **newm;        }
   double agefin, delaymax=50 ; /* Max number of years to converge */        printf("\n");
         fprintf(ficlog,"\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)  #endif
     for (j=1;j<=nlstate+ndeath;j++){      } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
         int k[2],l;
    cov[1]=1.;        k[0]=1;
          k[1]=-1;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf("Max: %.12e",(*func)(p));
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fprintf(ficlog,"Max: %.12e",(*func)(p));
     newm=savm;        for (j=1;j<=n;j++) {
     /* Covariates have to be included here again */          printf(" %.12e",p[j]);
      cov[2]=agefin;          fprintf(ficlog," %.12e",p[j]);
          }
       for (k=1; k<=cptcovn;k++) {        printf("\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/          for (j=1;j<=n;j++) {
       }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for (k=1; k<=cptcovage;k++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     savm=oldm;        }
     oldm=newm;  #endif
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  
       min=1.;        free_vector(xit,1,n); 
       max=0.;        free_vector(xits,1,n); 
       for(i=1; i<=nlstate; i++) {        free_vector(ptt,1,n); 
         sumnew=0;        free_vector(pt,1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        return; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      } 
         max=FMAX(max,prlim[i][j]);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         min=FMIN(min,prlim[i][j]);      for (j=1;j<=n;j++) { 
       }        ptt[j]=2.0*p[j]-pt[j]; 
       maxmin=max-min;        xit[j]=p[j]-pt[j]; 
       maxmax=FMAX(maxmax,maxmin);        pt[j]=p[j]; 
     }      } 
     if(maxmax < ftolpl){      fptt=(*func)(ptt); 
       return prlim;      if (fptt < fp) { 
     }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   }        if (t < 0.0) { 
 }          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
 /*************** transition probabilities **********/            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          }
 {  #ifdef DEBUG
   double s1, s2;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /*double t34;*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int i,j,j1, nc, ii, jj;          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     for(i=1; i<= nlstate; i++){            fprintf(ficlog," %.12e",xit[j]);
     for(j=1; j<i;j++){          }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          printf("\n");
         /*s2 += param[i][j][nc]*cov[nc];*/          fprintf(ficlog,"\n");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #endif
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        }
       }      } 
       ps[i][j]=s2;    } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  } 
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /**** Prevalence limit (stable prevalence)  ****************/
       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];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       ps[i][j]=s2;       matrix by transitions matrix until convergence is reached */
     }  
   }    int i, ii,j,k;
   for(i=1; i<= nlstate; i++){    double min, max, maxmin, maxmax,sumnew=0.;
      s1=0;    double **matprod2();
     for(j=1; j<i; j++)    double **out, cov[NCOVMAX], **pmij();
       s1+=exp(ps[i][j]);    double **newm;
     for(j=i+1; j<=nlstate+ndeath; j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<i; j++)      for (j=1;j<=nlstate+ndeath;j++){
       ps[i][j]= exp(ps[i][j])*ps[i][i];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=i+1; j<=nlstate+ndeath; j++)      }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */     cov[1]=1.;
   } /* end i */   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(jj=1; jj<= nlstate+ndeath; jj++){      newm=savm;
       ps[ii][jj]=0;      /* Covariates have to be included here again */
       ps[ii][ii]=1;       cov[2]=agefin;
     }    
   }        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          /*      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(jj=1; jj<= nlstate+ndeath; jj++){        }
      printf("%lf ",ps[ii][jj]);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    }        for (k=1; k<=cptcovprod;k++)
     printf("\n ");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
     printf("\n ");printf("%lf ",cov[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]);*/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   goto end;*/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     return ps;  
 }      savm=oldm;
       oldm=newm;
 /**************** Product of 2 matrices ******************/      maxmax=0.;
       for(j=1;j<=nlstate;j++){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        min=1.;
 {        max=0.;
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        for(i=1; i<=nlstate; i++) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          sumnew=0;
   /* in, b, out are matrice of pointers which should have been initialized          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      before: only the contents of out is modified. The function returns          prlim[i][j]= newm[i][j]/(1-sumnew);
      a pointer to pointers identical to out */          max=FMAX(max,prlim[i][j]);
   long i, j, k;          min=FMIN(min,prlim[i][j]);
   for(i=nrl; i<= nrh; i++)        }
     for(k=ncolol; k<=ncoloh; k++)        maxmin=max-min;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        maxmax=FMAX(maxmax,maxmin);
         out[i][k] +=in[i][j]*b[j][k];      }
       if(maxmax < ftolpl){
   return out;        return prlim;
 }      }
     }
   }
 /************* Higher Matrix Product ***************/  
   /*************** transition probabilities ***************/ 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  {
      duration (i.e. until    double s1, s2;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /*double t34;*/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    int i,j,j1, nc, ii, jj;
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be      for(i=1; i<= nlstate; i++){
      included manually here.      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];
   int i, j, d, h, k;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   double **out, cov[NCOVMAX];        }
   double **newm;        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   /* Hstepm could be zero and should return the unit matrix */      }
   for (i=1;i<=nlstate+ndeath;i++)      for(j=i+1; j<=nlstate+ndeath;j++){
     for (j=1;j<=nlstate+ndeath;j++){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       oldm[i][j]=(i==j ? 1.0 : 0.0);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       po[i][j][0]=(i==j ? 1.0 : 0.0);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     }        }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        ps[i][j]=s2;
   for(h=1; h <=nhstepm; h++){      }
     for(d=1; d <=hstepm; d++){    }
       newm=savm;      /*ps[3][2]=1;*/
       /* Covariates have to be included here again */  
       cov[1]=1.;    for(i=1; i<= nlstate; i++){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;       s1=0;
       if (cptcovn>0){      for(j=1; j<i; j++)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        s1+=exp(ps[i][j]);
     }      for(j=i+1; j<=nlstate+ndeath; j++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        s1+=exp(ps[i][j]);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      ps[i][i]=1./(s1+1.);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      for(j=1; j<i; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        ps[i][j]= exp(ps[i][j])*ps[i][i];
       savm=oldm;      for(j=i+1; j<=nlstate+ndeath; j++)
       oldm=newm;        ps[i][j]= exp(ps[i][j])*ps[i][i];
     }      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for(i=1; i<=nlstate+ndeath; i++)    } /* end i */
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      for(jj=1; jj<= nlstate+ndeath; jj++){
          */        ps[ii][jj]=0;
       }        ps[ii][ii]=1;
   } /* end h */      }
   return po;    }
 }  
   
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 /*************** log-likelihood *************/      for(jj=1; jj<= nlstate+ndeath; jj++){
 double func( double *x)       printf("%lf ",ps[ii][jj]);
 {     }
   int i, ii, j, k, mi, d, kk;      printf("\n ");
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      }
   double **out;      printf("\n ");printf("%lf ",cov[2]);*/
   double sw; /* Sum of weights */  /*
   double lli; /* Individual log likelihood */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   long ipmx;    goto end;*/
   /*extern weight */      return ps;
   /* We are differentiating ll according to initial status */  }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /**************** Product of 2 matrices ******************/
 printf(" %d\n",s[4][i]);  
   */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   cov[1]=1.;  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for(k=1; k<=nlstate; k++) ll[k]=0.;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    /* in, b, out are matrice of pointers which should have been initialized 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];       before: only the contents of out is modified. The function returns
        for(mi=1; mi<= wav[i]-1; mi++){       a pointer to pointers identical to out */
       for (ii=1;ii<=nlstate+ndeath;ii++)    long i, j, k;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for(i=nrl; i<= nrh; i++)
             for(d=0; d<dh[mi][i]; d++){      for(k=ncolol; k<=ncoloh; k++)
               newm=savm;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          out[i][k] +=in[i][j]*b[j][k];
               for (kk=1; kk<=cptcovage;kk++) {  
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    return out;
                  /*printf("%d %d",kk,Tage[kk]);*/  }
               }  
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/  
               /*cov[3]=pow(cov[2],2)/1000.;*/  /************* Higher Matrix Product ***************/
   
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  {
           savm=oldm;    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
           oldm=newm;       duration (i.e. until
        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 
       } /* end mult */       (typically every 2 years instead of every month which is too big).
           Model is determined by parameters x and covariates have to be 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       included manually here. 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;       */
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int i, j, d, h, k;
     } /* end of wave */    double **out, cov[NCOVMAX];
   } /* end of individual */    double **newm;
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* Hstepm could be zero and should return the unit matrix */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for (i=1;i<=nlstate+ndeath;i++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for (j=1;j<=nlstate+ndeath;j++){
   return -l;        oldm[i][j]=(i==j ? 1.0 : 0.0);
 }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /*********** Maximum Likelihood Estimation ***************/    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        newm=savm;
 {        /* Covariates have to be included here again */
   int i,j, iter;        cov[1]=1.;
   double **xi,*delti;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double fret;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   xi=matrix(1,npar,1,npar);        for (k=1; k<=cptcovage;k++)
   for (i=1;i<=npar;i++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovprod;k++)
       xi[i][j]=(i==j ? 1.0 : 0.0);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 }        savm=oldm;
         oldm=newm;
 /**** Computes Hessian and covariance matrix ***/      }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(i=1; i<=nlstate+ndeath; i++)
 {        for(j=1;j<=nlstate+ndeath;j++) {
   double  **a,**y,*x,pd;          po[i][j][h]=newm[i][j];
   double **hess;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   int i, j,jk;           */
   int *indx;        }
     } /* end h */
   double hessii(double p[], double delta, int theta, double delti[]);    return po;
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /*************** log-likelihood *************/
   double func( double *x)
   hess=matrix(1,npar,1,npar);  {
     int i, ii, j, k, mi, d, kk;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (i=1;i<=npar;i++){    double **out;
     printf("%d",i);fflush(stdout);    double sw; /* Sum of weights */
     hess[i][i]=hessii(p,ftolhess,i,delti);    double lli; /* Individual log likelihood */
     /*printf(" %f ",p[i]);*/    long ipmx;
   }    /*extern weight */
     /* We are differentiating ll according to initial status */
   for (i=1;i<=npar;i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for (j=1;j<=npar;j++)  {    /*for(i=1;i<imx;i++) 
       if (j>i) {      printf(" %d\n",s[4][i]);
         printf(".%d%d",i,j);fflush(stdout);    */
         hess[i][j]=hessij(p,delti,i,j);    cov[1]=1.;
         hess[j][i]=hess[i][j];  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("\n");      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          for(d=0; d<dh[mi][i]; d++){
   a=matrix(1,npar,1,npar);          newm=savm;
   y=matrix(1,npar,1,npar);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   x=vector(1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   indx=ivector(1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (i=1;i<=npar;i++)          }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          
   ludcmp(a,npar,indx,&pd);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (j=1;j<=npar;j++) {          savm=oldm;
     for (i=1;i<=npar;i++) x[i]=0;          oldm=newm;
     x[j]=1;          
     lubksb(a,npar,indx,x);          
     for (i=1;i<=npar;i++){        } /* end mult */
       matcov[i][j]=x[i];        
     }        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   }        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
         ipmx +=1;
   printf("\n#Hessian matrix#\n");        sw += weight[i];
   for (i=1;i<=npar;i++) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (j=1;j<=npar;j++) {      } /* end of wave */
       printf("%.3e ",hess[i][j]);    } /* end of individual */
     }  
     printf("\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /* Recompute Inverse */    return -l;
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  
   /*********** Maximum Likelihood Estimation ***************/
   /*  printf("\n#Hessian matrix recomputed#\n");  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   for (j=1;j<=npar;j++) {  {
     for (i=1;i<=npar;i++) x[i]=0;    int i,j, iter;
     x[j]=1;    double **xi,*delti;
     lubksb(a,npar,indx,x);    double fret;
     for (i=1;i<=npar;i++){    xi=matrix(1,npar,1,npar);
       y[i][j]=x[i];    for (i=1;i<=npar;i++)
       printf("%.3e ",y[i][j]);      for (j=1;j<=npar;j++)
     }        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   }    powell(p,xi,npar,ftol,&iter,&fret,func);
   */  
      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   free_matrix(a,1,npar,1,npar);    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_matrix(y,1,npar,1,npar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  }
   free_matrix(hess,1,npar,1,npar);  
   /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 }  {
     double  **a,**y,*x,pd;
 /*************** hessian matrix ****************/    double **hess;
 double hessii( double x[], double delta, int theta, double delti[])    int i, j,jk;
 {    int *indx;
   int i;  
   int l=1, lmax=20;    double hessii(double p[], double delta, int theta, double delti[]);
   double k1,k2;    double hessij(double p[], double delti[], int i, int j);
   double p2[NPARMAX+1];    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double res;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;    hess=matrix(1,npar,1,npar);
   int k=0,kmax=10;  
   double l1;    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   fx=func(x);    for (i=1;i<=npar;i++){
   for (i=1;i<=npar;i++) p2[i]=x[i];      printf("%d",i);fflush(stdout);
   for(l=0 ; l <=lmax; l++){      fprintf(ficlog,"%d",i);fflush(ficlog);
     l1=pow(10,l);      hess[i][i]=hessii(p,ftolhess,i,delti);
     delts=delt;      /*printf(" %f ",p[i]);*/
     for(k=1 ; k <kmax; k=k+1){      /*printf(" %lf ",hess[i][i]);*/
       delt = delta*(l1*k);    }
       p2[theta]=x[theta] +delt;    
       k1=func(p2)-fx;    for (i=1;i<=npar;i++) {
       p2[theta]=x[theta]-delt;      for (j=1;j<=npar;j++)  {
       k2=func(p2)-fx;        if (j>i) { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */          printf(".%d%d",i,j);fflush(stdout);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                hess[i][j]=hessij(p,delti,i,j);
 #ifdef DEBUG          hess[j][i]=hess[i][j];    
       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);          /*printf(" %lf ",hess[i][j]);*/
 #endif        }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    }
         k=kmax;    printf("\n");
       }    fprintf(ficlog,"\n");
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    
         delts=delt;    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
   }    indx=ivector(1,npar);
   delti[theta]=delts;    for (i=1;i<=npar;i++)
   return res;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      ludcmp(a,npar,indx,&pd);
 }  
     for (j=1;j<=npar;j++) {
 double hessij( double x[], double delti[], int thetai,int thetaj)      for (i=1;i<=npar;i++) x[i]=0;
 {      x[j]=1;
   int i;      lubksb(a,npar,indx,x);
   int l=1, l1, lmax=20;      for (i=1;i<=npar;i++){ 
   double k1,k2,k3,k4,res,fx;        matcov[i][j]=x[i];
   double p2[NPARMAX+1];      }
   int k;    }
   
   fx=func(x);    printf("\n#Hessian matrix#\n");
   for (k=1; k<=2; k++) {    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) p2[i]=x[i];    for (i=1;i<=npar;i++) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;      for (j=1;j<=npar;j++) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        printf("%.3e ",hess[i][j]);
     k1=func(p2)-fx;        fprintf(ficlog,"%.3e ",hess[i][j]);
        }
     p2[thetai]=x[thetai]+delti[thetai]/k;      printf("\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      fprintf(ficlog,"\n");
     k2=func(p2)-fx;    }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    /* Recompute Inverse */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for (i=1;i<=npar;i++)
     k3=func(p2)-fx;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ludcmp(a,npar,indx,&pd);
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    /*  printf("\n#Hessian matrix recomputed#\n");
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    for (j=1;j<=npar;j++) {
 #ifdef DEBUG      for (i=1;i<=npar;i++) x[i]=0;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      x[j]=1;
 #endif      lubksb(a,npar,indx,x);
   }      for (i=1;i<=npar;i++){ 
   return res;        y[i][j]=x[i];
 }        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
 /************** Inverse of matrix **************/      }
 void ludcmp(double **a, int n, int *indx, double *d)      printf("\n");
 {      fprintf(ficlog,"\n");
   int i,imax,j,k;    }
   double big,dum,sum,temp;    */
   double *vv;  
      free_matrix(a,1,npar,1,npar);
   vv=vector(1,n);    free_matrix(y,1,npar,1,npar);
   *d=1.0;    free_vector(x,1,npar);
   for (i=1;i<=n;i++) {    free_ivector(indx,1,npar);
     big=0.0;    free_matrix(hess,1,npar,1,npar);
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  }
     vv[i]=1.0/big;  
   }  /*************** hessian matrix ****************/
   for (j=1;j<=n;j++) {  double hessii( double x[], double delta, int theta, double delti[])
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    int i;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    int l=1, lmax=20;
       a[i][j]=sum;    double k1,k2;
     }    double p2[NPARMAX+1];
     big=0.0;    double res;
     for (i=j;i<=n;i++) {    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       sum=a[i][j];    double fx;
       for (k=1;k<j;k++)    int k=0,kmax=10;
         sum -= a[i][k]*a[k][j];    double l1;
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {    fx=func(x);
         big=dum;    for (i=1;i<=npar;i++) p2[i]=x[i];
         imax=i;    for(l=0 ; l <=lmax; l++){
       }      l1=pow(10,l);
     }      delts=delt;
     if (j != imax) {      for(k=1 ; k <kmax; k=k+1){
       for (k=1;k<=n;k++) {        delt = delta*(l1*k);
         dum=a[imax][k];        p2[theta]=x[theta] +delt;
         a[imax][k]=a[j][k];        k1=func(p2)-fx;
         a[j][k]=dum;        p2[theta]=x[theta]-delt;
       }        k2=func(p2)-fx;
       *d = -(*d);        /*res= (k1-2.0*fx+k2)/delt/delt; */
       vv[imax]=vv[j];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     }        
     indx[j]=imax;  #ifdef DEBUG
     if (a[j][j] == 0.0) a[j][j]=TINY;        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 != n) {        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);
       dum=1.0/(a[j][j]);  #endif
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   }          k=kmax;
   free_vector(vv,1,n);  /* Doesn't work */        }
 ;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 }          k=kmax; l=lmax*10.;
         }
 void lubksb(double **a, int n, int *indx, double b[])        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 {          delts=delt;
   int i,ii=0,ip,j;        }
   double sum;      }
      }
   for (i=1;i<=n;i++) {    delti[theta]=delts;
     ip=indx[i];    return res; 
     sum=b[ip];    
     b[ip]=b[i];  }
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  double hessij( double x[], double delti[], int thetai,int thetaj)
     else if (sum) ii=i;  {
     b[i]=sum;    int i;
   }    int l=1, l1, lmax=20;
   for (i=n;i>=1;i--) {    double k1,k2,k3,k4,res,fx;
     sum=b[i];    double p2[NPARMAX+1];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int k;
     b[i]=sum/a[i][i];  
   }    fx=func(x);
 }    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
 /************ Frequencies ********************/      p2[thetai]=x[thetai]+delti[thetai]/k;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 {  /* Some frequencies */      k1=func(p2)-fx;
      
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double ***freq; /* Frequencies */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double *pp;      k2=func(p2)-fx;
   double pos;    
   FILE *ficresp;      p2[thetai]=x[thetai]-delti[thetai]/k;
   char fileresp[FILENAMELENGTH];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   pp=vector(1,nlstate);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   strcpy(fileresp,"p");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   strcat(fileresp,fileres);      k4=func(p2)-fx;
   if((ficresp=fopen(fileresp,"w"))==NULL) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     printf("Problem with prevalence resultfile: %s\n", fileresp);  #ifdef DEBUG
     exit(0);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  #endif
   j1=0;    }
     return res;
   j=cptcovn;  }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   /************** Inverse of matrix **************/
   for(k1=1; k1<=j;k1++){  void ludcmp(double **a, int n, int *indx, double *d) 
    for(i1=1; i1<=ncodemax[k1];i1++){  { 
        j1++;    int i,imax,j,k; 
     double big,dum,sum,temp; 
         for (i=-1; i<=nlstate+ndeath; i++)      double *vv; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)     
            for(m=agemin; m <= agemax+3; m++)    vv=vector(1,n); 
              freq[i][jk][m]=0;    *d=1.0; 
            for (i=1;i<=n;i++) { 
        for (i=1; i<=imx; i++) {      big=0.0; 
          bool=1;      for (j=1;j<=n;j++) 
          if  (cptcovn>0) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
            for (z1=1; z1<=cptcovn; z1++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;      vv[i]=1.0/big; 
          }    } 
           if (bool==1) {    for (j=1;j<=n;j++) { 
            for(m=firstpass; m<=lastpass-1; m++){      for (i=1;i<j;i++) { 
              if(agev[m][i]==0) agev[m][i]=agemax+1;        sum=a[i][j]; 
              if(agev[m][i]==1) agev[m][i]=agemax+2;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        a[i][j]=sum; 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      } 
            }      big=0.0; 
          }      for (i=j;i<=n;i++) { 
        }        sum=a[i][j]; 
         if  (cptcovn>0) {        for (k=1;k<j;k++) 
          fprintf(ficresp, "\n#Variable");          sum -= a[i][k]*a[k][j]; 
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);        a[i][j]=sum; 
        }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
        fprintf(ficresp, "\n#");          big=dum; 
        for(i=1; i<=nlstate;i++)          imax=i; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        } 
        fprintf(ficresp, "\n");      } 
              if (j != imax) { 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for (k=1;k<=n;k++) { 
     if(i==(int)agemax+3)          dum=a[imax][k]; 
       printf("Total");          a[imax][k]=a[j][k]; 
     else          a[j][k]=dum; 
       printf("Age %d", i);        } 
     for(jk=1; jk <=nlstate ; jk++){        *d = -(*d); 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        vv[imax]=vv[j]; 
         pp[jk] += freq[jk][m][i];      } 
     }      indx[j]=imax; 
     for(jk=1; jk <=nlstate ; jk++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(m=-1, pos=0; m <=0 ; m++)      if (j != n) { 
         pos += freq[jk][m][i];        dum=1.0/(a[j][j]); 
       if(pp[jk]>=1.e-10)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      } 
       else    } 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
     for(jk=1; jk <=nlstate ; jk++){  } 
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];  void lubksb(double **a, int n, int *indx, double b[]) 
     }  { 
     for(jk=1,pos=0; jk <=nlstate ; jk++)    int i,ii=0,ip,j; 
       pos += pp[jk];    double sum; 
     for(jk=1; jk <=nlstate ; jk++){   
       if(pos>=1.e-5)    for (i=1;i<=n;i++) { 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      ip=indx[i]; 
       else      sum=b[ip]; 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      b[ip]=b[i]; 
       if( i <= (int) agemax){      if (ii) 
         if(pos>=1.e-5)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      else if (sum) ii=i; 
       else      b[i]=sum; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    } 
       }    for (i=n;i>=1;i--) { 
     }      sum=b[i]; 
     for(jk=-1; jk <=nlstate+ndeath; jk++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       for(m=-1; m <=nlstate+ndeath; m++)      b[i]=sum/a[i][i]; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    } 
     if(i <= (int) agemax)  } 
       fprintf(ficresp,"\n");  
     printf("\n");  /************ Frequencies ********************/
     }  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
     }  {  /* Some frequencies */
  }    
      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   fclose(ficresp);    int first;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double ***freq; /* Frequencies */
   free_vector(pp,1,nlstate);    double *pp;
     double pos, k2, dateintsum=0,k2cpt=0;
 }  /* End of Freq */    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
 /************* Waves Concatenation ***************/    
     pp=vector(1,nlstate);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 {    strcpy(fileresp,"p");
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    strcat(fileresp,fileres);
      Death is a valid wave (if date is known).    if((ficresp=fopen(fileresp,"w"))==NULL) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      printf("Problem with prevalence resultfile: %s\n", fileresp);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      and mw[mi+1][i]. dh depends on stepm.      exit(0);
      */    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   int i, mi, m;    j1=0;
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    
 float sum=0.;    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for(i=1; i<=imx; i++){  
     mi=0;    first=1;
     m=firstpass;  
     while(s[m][i] <= nlstate){    for(k1=1; k1<=j;k1++){
       if(s[m][i]>=1)      for(i1=1; i1<=ncodemax[k1];i1++){
         mw[++mi][i]=m;        j1++;
       if(m >=lastpass)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         break;          scanf("%d", i);*/
       else        for (i=-1; i<=nlstate+ndeath; i++)  
         m++;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     }/* end while */            for(m=agemin; m <= agemax+3; m++)
     if (s[m][i] > nlstate){              freq[i][jk][m]=0;
       mi++;     /* Death is another wave */        
       /* if(mi==0)  never been interviewed correctly before death */        dateintsum=0;
          /* Only death is a correct wave */        k2cpt=0;
       mw[mi][i]=m;        for (i=1; i<=imx; i++) {
     }          bool=1;
           if  (cptcovn>0) {
     wav[i]=mi;            for (z1=1; z1<=cptcoveff; z1++) 
     if(mi==0)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);                bool=0;
   }          }
           if (bool==1) {
   for(i=1; i<=imx; i++){            for(m=firstpass; m<=lastpass; m++){
     for(mi=1; mi<wav[i];mi++){              k2=anint[m][i]+(mint[m][i]/12.);
       if (stepm <=0)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         dh[mi][i]=1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
       else{                if(agev[m][i]==1) agev[m][i]=agemax+2;
         if (s[mw[mi+1][i]][i] > nlstate) {                if (m<lastpass) {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           if(j=0) j=1;  /* Survives at least one month after exam */                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
         }                }
         else{                
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           k=k+1;                  dateintsum=dateintsum+k2;
           if (j >= jmax) jmax=j;                  k2cpt++;
           else if (j <= jmin)jmin=j;                }
           sum=sum+j;              }
         }            }
         jk= j/stepm;          }
         jl= j -jk*stepm;        }
         ju= j -(jk+1)*stepm;         
         if(jl <= -ju)        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
           dh[mi][i]=jk;  
         else        if  (cptcovn>0) {
           dh[mi][i]=jk+1;          fprintf(ficresp, "\n#********** Variable "); 
         if(dh[mi][i]==0)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           dh[mi][i]=1; /* At least one step */          fprintf(ficresp, "**********\n#");
       }        }
     }        for(i=1; i<=nlstate;i++) 
   }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);        fprintf(ficresp, "\n");
 }        
 /*********** Tricode ****************************/        for(i=(int)agemin; i <= (int)agemax+3; i++){
 void tricode(int *Tvar, int **nbcode, int imx)          if(i==(int)agemax+3){
 {            fprintf(ficlog,"Total");
   int Ndum[80],ij=1, k, j, i, Ntvar[20];          }else{
   int cptcode=0;            if(first==1){
   for (k=0; k<79; k++) Ndum[k]=0;              first=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;              printf("See log file for details...\n");
             }
   for (j=1; j<=cptcovn; j++) {            fprintf(ficlog,"Age %d", i);
     for (i=1; i<=imx; i++) {          }
       ij=(int)(covar[Tvar[j]][i]);          for(jk=1; jk <=nlstate ; jk++){
       Ndum[ij]++;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       if (ij > cptcode) cptcode=ij;              pp[jk] += freq[jk][m][i]; 
     }          }
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/          for(jk=1; jk <=nlstate ; jk++){
     for (i=0; i<=cptcode; i++) {            for(m=-1, pos=0; m <=0 ; m++)
       if(Ndum[i]!=0) ncodemax[j]++;              pos += freq[jk][m][i];
     }            if(pp[jk]>=1.e-10){
                if(first==1){
     ij=1;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for (i=1; i<=ncodemax[j]; i++) {              }
       for (k=0; k<=79; k++) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         if (Ndum[k] != 0) {            }else{
           nbcode[Tvar[j]][ij]=k;              if(first==1)
           ij++;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         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];
           }
 /*********** Health Expectancies ****************/  
           for(jk=1,pos=0; jk <=nlstate ; jk++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            pos += pp[jk];
 {          for(jk=1; jk <=nlstate ; jk++){
   /* Health expectancies */            if(pos>=1.e-5){
   int i, j, nhstepm, hstepm, h;              if(first==1)
   double age, agelim,hf;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double ***p3mat;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
   fprintf(ficreseij,"# Health expectancies\n");              if(first==1)
   fprintf(ficreseij,"# Age");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficreseij," %1d-%1d",i,j);            if( i <= (int) agemax){
   fprintf(ficreseij,"\n");              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
   hstepm=1*YEARM; /*  Every j years of age (in month) */                probs[i][jk][j1]= pp[jk]/pos;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
   agelim=AGESUP;              else
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
     /* nhstepm age range expressed in number of stepm */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          }
     /* Typically if 20 years = 20*12/6=40 stepm */          
     if (stepm >= YEARM) hstepm=1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            for(m=-1; m <=nlstate+ndeath; m++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if(freq[jk][m][i] !=0 ) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              if(first==1)
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
           if(i <= (int) agemax)
     for(i=1; i<=nlstate;i++)            fprintf(ficresp,"\n");
       for(j=1; j<=nlstate;j++)          if(first==1)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            printf("Others in log...\n");
           eij[i][j][(int)age] +=p3mat[i][j][h];          fprintf(ficlog,"\n");
         }        }
          }
     hf=1;    }
     if (stepm >= YEARM) hf=stepm/YEARM;    dateintmean=dateintsum/k2cpt; 
     fprintf(ficreseij,"%.0f",age );   
     for(i=1; i<=nlstate;i++)    fclose(ficresp);
       for(j=1; j<=nlstate;j++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    free_vector(pp,1,nlstate);
       }    
     fprintf(ficreseij,"\n");    /* End of Freq */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
   }  
 }  /************ Prevalence ********************/
   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)
 /************ Variance ******************/  {  /* Some frequencies */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)   
 {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   /* Variance of health expectancies */    double ***freq; /* Frequencies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double *pp;
   double **newm;    double pos, k2;
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;    pp=vector(1,nlstate);
   int k, cptcode;    
    double *xp;    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   double **gp, **gm;    j1=0;
   double ***gradg, ***trgradg;    
   double ***p3mat;    j=cptcoveff;
   double age,agelim;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int theta;    
     for(k1=1; k1<=j;k1++){
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficresvij,"# Age");        j1++;
   for(i=1; i<=nlstate;i++)        
     for(j=1; j<=nlstate;j++)        for (i=-1; i<=nlstate+ndeath; i++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   fprintf(ficresvij,"\n");            for(m=agemin; m <= agemax+3; m++)
               freq[i][jk][m]=0;
   xp=vector(1,npar);       
   dnewm=matrix(1,nlstate,1,npar);        for (i=1; i<=imx; i++) {
   doldm=matrix(1,nlstate,1,nlstate);          bool=1;
            if  (cptcovn>0) {
   hstepm=1*YEARM; /* Every year of age */            for (z1=1; z1<=cptcoveff; z1++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   agelim = AGESUP;                bool=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          } 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          if (bool==1) { 
     if (stepm >= YEARM) hstepm=1;            for(m=firstpass; m<=lastpass; m++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              k2=anint[m][i]+(mint[m][i]/12.);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                if(agev[m][i]==0) agev[m][i]=agemax+1;
     gp=matrix(0,nhstepm,1,nlstate);                if(agev[m][i]==1) agev[m][i]=agemax+2;
     gm=matrix(0,nhstepm,1,nlstate);                if (m<lastpass) {
                   if (calagedate>0) 
     for(theta=1; theta <=npar; theta++){                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */                  else
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                    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]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              }
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
         }          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                  pp[jk] += freq[jk][m][i]; 
       for(i=1; i<=npar; i++) /* Computes gradient */          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(jk=1; jk <=nlstate ; jk++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for(m=-1, pos=0; m <=0 ; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              pos += freq[jk][m][i];
       for(j=1; j<= nlstate; j++){          }
         for(h=0; h<=nhstepm; h++){          
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         }              pp[jk] += freq[jk][m][i];
       }          }
       for(j=1; j<= nlstate; j++)          
         for(h=0; h<=nhstepm; h++){          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          
         }          for(jk=1; jk <=nlstate ; jk++){    
     } /* End theta */            if( i <= (int) agemax){
               if(pos>=1.e-5){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);                probs[i][jk][j1]= pp[jk]/pos;
               }
     for(h=0; h<=nhstepm; h++)            }
       for(j=1; j<=nlstate;j++)          }/* end jk */
         for(theta=1; theta <=npar; theta++)        }/* end i */
           trgradg[h][j][theta]=gradg[h][theta][j];      } /* end i1 */
     } /* end k1 */
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    
         vareij[i][j][(int)age] =0.;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     for(h=0;h<=nhstepm;h++){    free_vector(pp,1,nlstate);
       for(k=0;k<=nhstepm;k++){    
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  }  /* End of Freq */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)  /************* Waves Concatenation ***************/
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       }  {
     }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     h=1;       Death is a valid wave (if date is known).
     if (stepm >= YEARM) h=stepm/YEARM;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     fprintf(ficresvij,"%.0f ",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(ficresvij," %.4f", h*vareij[i][j][(int)age]);  
       }    int i, mi, m;
     fprintf(ficresvij,"\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     free_matrix(gp,0,nhstepm,1,nlstate);       double sum=0., jmean=0.;*/
     free_matrix(gm,0,nhstepm,1,nlstate);    int first;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int j, k=0,jk, ju, jl;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double sum=0.;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    first=0;
   } /* End age */    jmin=1e+5;
      jmax=-1;
   free_vector(xp,1,npar);    jmean=0.;
   free_matrix(doldm,1,nlstate,1,npar);    for(i=1; i<=imx; i++){
   free_matrix(dnewm,1,nlstate,1,nlstate);      mi=0;
       m=firstpass;
 }      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
 /************ Variance of prevlim ******************/          mw[++mi][i]=m;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        if(m >=lastpass)
 {          break;
   /* Variance of prevalence limit */        else
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          m++;
   double **newm;      }/* end while */
   double **dnewm,**doldm;      if (s[m][i] > nlstate){
   int i, j, nhstepm, hstepm;        mi++;     /* Death is another wave */
   int k, cptcode;        /* if(mi==0)  never been interviewed correctly before death */
   double *xp;           /* Only death is a correct wave */
   double *gp, *gm;        mw[mi][i]=m;
   double **gradg, **trgradg;      }
   double age,agelim;  
   int theta;      wav[i]=mi;
          if(mi==0){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        if(first==0){
   fprintf(ficresvpl,"# Age");          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
   for(i=1; i<=nlstate;i++)          first=1;
       fprintf(ficresvpl," %1d-%1d",i,i);        }
   fprintf(ficresvpl,"\n");        if(first==1){
           fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   xp=vector(1,npar);        }
   dnewm=matrix(1,nlstate,1,npar);      } /* end mi==0 */
   doldm=matrix(1,nlstate,1,nlstate);    }
    
   hstepm=1*YEARM; /* Every year of age */    for(i=1; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(mi=1; mi<wav[i];mi++){
   agelim = AGESUP;        if (stepm <=0)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          dh[mi][i]=1;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        else{
     if (stepm >= YEARM) hstepm=1;          if (s[mw[mi+1][i]][i] > nlstate) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            if (agedc[i] < 2*AGESUP) {
     gradg=matrix(1,npar,1,nlstate);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     gp=vector(1,nlstate);            if(j==0) j=1;  /* Survives at least one month after exam */
     gm=vector(1,nlstate);            k=k+1;
             if (j >= jmax) jmax=j;
     for(theta=1; theta <=npar; theta++){            if (j <= jmin) jmin=j;
       for(i=1; i<=npar; i++){ /* Computes gradient */            sum=sum+j;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       }            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
       for(i=1;i<=nlstate;i++)          else{
         gp[i] = prlim[i][i];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                k=k+1;
       for(i=1; i<=npar; i++) /* Computes gradient */            if (j >= jmax) jmax=j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            else if (j <= jmin)jmin=j;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(i=1;i<=nlstate;i++)            sum=sum+j;
         gm[i] = prlim[i][i];          }
           jk= j/stepm;
       for(i=1;i<=nlstate;i++)          jl= j -jk*stepm;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          ju= j -(jk+1)*stepm;
     } /* End theta */          if(jl <= -ju)
             dh[mi][i]=jk;
     trgradg =matrix(1,nlstate,1,npar);          else
             dh[mi][i]=jk+1;
     for(j=1; j<=nlstate;j++)          if(dh[mi][i]==0)
       for(theta=1; theta <=npar; theta++)            dh[mi][i]=1; /* At least one step */
         trgradg[j][theta]=gradg[theta][j];        }
       }
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] =0.;    jmean=sum/k;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     for(i=1;i<=nlstate;i++)   }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
   /*********** Tricode ****************************/
     fprintf(ficresvpl,"%.0f ",age );  void tricode(int *Tvar, int **nbcode, int imx)
     for(i=1; i<=nlstate;i++)  {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    int Ndum[20],ij=1, k, j, i;
     fprintf(ficresvpl,"\n");    int cptcode=0;
     free_vector(gp,1,nlstate);    cptcoveff=0; 
     free_vector(gm,1,nlstate);   
     free_matrix(gradg,1,npar,1,nlstate);    for (k=0; k<19; k++) Ndum[k]=0;
     free_matrix(trgradg,1,nlstate,1,npar);    for (k=1; k<=7; k++) ncodemax[k]=0;
   } /* End age */  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   free_vector(xp,1,npar);      for (i=1; i<=imx; i++) {
   free_matrix(doldm,1,nlstate,1,npar);        ij=(int)(covar[Tvar[j]][i]);
   free_matrix(dnewm,1,nlstate,1,nlstate);        Ndum[ij]++; 
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 }        if (ij > cptcode) cptcode=ij; 
       }
   
       for (i=0; i<=cptcode; i++) {
 /***********************************************/        if(Ndum[i]!=0) ncodemax[j]++;
 /**************** Main Program *****************/      }
 /***********************************************/      ij=1; 
   
 /*int main(int argc, char *argv[])*/  
 int main()      for (i=1; i<=ncodemax[j]; i++) {
 {        for (k=0; k<=19; k++) {
           if (Ndum[k] != 0) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;            nbcode[Tvar[j]][ij]=k; 
   double agedeb, agefin,hf;            
   double agemin=1.e20, agemax=-1.e20;            ij++;
           }
   double fret;          if (ij > ncodemax[j]) break; 
   double **xi,tmp,delta;        }  
       } 
   double dum; /* Dummy variable */    }  
   double ***p3mat;  
   int *indx;   for (k=0; k<19; k++) Ndum[k]=0;
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];   for (i=1; i<=ncovmodel-2; i++) {
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];     ij=Tvar[i];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];     Ndum[ij]++; 
   char filerest[FILENAMELENGTH];   }
   char fileregp[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];   ij=1;
   int firstobs=1, lastobs=10;   for (i=1; i<=10; i++) {
   int sdeb, sfin; /* Status at beginning and end */     if((Ndum[i]!=0) && (i<=ncovcol)){
   int c,  h , cpt,l;       Tvaraff[ij]=i; 
   int ju,jl, mi;       ij++;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;     }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;   }
     
   int hstepm, nhstepm;   cptcoveff=ij-1;
   double bage, fage, age, agelim, agebase;  }
   double ftolpl=FTOL;  
   double **prlim;  /*********** Health Expectancies ****************/
   double *severity;  
   double ***param; /* Matrix of parameters */  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 )
   double  *p;  
   double **matcov; /* Matrix of covariance */  {
   double ***delti3; /* Scale */    /* Health expectancies */
   double *delti; /* Scale */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   double ***eij, ***vareij;    double age, agelim, hf;
   double **varpl; /* Variances of prevalence limits by age */    double ***p3mat,***varhe;
   double *epj, vepp;    double **dnewm,**doldm;
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";    double *xp;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double **gp, **gm;
     double ***gradg, ***trgradg;
   char z[1]="c", occ;    int theta;
 #include <sys/time.h>  
 #include <time.h>    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    xp=vector(1,npar);
   /* long total_usecs;    dnewm=matrix(1,nlstate*2,1,npar);
   struct timeval start_time, end_time;    doldm=matrix(1,nlstate*2,1,nlstate*2);
      
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
   printf("\nIMACH, Version 0.64a");      for(j=1; j<=nlstate;j++)
   printf("\nEnter the parameter file name: ");        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
 #ifdef windows  
   scanf("%s",pathtot);    if(estepm < stepm){
   getcwd(pathcd, size);      printf ("Problem %d lower than %d\n",estepm, stepm);
   /*cygwin_split_path(pathtot,path,optionfile);    }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    else  hstepm=estepm;   
   /* cutv(path,optionfile,pathtot,'\\');*/    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 split(pathtot, path,optionfile);     * if stepm=24 months pijx are given only every 2 years and by summing them
   chdir(path);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   replace(pathc,path);     * progression inbetween and thus overestimating or underestimating according
 #endif     * to the curvature of the survival function. If, for the same date, we 
 #ifdef unix     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   scanf("%s",optionfile);     * to compare the new estimate of Life expectancy with the same linear 
 #endif     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
 /*-------- arguments in the command line --------*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(fileres,"r");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(fileres, optionfile);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   /*---------arguments file --------*/       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     printf("Problem with optionfile %s\n",optionfile);       survival function given by stepm (the optimization length). Unfortunately it
     goto end;       means that if the survival funtion is printed only each two years of age and if
   }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
   strcpy(filereso,"o");    */
   strcat(filereso,fileres);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    agelim=AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
   /* Reads comments: lines beginning with '#' */      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     ungetc(c,ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
     fgets(line, MAXLINE, ficpar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     puts(line);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   }      gp=matrix(0,nhstepm,1,nlstate*2);
   ungetc(c,ficpar);      gm=matrix(0,nhstepm,1,nlstate*2);
   
   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);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   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);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   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);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   covar=matrix(0,NCOVMAX,1,n);      
   if (strlen(model)<=1) cptcovn=0;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else {  
     j=0;      /* Computing Variances of health expectancies */
     j=nbocc(model,'+');  
     cptcovn=j+1;       for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   ncovmodel=2+cptcovn;        }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
   /* Read guess parameters */        cptj=0;
   /* Reads comments: lines beginning with '#' */        for(j=1; j<= nlstate; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1; i<=nlstate; i++){
     ungetc(c,ficpar);            cptj=cptj+1;
     fgets(line, MAXLINE, ficpar);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     puts(line);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);        }
         
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       
     for(i=1; i <=nlstate; i++)        for(i=1; i<=npar; i++) 
     for(j=1; j <=nlstate+ndeath-1; j++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficparo,"%1d%1d",i1,j1);        
       printf("%1d%1d",i,j);        cptj=0;
       for(k=1; k<=ncovmodel;k++){        for(j=1; j<= nlstate; j++){
         fscanf(ficpar," %lf",&param[i][j][k]);          for(i=1;i<=nlstate;i++){
         printf(" %lf",param[i][j][k]);            cptj=cptj+1;
         fprintf(ficparo," %lf",param[i][j][k]);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       fscanf(ficpar,"\n");            }
       printf("\n");          }
       fprintf(ficparo,"\n");        }
     }        for(j=1; j<= nlstate*2; j++)
            for(h=0; h<=nhstepm-1; h++){
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   p=param[1][1];          }
         } 
   /* Reads comments: lines beginning with '#' */     
   while((c=getc(ficpar))=='#' && c!= EOF){  /* End theta */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
     puts(line);  
     fputs(line,ficparo);       for(h=0; h<=nhstepm-1; h++)
   }        for(j=1; j<=nlstate*2;j++)
   ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   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(i=1;i<=nlstate*2;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1;j<=nlstate*2;j++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);          varhe[i][j][(int)age] =0.;
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);       printf("%d|",(int)age);fflush(stdout);
       for(k=1; k<=ncovmodel;k++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         fscanf(ficpar,"%le",&delti3[i][j][k]);       for(h=0;h<=nhstepm-1;h++){
         printf(" %le",delti3[i][j][k]);        for(k=0;k<=nhstepm-1;k++){
         fprintf(ficparo," %le",delti3[i][j][k]);          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
       fscanf(ficpar,"\n");          for(i=1;i<=nlstate*2;i++)
       printf("\n");            for(j=1;j<=nlstate*2;j++)
       fprintf(ficparo,"\n");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     }        }
   }      }
   delti=delti3[1][1];      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */        for(j=1; j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     ungetc(c,ficpar);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fgets(line, MAXLINE, ficpar);            
     puts(line);  /* 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]);*/
     fputs(line,ficparo);  
   }          }
   ungetc(c,ficpar);  
        fprintf(ficreseij,"%3.0f",age );
   matcov=matrix(1,npar,1,npar);      cptj=0;
   for(i=1; i <=npar; i++){      for(i=1; i<=nlstate;i++)
     fscanf(ficpar,"%s",&str);        for(j=1; j<=nlstate;j++){
     printf("%s",str);          cptj++;
     fprintf(ficparo,"%s",str);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     for(j=1; j <=i; j++){        }
       fscanf(ficpar," %le",&matcov[i][j]);      fprintf(ficreseij,"\n");
       printf(" %.5le",matcov[i][j]);     
       fprintf(ficparo," %.5le",matcov[i][j]);      free_matrix(gm,0,nhstepm,1,nlstate*2);
     }      free_matrix(gp,0,nhstepm,1,nlstate*2);
     fscanf(ficpar,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
     printf("\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
     fprintf(ficparo,"\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    }
   for(i=1; i <=npar; i++)    printf("\n");
     for(j=i+1;j<=npar;j++)    fprintf(ficlog,"\n");
       matcov[i][j]=matcov[j][i];  
        free_vector(xp,1,npar);
   printf("\n");    free_matrix(dnewm,1,nlstate*2,1,npar);
     free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
     /*-------- data file ----------*/  }
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  /************ Variance ******************/
     }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     fprintf(ficres,"#%s\n",version);  {
        /* Variance of health expectancies */
     if((fic=fopen(datafile,"r"))==NULL)    {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       printf("Problem with datafile: %s\n", datafile);goto end;    /* double **newm;*/
     }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     n= lastobs;    int i, j, nhstepm, hstepm, h, nstepm ;
     severity = vector(1,maxwav);    int k, cptcode;
     outcome=imatrix(1,maxwav+1,1,n);    double *xp;
     num=ivector(1,n);    double **gp, **gm;  /* for var eij */
     moisnais=vector(1,n);    double ***gradg, ***trgradg; /*for var eij */
     annais=vector(1,n);    double **gradgp, **trgradgp; /* for var p point j */
     moisdc=vector(1,n);    double *gpp, *gmp; /* for var p point j */
     andc=vector(1,n);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     agedc=vector(1,n);    double ***p3mat;
     cod=ivector(1,n);    double age,agelim, hf;
     weight=vector(1,n);    double ***mobaverage;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    int theta;
     mint=matrix(1,maxwav,1,n);    char digit[4];
     anint=matrix(1,maxwav,1,n);    char digitp[25];
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);        char fileresprobmorprev[FILENAMELENGTH];
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    if(popbased==1){
       if(mobilav==1)
     i=1;        strcpy(digitp,"-populbased-mobilav-");
     while (fgets(line, MAXLINE, fic) != NULL)    {      else strcpy(digitp,"-populbased-nomobil-");
       if ((i >= firstobs) && (i <=lastobs)) {    }
            else 
         for (j=maxwav;j>=1;j--){      strcpy(digitp,"-stablbased-");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    if (mobilav!=0) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      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);
         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);    strcpy(fileresprobmorprev,"prmorprev"); 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         for (j=ncov;j>=1;j--){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    strcat(fileresprobmorprev,fileres);
         }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         num[i]=atol(stra);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         /*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]));*/    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         i=i+1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     /*scanf("%d",i);*/      fprintf(ficresprobmorprev," p.%-d SE",j);
   imx=i-1; /* Number of individuals */      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   /* Calculation of the number of parameter from char model*/    }  
   Tvar=ivector(1,15);        fprintf(ficresprobmorprev,"\n");
   Tage=ivector(1,15);          if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
          printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   if (strlen(model) >1){      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     j=0, j1=0;      exit(0);
     j=nbocc(model,'+');    }
     j1=nbocc(model,'*');    else{
     cptcovn=j+1;      fprintf(ficgp,"\n# Routine varevsij");
        }
     strcpy(modelsav,model);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     if (j==0) {      printf("Problem with html file: %s\n", optionfilehtm);
       if (j1==0){      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        cutv(stra,strb,modelsav,'V');      exit(0);
        Tvar[1]=atoi(strb);    }
       }    else{
       else if (j1==1) {      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");
        cutv(stra,strb,modelsav,'*');      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
        /*      printf("stra=%s strb=%s modelsav=%s ",stra,strb,modelsav);*/    }
        Tage[1]=1; cptcovage++;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        if (strcmp(stra,"age")==0) {  
          cutv(strd,strc,strb,'V');    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");
          Tvar[1]=atoi(strc);    fprintf(ficresvij,"# Age");
        }    for(i=1; i<=nlstate;i++)
        else if (strcmp(strb,"age")==0) {      for(j=1; j<=nlstate;j++)
          cutv(strd,strc,stra,'V');        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
          Tvar[1]=atoi(strc);    fprintf(ficresvij,"\n");
        }  
        else {printf("Error"); exit(0);}    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     else {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for(i=j; i>=1;i--){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         cutv(stra,strb,modelsav,'+');  
         /*printf("%s %s %s\n", stra,strb,modelsav);*/    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         if (strchr(strb,'*')) {    gpp=vector(nlstate+1,nlstate+ndeath);
           cutv(strd,strc,strb,'*');    gmp=vector(nlstate+1,nlstate+ndeath);
           if (strcmp(strc,"age")==0) {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             cutv(strb,stre,strd,'V');    
             Tvar[i+1]=atoi(stre);    if(estepm < stepm){
             cptcovage++;      printf ("Problem %d lower than %d\n",estepm, stepm);
             Tage[cptcovage]=i+1;    }
             printf("stre=%s ", stre);    else  hstepm=estepm;   
           }    /* For example we decided to compute the life expectancy with the smallest unit */
           else if (strcmp(strd,"age")==0) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             cutv(strb,stre,strc,'V');       nhstepm is the number of hstepm from age to agelim 
             Tvar[i+1]=atoi(stre);       nstepm is the number of stepm from age to agelin. 
             cptcovage++;       Look at hpijx to understand the reason of that which relies in memory size
             Tage[cptcovage]=i+1;       and note for a fixed period like k years */
           }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           else {       survival function given by stepm (the optimization length). Unfortunately it
             cutv(strb,stre,strc,'V');       means that if the survival funtion is printed only each two years of age and if
             Tvar[i+1]=ncov+1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             cutv(strb,strc,strd,'V');       results. So we changed our mind and took the option of the best precision.
             for (k=1; k<=lastobs;k++)    */
               covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }    agelim = AGESUP;
         }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         else {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           cutv(strd,strc,strb,'V');      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           /* printf("%s %s %s", strd,strc,strb);*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         Tvar[i+1]=atoi(strc);      gp=matrix(0,nhstepm,1,nlstate);
         }      gm=matrix(0,nhstepm,1,nlstate);
         strcpy(modelsav,stra);    
       }  
       cutv(strd,strc,stra,'V');      for(theta=1; theta <=npar; theta++){
       Tvar[1]=atoi(strc);        for(i=1; i<=npar; i++){ /* Computes gradient */
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      scanf("%d ",i);*/  
     fclose(fic);        if (popbased==1) {
           if(mobilav ==0){
    if(mle==1){            for(i=1; i<=nlstate;i++)
     if (weightopt != 1) { /* Maximisation without weights*/              prlim[i][i]=probs[(int)age][i][ij];
       for(i=1;i<=n;i++) weight[i]=1.0;          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     /*-calculation of age at interview from date of interview and age at death -*/              prlim[i][i]=mobaverage[(int)age][i][ij];
     agev=matrix(1,maxwav,1,imx);          }
            }
     for (i=1; i<=imx; i++)  {    
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(j=1; j<= nlstate; j++){
       for(m=1; (m<= maxwav); m++){          for(h=0; h<=nhstepm; h++){
         if(s[m][i] >0){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           if (s[m][i] == nlstate+1) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
             if(agedc[i]>0)          }
               if(moisdc[i]!=99 && andc[i]!=9999)        }
               agev[m][i]=agedc[i];        /* This for computing forces of mortality (h=1)as a weighted average */
             else{        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          for(i=1; i<= nlstate; i++)
               agev[m][i]=-1;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             }        }    
           }        /* end force of mortality */
           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]);        for(i=1; i<=npar; i++) /* Computes gradient */
             if(mint[m][i]==99 || anint[m][i]==9999)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               agev[m][i]=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             else if(agev[m][i] <agemin){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               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);*/        if (popbased==1) {
             }          if(mobilav ==0){
             else if(agev[m][i] >agemax){            for(i=1; i<=nlstate;i++)
               agemax=agev[m][i];              prlim[i][i]=probs[(int)age][i][ij];
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          }else{ /* mobilav */ 
             }            for(i=1; i<=nlstate;i++)
             /*agev[m][i]=anint[m][i]-annais[i];*/              prlim[i][i]=mobaverage[(int)age][i][ij];
             /*   agev[m][i] = age[i]+2*m;*/          }
           }        }
           else { /* =9 */  
             agev[m][i]=1;        for(j=1; j<= nlstate; j++){
             s[m][i]=-1;          for(h=0; h<=nhstepm; h++){
           }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         else /*= 0 Unknown */          }
           agev[m][i]=1;        }
       }        /* This for computing force of mortality (h=1)as a weighted average */
            for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     }          for(i=1; i<= nlstate; i++)
     for (i=1; i<=imx; i++)  {            gmp[j] += prlim[i][i]*p3mat[i][j][1];
       for(m=1; (m<= maxwav); m++){        }    
         if (s[m][i] > (nlstate+ndeath)) {        /* end force of mortality */
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;        for(j=1; j<= nlstate; j++) /* vareij */
         }          for(h=0; h<=nhstepm; h++){
       }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     }          }
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);      } /* End theta */
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n);      for(h=0; h<=nhstepm; h++) /* veij */
     free_vector(moisdc,1,n);        for(j=1; j<=nlstate;j++)
     free_vector(andc,1,n);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
      
     wav=ivector(1,imx);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(theta=1; theta <=npar; theta++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          trgradgp[j][theta]=gradgp[theta][j];
      
     /* Concatenates waves */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
       Tcode=ivector(1,100);  
    nbcode=imatrix(1,nvar,1,8);        for(h=0;h<=nhstepm;h++){
    ncodemax[1]=1;        for(k=0;k<=nhstepm;k++){
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
    codtab=imatrix(1,100,1,10);          for(i=1;i<=nlstate;i++)
    h=0;            for(j=1;j<=nlstate;j++)
    m=pow(2,cptcovn);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
    for(k=1;k<=cptcovn; k++){      }
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){      /* pptj */
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            h++;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
            if (h>m) h=1;codtab[h][k]=j;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
          }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
        }          varppt[j][i]=doldmp[j][i];
      }      /* end ppptj */
    }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    /* for(i=1; i <=m ;i++){   
      for(k=1; k <=cptcovn; k++){      if (popbased==1) {
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);        if(mobilav ==0){
      }          for(i=1; i<=nlstate;i++)
      printf("\n");            prlim[i][i]=probs[(int)age][i][ij];
    }        }else{ /* mobilav */ 
    scanf("%d",i);*/          for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
    /* Calculates basic frequencies. Computes observed prevalence at single age        }
        and prints on file fileres'p'. */      }
    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);      
       /* This for computing force of mortality (h=1)as a weighted average */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1; i<= nlstate; i++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }    
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      /* end force of mortality */
      
     /* For Powell, parameters are in a vector p[] starting at p[1]      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
            for(i=1; i<=nlstate;i++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
          } 
     /*--------- results files --------------*/      fprintf(ficresprobmorprev,"\n");
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  
          fprintf(ficresvij,"%.0f ",age );
    jk=1;      for(i=1; i<=nlstate;i++)
    fprintf(ficres,"# Parameters\n");        for(j=1; j<=nlstate;j++){
    printf("# Parameters\n");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
    for(i=1,jk=1; i <=nlstate; i++){        }
      for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficresvij,"\n");
        if (k != i)      free_matrix(gp,0,nhstepm,1,nlstate);
          {      free_matrix(gm,0,nhstepm,1,nlstate);
            printf("%d%d ",i,k);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
            fprintf(ficres,"%1d%1d ",i,k);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
            for(j=1; j <=ncovmodel; j++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              printf("%f ",p[jk]);    } /* End age */
              fprintf(ficres,"%f ",p[jk]);    free_vector(gpp,nlstate+1,nlstate+ndeath);
              jk++;    free_vector(gmp,nlstate+1,nlstate+ndeath);
            }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
            printf("\n");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
            fprintf(ficres,"\n");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
          }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
     /* Computing hessian and covariance matrix */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
     ftolhess=ftol; /* Usually correct */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
     fprintf(ficres,"# Scales\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);
     printf("# Scales\n");  */
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    free_vector(xp,1,npar);
           fprintf(ficres,"%1d%1d",i,j);    free_matrix(doldm,1,nlstate,1,nlstate);
           printf("%1d%1d",i,j);    free_matrix(dnewm,1,nlstate,1,npar);
           for(k=1; k<=ncovmodel;k++){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             printf(" %.5e",delti[jk]);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             fprintf(ficres," %.5e",delti[jk]);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             jk++;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           }    fclose(ficresprobmorprev);
           printf("\n");    fclose(ficgp);
           fprintf(ficres,"\n");    fclose(fichtm);
         }  }
       }  
       }  /************ Variance of prevlim ******************/
      void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     k=1;  {
     fprintf(ficres,"# Covariance\n");    /* Variance of prevalence limit */
     printf("# Covariance\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     for(i=1;i<=npar;i++){    double **newm;
       /*  if (k>nlstate) k=1;    double **dnewm,**doldm;
       i1=(i-1)/(ncovmodel*nlstate)+1;    int i, j, nhstepm, hstepm;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    int k, cptcode;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double *xp;
       fprintf(ficres,"%3d",i);    double *gp, *gm;
       printf("%3d",i);    double **gradg, **trgradg;
       for(j=1; j<=i;j++){    double age,agelim;
         fprintf(ficres," %.5e",matcov[i][j]);    int theta;
         printf(" %.5e",matcov[i][j]);     
       }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       fprintf(ficres,"\n");    fprintf(ficresvpl,"# Age");
       printf("\n");    for(i=1; i<=nlstate;i++)
       k++;        fprintf(ficresvpl," %1d-%1d",i,i);
     }    fprintf(ficresvpl,"\n");
      
     while((c=getc(ficpar))=='#' && c!= EOF){    xp=vector(1,npar);
       ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
       fgets(line, MAXLINE, ficpar);    doldm=matrix(1,nlstate,1,nlstate);
       puts(line);    
       fputs(line,ficparo);    hstepm=1*YEARM; /* Every year of age */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     ungetc(c,ficpar);    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          if (stepm >= YEARM) hstepm=1;
     if (fage <= 2) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       bage = agemin;      gradg=matrix(1,npar,1,nlstate);
       fage = agemax;      gp=vector(1,nlstate);
     }      gm=vector(1,nlstate);
   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for(theta=1; theta <=npar; theta++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for(i=1; i<=npar; i++){ /* Computes gradient */
 /*------------ gnuplot -------------*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 chdir(pathcd);        }
   if((ficgp=fopen("graph.plt","w"))==NULL) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with file graph.gp");goto end;        for(i=1;i<=nlstate;i++)
   }          gp[i] = prlim[i][i];
 #ifdef windows      
   fprintf(ficgp,"cd \"%s\" \n",pathc);        for(i=1; i<=npar; i++) /* Computes gradient */
 #endif          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 m=pow(2,cptcovn);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
  /* 1eme*/          gm[i] = prlim[i][i];
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 #ifdef windows      } /* End theta */
     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);  
 #endif      trgradg =matrix(1,nlstate,1,npar);
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      for(j=1; j<=nlstate;j++)
 #endif        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1;i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        varpl[i][(int)age] =0.;
 }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     for (i=1; i<= nlstate ; i ++) {      for(i=1;i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      fprintf(ficresvpl,"%.0f ",age );
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(i=1; i<=nlstate;i++)
      for (i=1; i<= nlstate ; i ++) {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresvpl,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_vector(gp,1,nlstate);
 }        free_vector(gm,1,nlstate);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      free_matrix(gradg,1,npar,1,nlstate);
 #ifdef unix      free_matrix(trgradg,1,nlstate,1,npar);
 fprintf(ficgp,"\nset ter gif small size 400,300");    } /* End age */
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_vector(xp,1,npar);
    }    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   /*2 eme*/  
   }
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  /************ Variance of one-step probabilities  ******************/
      void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     for (i=1; i<= nlstate+1 ; i ++) {  {
       k=2*i;    int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    int k2, l2, j1,  z1;
       for (j=1; j<= nlstate+1 ; j ++) {    int k=0,l, cptcode;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int first=1, first1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 }      double **dnewm,**doldm;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double *xp;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double *gp, *gm;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double **gradg, **trgradg;
       for (j=1; j<= nlstate+1 ; j ++) {    double **mu;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double age,agelim, cov[NCOVMAX];
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 }      int theta;
       fprintf(ficgp,"\" t\"\" w l 0,");    char fileresprob[FILENAMELENGTH];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    char fileresprobcov[FILENAMELENGTH];
       for (j=1; j<= nlstate+1 ; j ++) {    char fileresprobcor[FILENAMELENGTH];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***varpij;
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    strcpy(fileresprob,"prob"); 
       else fprintf(ficgp,"\" t\"\" w l 0,");    strcat(fileresprob,fileres);
     }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      printf("Problem with resultfile: %s\n", fileresprob);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
   /*3eme*/    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
   for (k1=1; k1<= m ; k1 ++) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {      printf("Problem with resultfile: %s\n", fileresprobcov);
       k=2+nlstate*(cpt-1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    }
       for (i=1; i< nlstate ; i ++) {    strcpy(fileresprobcor,"probcor"); 
         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);    strcat(fileresprobcor,fileres);
       }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      printf("Problem with resultfile: %s\n", fileresprobcor);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   /* CV preval stat */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   for (k1=1; k1<= m ; k1 ++) {    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for (cpt=1; cpt<nlstate ; cpt ++) {    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       k=3;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       for (i=1; i< nlstate ; i ++)    
         fprintf(ficgp,"+$%d",k+i+1);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    fprintf(ficresprob,"# Age");
          fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       l=3+(nlstate+ndeath)*cpt;    fprintf(ficresprobcov,"# Age");
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       for (i=1; i< nlstate ; i ++) {    fprintf(ficresprobcov,"# Age");
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);  
       }    for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
   /* proba elementaires */    fprintf(ficresprob,"\n");
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficresprobcov,"\n");
     for(k=1; k <=(nlstate+ndeath); k++){    fprintf(ficresprobcor,"\n");
       if (k != i) {    xp=vector(1,npar);
         for(j=1; j <=ncovmodel; j++){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           /*fprintf(ficgp,"%s",alph[1]);*/    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           jk++;    first=1;
           fprintf(ficgp,"\n");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
         }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     }      exit(0);
     }    }
     else{
   for(jk=1; jk <=m; jk++) {      fprintf(ficgp,"\n# Routine varprob");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    }
    i=1;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    for(k2=1; k2<=nlstate; k2++) {      printf("Problem with html file: %s\n", optionfilehtm);
      k3=i;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      for(k=1; k<=(nlstate+ndeath); k++) {      exit(0);
        if (k != k2){    }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    else{
       fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         for(j=3; j <=ncovmodel; j++)      fprintf(fichtm,"\n");
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         fprintf(ficgp,")/(1");      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");
         for(k1=1; k1 <=nlstate; k1++){        fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
           for(j=3; j <=ncovmodel; j++)    }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
           fprintf(ficgp,")");   
         }    cov[1]=1;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    tj=cptcoveff;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         i=i+ncovmodel;    j1=0;
        }    for(t=1; t<=tj;t++){
      }      for(i1=1; i1<=ncodemax[t];i1++){ 
    }        j1++;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        
   }        if  (cptcovn>0) {
              fprintf(ficresprob, "\n#********** Variable "); 
   fclose(ficgp);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprob, "**********\n#");
 chdir(path);          fprintf(ficresprobcov, "\n#********** Variable "); 
     free_matrix(agev,1,maxwav,1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_ivector(wav,1,imx);          fprintf(ficresprobcov, "**********\n#");
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          fprintf(ficgp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficgp, "**********\n#");
              
              
     free_ivector(num,1,n);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     free_vector(agedc,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(weight,1,n);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          
     fclose(ficparo);          fprintf(ficresprobcor, "\n#********** Variable ");    
     fclose(ficres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    }          fprintf(ficgp, "**********\n#");    
            }
    /*________fin mle=1_________*/        
            for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
     /* No more information from the sample is required now */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     ungetc(c,ficpar);          for (k=1; k<=cptcovprod;k++)
     fgets(line, MAXLINE, ficpar);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     puts(line);          
     fputs(line,ficparo);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   ungetc(c,ficpar);          gp=vector(1,(nlstate)*(nlstate+ndeath));
            gm=vector(1,(nlstate)*(nlstate+ndeath));
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          for(theta=1; theta <=npar; theta++){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            for(i=1; i<=npar; i++)
 /*--------- index.htm --------*/              xp[i] = x[i] + (i==theta ?delti[theta]:0);
             
   if((fichtm=fopen("index.htm","w"))==NULL)    {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     printf("Problem with index.htm \n");goto end;            
   }            k=0;
             for(i=1; i<= (nlstate); i++){
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n              for(j=1; j<=(nlstate+ndeath);j++){
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                k=k+1;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                gp[k]=pmmij[i][j];
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            }
         - 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>            for(i=1; i<=npar; i++)
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              xp[i] = x[i] - (i==theta ?delti[theta]:0);
         - 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><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
  fprintf(fichtm," <li>Graphs</li>\n<p>");            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
  m=cptcovn;                k=k+1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                gm[k]=pmmij[i][j];
               }
  j1=0;            }
  for(k1=1; k1<=m;k1++){       
    for(i1=1; i1<=ncodemax[k1];i1++){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
        j1++;              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
        if (cptcovn > 0) {          }
          fprintf(fichtm,"<hr>************ Results for covariates");  
          for (cpt=1; cpt<=cptcovn;cpt++)          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);            for(theta=1; theta <=npar; theta++)
          fprintf(fichtm," ************\n<hr>");              trgradg[j][theta]=gradg[theta][j];
        }          
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
        for(cpt=1; cpt<nlstate;cpt++){          
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          pmij(pmmij,cov,ncovmodel,x,nlstate);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          
        }          k=0;
     for(cpt=1; cpt<=nlstate;cpt++) {          for(i=1; i<=(nlstate); i++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            for(j=1; j<=(nlstate+ndeath);j++){
 interval) in state (%d): v%s%d%d.gif <br>              k=k+1;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                mu[k][(int) age]=pmmij[i][j];
      }            }
      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(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
      }              varpij[i][j][(int)age] = doldm[i][j];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>          /*printf("\n%d ",(int)age);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);       for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 fprintf(fichtm,"\n</body>");         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    }         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  }       }*/
 fclose(fichtm);  
           fprintf(ficresprob,"\n%d ",(int)age);
   /*--------------- Prevalence limit --------------*/          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   fprintf(ficrespl,"#Prevalence limit\n");          }
   fprintf(ficrespl,"#Age ");          i=0;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          for (k=1; k<=(nlstate);k++){
   fprintf(ficrespl,"\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
   prlim=matrix(1,nlstate,1,nlstate);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for (j=1; j<=i;j++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              }
   k=0;            }
   agebase=agemin;          }/* end of loop for state */
   agelim=agemax;        } /* end of loop for age */
   ftolpl=1.e-10;  
   i1=cptcovn;        /* Confidence intervalle of pij  */
   if (cptcovn < 1){i1=1;}        /*
         fprintf(ficgp,"\nset noparametric;unset label");
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         k=k+1;        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);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         fprintf(ficrespl,"\n#******");        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         for(j=1;j<=cptcovn;j++)        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           fprintf(ficrespl," V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);        */
         fprintf(ficrespl,"******\n");  
                /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         for (age=agebase; age<=agelim; age++){        first1=1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for (k2=1; k2<=(nlstate);k2++){
           fprintf(ficrespl,"%.0f",age );          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           for(i=1; i<=nlstate;i++)            if(l2==k2) continue;
           fprintf(ficrespl," %.5f", prlim[i][i]);            j=(k2-1)*(nlstate+ndeath)+l2;
           fprintf(ficrespl,"\n");            for (k1=1; k1<=(nlstate);k1++){
         }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       }                if(l1==k1) continue;
     }                i=(k1-1)*(nlstate+ndeath)+l1;
   fclose(ficrespl);                if(i<=j) continue;
   /*------------- h Pij x at various ages ------------*/                for (age=bage; age<=fage; age ++){ 
                    if ((int)age %5==0){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    mu1=mu[i][(int) age]/stepm*YEARM ;
   printf("Computing pij: result on file '%s' \n", filerespij);                    mu2=mu[j][(int) age]/stepm*YEARM;
                      c12=cv12/sqrt(v1*v2);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    /* Computing eigen value of matrix of covariance */
   if (stepm<=24) stepsize=2;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   agelim=AGESUP;                    /* Eigen vectors */
   hstepm=stepsize*YEARM; /* Every year of age */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                    /*v21=sqrt(1.-v11*v11); *//* error */
                      v21=(lc1-v1)/cv12*v11;
   k=0;                    v12=-v21;
   for(cptcov=1;cptcov<=i1;cptcov++){                    v22=v11;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    tnalp=v21/v11;
       k=k+1;                    if(first1==1){
         fprintf(ficrespij,"\n#****** ");                      first1=0;
         for(j=1;j<=cptcovn;j++)                      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);
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);                    }
         fprintf(ficrespij,"******\n");                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                            /*printf(fignu*/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                    if(first==1){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      first=0;
           oldm=oldms;savm=savms;                      fprintf(ficgp,"\nset parametric;unset label");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                        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(ficrespij,"# Age");                      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);
             for(j=1; j<=nlstate+ndeath;j++)                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
               fprintf(ficrespij," %1d-%1d",i,j);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           fprintf(ficrespij,"\n");                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           for (h=0; h<=nhstepm; h++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             for(i=1; i<=nlstate;i++)                      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",\
               for(j=1; j<=nlstate+ndeath;j++)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
             fprintf(ficrespij,"\n");                    }else{
           }                      first=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
           fprintf(ficrespij,"\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fclose(ficrespij);                    }/* if first */
                   } /* age mod 5 */
   /*---------- Health expectancies and variances ------------*/                } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   strcpy(filerest,"t");                first=1;
   strcat(filerest,fileres);              } /*l12 */
   if((ficrest=fopen(filerest,"w"))==NULL) {            } /* k12 */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          } /*l1 */
   }        }/* k1 */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      } /* loop covariates */
       free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   strcpy(filerese,"e");      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   strcat(filerese,fileres);      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }    }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    free_vector(xp,1,npar);
     fclose(ficresprob);
  strcpy(fileresv,"v");    fclose(ficresprobcov);
   strcat(fileresv,fileres);    fclose(ficresprobcor);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fclose(ficgp);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fclose(fichtm);
   }  }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   
   k=0;  /******************* Printing html file ***********/
   for(cptcov=1;cptcov<=i1;cptcov++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    int lastpass, int stepm, int weightopt, char model[],\
       k=k+1;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       fprintf(ficrest,"\n#****** ");                    int popforecast, int estepm ,\
       for(j=1;j<=cptcovn;j++)                    double jprev1, double mprev1,double anprev1, \
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);                    double jprev2, double mprev2,double anprev2){
       fprintf(ficrest,"******\n");    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
       fprintf(ficreseij,"\n#****** ");    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       for(j=1;j<=cptcovn;j++)      printf("Problem with %s \n",optionfilehtm), exit(0);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficreseij,"******\n");    }
   
       fprintf(ficresvij,"\n#****** ");     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
       for(j=1;j<=cptcovn;j++)   - 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(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       fprintf(ficresvij,"******\n");   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
       oldm=oldms;savm=savms;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       oldm=oldms;savm=savms;  
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   m=cptcoveff;
         if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   jj1=0;
       fprintf(ficrest,"\n");   for(k1=1; k1<=m;k1++){
             for(i1=1; i1<=ncodemax[k1];i1++){
       hf=1;       jj1++;
       if (stepm >= YEARM) hf=stepm/YEARM;       if (cptcovn > 0) {
       epj=vector(1,nlstate+1);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       for(age=bage; age <=fage ;age++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         fprintf(ficrest," %.0f",age);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       /* Pij */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
           }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           epj[nlstate+1] +=epj[j];       /* Quasi-incidences */
         }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
         for(i=1, vepp=0.;i <=nlstate;i++)  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           for(j=1;j <=nlstate;j++)         /* Stable prevalence in each health state */
             vepp += vareij[i][j][(int)age];         for(cpt=1; cpt<nlstate;cpt++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
         for(j=1;j <=nlstate;j++){  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));         }
         }       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(ficrest,"\n");          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
       }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     }       }
   }       fprintf(fichtm,"\n<br>- Total life expectancy by age and
          health expectancies in states (1) and (2): e%s%d.png<br>
  fclose(ficreseij);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
  fclose(ficresvij);     } /* end i1 */
   fclose(ficrest);   }/* End k1 */
   fclose(ficpar);   fprintf(fichtm,"</ul>");
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */  
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   /*------- Variance limit prevalence------*/     - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
 strcpy(fileresvpl,"vpl");   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
   strcat(fileresvpl,fileres);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     exit(0);   - 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);
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   if(popforecast==1) fprintf(fichtm,"\n
    - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
  k=0;   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
  for(cptcov=1;cptcov<=i1;cptcov++){          <br>",fileres,fileres,fileres,fileres);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   else 
      k=k+1;     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(ficresvpl,"\n#****** ");  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
      for(j=1;j<=cptcovn;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);   m=cptcoveff;
      fprintf(ficresvpl,"******\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);   jj1=0;
      oldm=oldms;savm=savms;   for(k1=1; k1<=m;k1++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     for(i1=1; i1<=ncodemax[k1];i1++){
    }       jj1++;
  }       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   fclose(ficresvpl);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /*---------- End : free ----------------*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       }
         for(cpt=1; cpt<=nlstate;cpt++) {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  interval) in state (%d): v%s%d%d.png <br>
    <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
         }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     } /* end i1 */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);   }/* End k1 */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm,"</ul>");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  fclose(fichtm);
    }
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);  /******************* Gnuplot file **************/
    void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   printf("End of Imach\n");    int ng;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        printf("Problem with file %s",optionfilegnuplot);
   /* 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);*/      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    }
   /*------ End -----------*/  
     /*#ifdef windows */
  end:      fprintf(ficgp,"cd \"%s\" \n",pathc);
 #ifdef windows      /*#endif */
  chdir(pathcd);  m=pow(2,cptcoveff);
 #endif    
  system("wgnuplot graph.plt");   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
 #ifdef windows     for (k1=1; k1<= m ; k1 ++) {
   while (z[0] != 'q') {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     chdir(pathcd);       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);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);       for (i=1; i<= nlstate ; i ++) {
     if (z[0] == 'c') system("./imach");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     else if (z[0] == 'e') {         else fprintf(ficgp," \%%*lf (\%%*lf)");
       chdir(path);       }
       system("index.htm");       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
     }       for (i=1; i<= nlstate ; i ++) {
     else if (z[0] == 'q') exit(0);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
 #endif       } 
 }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int mobilavrange, mob;
     double age;
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
    agelim=AGESUP;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
     
     fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     
     for(cptcov=1;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         
         
         for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                   
                 }
                 if (h==(int)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
                           
                 }
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       }
     }
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   /************** Forecasting ******************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedate+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedate+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (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.1.6  
changed lines
  Added in v.1.56


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