Diff for /imach/src/imach.c between versions 1.5 and 1.57

version 1.5, 2001/05/02 17:42:45 version 1.57, 2002/07/25 07:37:44
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 MAXLINE 256
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define GNUPLOTPROGRAM "gnuplot"
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 80
 #define NINTERVMAX 8  /*#define DEBUG*/
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define windows
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define AGESUP 130  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define AGEBASE 40  
   #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int nvar;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 static int cptcov;  #define NCOVMAX 8 /* Maximum number of covariates */
 int cptcovn;  #define MAXN 20000
 int npar=NPARMAX;  #define YEARM 12. /* Number of months per year */
 int nlstate=2; /* Number of live states */  #define AGESUP 130
 int ndeath=1; /* Number of dead states */  #define AGEBASE 40
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #ifdef windows
   #define DIRSEPARATOR '\\'
 int *wav; /* Number of waves for this individuual 0 is possible */  #define ODIRSEPARATOR '/'
 int maxwav; /* Maxim number of waves */  #else
 int mle, weightopt;  #define DIRSEPARATOR '/'
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define ODIRSEPARATOR '\\'
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #endif
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  int erreur; /* Error number */
 FILE *ficgp, *fichtm;  int nvar;
 FILE *ficreseij;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   char filerese[FILENAMELENGTH];  int npar=NPARMAX;
  FILE  *ficresvij;  int nlstate=2; /* Number of live states */
   char fileresv[FILENAMELENGTH];  int ndeath=1; /* Number of dead states */
  FILE  *ficresvpl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   char fileresvpl[FILENAMELENGTH];  int popbased=0;
   
   int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 #define NR_END 1  int mle, weightopt;
 #define FREE_ARG char*  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define FTOL 1.0e-10  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double jmean; /* Mean space between 2 waves */
 #define NRANSI  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define ITMAX 200  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define TOL 2.0e-4  FILE *ficlog;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define CGOLD 0.3819660  FILE *ficresprobmorprev;
 #define ZEPS 1.0e-10  FILE *fichtm; /* Html File */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define GOLD 1.618034  FILE  *ficresvij;
 #define GLIMIT 100.0  char fileresv[FILENAMELENGTH];
 #define TINY 1.0e-20  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 static double maxarg1,maxarg2;  char title[MAXLINE];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 static double sqrarg;  char fileregp[FILENAMELENGTH];
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char popfile[FILENAMELENGTH];
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 int imx;  
 int stepm;  #define NR_END 1
 /* Stepm, step in month: minimum step interpolation*/  #define FREE_ARG char*
   #define FTOL 1.0e-10
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  #define NRANSI 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define ITMAX 200 
 double **pmmij;  
   #define TOL 2.0e-4 
 double *weight;  
 int **s; /* Status */  #define CGOLD 0.3819660 
 double *agedc, **covar, idx;  #define ZEPS 1.0e-10 
 int **nbcode, *Tcode, *Tvar, **codtab;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define GOLD 1.618034 
 double ftolhess; /* Tolerance for computing hessian */  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
   
 static  int split( char *path, char *dirc, char *name )  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    char *s;                             /* pointer */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    int  l1, l2;                         /* length counters */    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    l1 = strlen( path );                 /* length of path */  #define rint(a) floor(a+0.5)
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */  static double sqrarg;
    if ( s == NULL ) {                   /* no directory, so use current */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #if     defined(__bsd__)                /* get current working directory */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       extern char       *getwd( );  
   int imx; 
       if ( getwd( dirc ) == NULL ) {  int stepm;
 #else  /* Stepm, step in month: minimum step interpolation*/
       extern char       *getcwd( );  
   int estepm;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #endif  
          return( GLOCK_ERROR_GETCWD );  int m,nb;
       }  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       strcpy( name, path );             /* we've got it */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    } else {                             /* strip direcotry from path */  double **pmmij, ***probs;
       s++;                              /* after this, the filename */  double dateintmean=0;
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double *weight;
       strcpy( name, s );                /* save file name */  int **s; /* Status */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  double *agedc, **covar, idx;
       dirc[l1-l2] = 0;                  /* add zero */  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    }  
    l1 = strlen( dirc );                 /* length of directory */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  double ftolhess; /* Tolerance for computing hessian */
    return( 0 );                         /* we're done */  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /******************************************/     char *s;                             /* pointer */
      int  l1, l2;                         /* length counters */
 void replace(char *s, char*t)  
 {     l1 = strlen( path );                 /* length of path */
   int i;     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int lg=20;     s= strrchr( path, DIRSEPARATOR );            /* find last / */
   i=0;     if ( s == NULL ) {                   /* no directory, so use current */
   lg=strlen(t);       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for(i=0; i<= lg; i++) {         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     (s[i] = t[i]);  #if     defined(__bsd__)                /* get current working directory */
     if (t[i]== '\\') s[i]='/';        extern char       *getwd( );
   }  
 }        if ( getwd( dirc ) == NULL ) {
   #else
 int nbocc(char *s, char occ)        extern char       *getcwd( );
 {  
   int i,j=0;        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int lg=20;  #endif
   i=0;           return( GLOCK_ERROR_GETCWD );
   lg=strlen(s);        }
   for(i=0; i<= lg; i++) {        strcpy( name, path );             /* we've got it */
   if  (s[i] == occ ) j++;     } else {                             /* strip direcotry from path */
   }        s++;                              /* after this, the filename */
   return j;        l2 = strlen( s );                 /* length of filename */
 }        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         strcpy( name, s );                /* save file name */
 void cutv(char *u,char *v, char*t, char occ)        strncpy( dirc, path, l1 - l2 );   /* now the directory */
 {        dirc[l1-l2] = 0;                  /* add zero */
   int i,lg,j,p;     }
   i=0;     l1 = strlen( dirc );                 /* length of directory */
   for(j=0; j<=strlen(t)-1; j++) {  #ifdef windows
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   }  #else
      if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   lg=strlen(t);  #endif
   for(j=0; j<p; j++) {     s = strrchr( name, '.' );            /* find last / */
     (u[j] = t[j]);     s++;
     u[p]='\0';     strcpy(ext,s);                       /* save extension */
   }     l1= strlen( name);
      l2= strlen( s)+1;
    for(j=0; j<= lg; j++) {     strncpy( finame, name, l1-l2);
     if (j>=(p+1))(v[j-p-1] = t[j]);     finame[l1-l2]= 0;
   }     return( 0 );                         /* we're done */
 }  }
   
 /********************** nrerror ********************/  
   /******************************************/
 void nrerror(char error_text[])  
 {  void replace(char *s, char*t)
   fprintf(stderr,"ERREUR ...\n");  {
   fprintf(stderr,"%s\n",error_text);    int i;
   exit(1);    int lg=20;
 }    i=0;
 /*********************** vector *******************/    lg=strlen(t);
 double *vector(int nl, int nh)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   double *v;      if (t[i]== '\\') s[i]='/';
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    }
   if (!v) nrerror("allocation failure in vector");  }
   return v-nl+NR_END;  
 }  int nbocc(char *s, char occ)
   {
 /************************ free vector ******************/    int i,j=0;
 void free_vector(double*v, int nl, int nh)    int lg=20;
 {    i=0;
   free((FREE_ARG)(v+nl-NR_END));    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /************************ivector *******************************/    }
 int *ivector(long nl,long nh)    return j;
 {  }
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  void cutv(char *u,char *v, char*t, char occ)
   if (!v) nrerror("allocation failure in ivector");  {
   return v-nl+NR_END;    /* cuts string t into u and v where u is ended by char occ excluding it
 }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
        gives u="abcedf" and v="ghi2j" */
 /******************free ivector **************************/    int i,lg,j,p=0;
 void free_ivector(int *v, long nl, long nh)    i=0;
 {    for(j=0; j<=strlen(t)-1; j++) {
   free((FREE_ARG)(v+nl-NR_END));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /******************* imatrix *******************************/    lg=strlen(t);
 int **imatrix(long nrl, long nrh, long ncl, long nch)    for(j=0; j<p; j++) {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */      (u[j] = t[j]);
 {    }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;       u[p]='\0';
   int **m;  
       for(j=0; j<= lg; j++) {
   /* allocate pointers to rows */      if (j>=(p+1))(v[j-p-1] = t[j]);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /********************** nrerror ********************/
    
    void nrerror(char error_text[])
   /* allocate rows and set pointers to them */  {
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    fprintf(stderr,"ERREUR ...\n");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    fprintf(stderr,"%s\n",error_text);
   m[nrl] += NR_END;    exit(1);
   m[nrl] -= ncl;  }
    /*********************** vector *******************/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double *vector(int nl, int nh)
    {
   /* return pointer to array of pointers to rows */    double *v;
   return m;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /****************** free_imatrix *************************/  }
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /************************ free vector ******************/
       long nch,ncl,nrh,nrl;  void free_vector(double*v, int nl, int nh)
      /* free an int matrix allocated by imatrix() */  {
 {    free((FREE_ARG)(v+nl-NR_END));
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  }
   free((FREE_ARG) (m+nrl-NR_END));  
 }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 /******************* matrix *******************************/  {
 double **matrix(long nrl, long nrh, long ncl, long nch)    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if (!v) nrerror("allocation failure in ivector");
   double **m;    return v-nl+NR_END;
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /******************free ivector **************************/
   m += NR_END;  void free_ivector(int *v, long nl, long nh)
   m -= nrl;  {
     free((FREE_ARG)(v+nl-NR_END));
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /******************* imatrix *******************************/
   m[nrl] -= ncl;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  { 
   return m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 }    int **m; 
     
 /*************************free matrix ************************/    /* allocate pointers to rows */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m += NR_END; 
   free((FREE_ARG)(m+nrl-NR_END));    m -= nrl; 
 }    
     
 /******************* ma3x *******************************/    /* allocate rows and set pointers to them */ 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m[nrl] += NR_END; 
   double ***m;    m[nrl] -= ncl; 
     
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    /* return pointer to array of pointers to rows */ 
   m -= nrl;    return m; 
   } 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /****************** free_imatrix *************************/
   m[nrl] += NR_END;  void free_imatrix(m,nrl,nrh,ncl,nch)
   m[nrl] -= ncl;        int **m;
         long nch,ncl,nrh,nrl; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;       /* free an int matrix allocated by imatrix() */ 
   { 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    free((FREE_ARG) (m+nrl-NR_END)); 
   m[nrl][ncl] += NR_END;  } 
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /******************* matrix *******************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  double **matrix(long nrl, long nrh, long ncl, long nch)
    {
   for (i=nrl+1; i<=nrh; i++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    double **m;
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
   return m;    m += NR_END;
 }    m -= nrl;
   
 /*************************free ma3x ************************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl] -= ncl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }    return m;
   }
 /***************** f1dim *************************/  
 extern int ncom;  /*************************free matrix ************************/
 extern double *pcom,*xicom;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 extern double (*nrfunc)(double []);  {
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double f1dim(double x)    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   int j;  
   double f;  /******************* ma3x *******************************/
   double *xt;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
   xt=vector(1,ncom);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    double ***m;
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   return f;    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int iter;    m[nrl] += NR_END;
   double a,b,d,etemp;    m[nrl] -= ncl;
   double fu,fv,fw,fx;  
   double ftemp;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   a=(ax < cx ? ax : cx);    m[nrl][ncl] += NR_END;
   b=(ax > cx ? ax : cx);    m[nrl][ncl] -= nll;
   x=w=v=bx;    for (j=ncl+1; j<=nch; j++) 
   fw=fv=fx=(*f)(x);      m[nrl][j]=m[nrl][j-1]+nlay;
   for (iter=1;iter<=ITMAX;iter++) {    
     xm=0.5*(a+b);    for (i=nrl+1; i<=nrh; i++) {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      for (j=ncl+1; j<=nch; j++) 
     printf(".");fflush(stdout);        m[i][j]=m[i][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);    return m;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /*************************free ma3x ************************/
       *xmin=x;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       return fx;  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     ftemp=fu;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if (fabs(e) > tol1) {    free((FREE_ARG)(m+nrl-NR_END));
       r=(x-w)*(fx-fv);  }
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  /***************** f1dim *************************/
       q=2.0*(q-r);  extern int ncom; 
       if (q > 0.0) p = -p;  extern double *pcom,*xicom;
       q=fabs(q);  extern double (*nrfunc)(double []); 
       etemp=e;   
       e=d;  double f1dim(double x) 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    int j; 
       else {    double f;
         d=p/q;    double *xt; 
         u=x+d;   
         if (u-a < tol2 || b-u < tol2)    xt=vector(1,ncom); 
           d=SIGN(tol1,xm-x);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
     } else {    free_vector(xt,1,ncom); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return f; 
     }  } 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /*****************brent *************************/
     if (fu <= fx) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       if (u >= x) a=x; else b=x;  { 
       SHFT(v,w,x,u)    int iter; 
         SHFT(fv,fw,fx,fu)    double a,b,d,etemp;
         } else {    double fu,fv,fw,fx;
           if (u < x) a=u; else b=u;    double ftemp;
           if (fu <= fw || w == x) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
             v=w;    double e=0.0; 
             w=u;   
             fv=fw;    a=(ax < cx ? ax : cx); 
             fw=fu;    b=(ax > cx ? ax : cx); 
           } else if (fu <= fv || v == x || v == w) {    x=w=v=bx; 
             v=u;    fw=fv=fx=(*f)(x); 
             fv=fu;    for (iter=1;iter<=ITMAX;iter++) { 
           }      xm=0.5*(a+b); 
         }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   nrerror("Too many iterations in brent");      printf(".");fflush(stdout);
   *xmin=x;      fprintf(ficlog,".");fflush(ficlog);
   return fx;  #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);
       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);
 /****************** mnbrak ***********************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
             double (*func)(double))        *xmin=x; 
 {        return fx; 
   double ulim,u,r,q, dum;      } 
   double fu;      ftemp=fu;
        if (fabs(e) > tol1) { 
   *fa=(*func)(*ax);        r=(x-w)*(fx-fv); 
   *fb=(*func)(*bx);        q=(x-v)*(fx-fw); 
   if (*fb > *fa) {        p=(x-v)*q-(x-w)*r; 
     SHFT(dum,*ax,*bx,dum)        q=2.0*(q-r); 
       SHFT(dum,*fb,*fa,dum)        if (q > 0.0) p = -p; 
       }        q=fabs(q); 
   *cx=(*bx)+GOLD*(*bx-*ax);        etemp=e; 
   *fc=(*func)(*cx);        e=d; 
   while (*fb > *fc) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     r=(*bx-*ax)*(*fb-*fc);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     q=(*bx-*cx)*(*fb-*fa);        else { 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/          d=p/q; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));          u=x+d; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);          if (u-a < tol2 || b-u < tol2) 
     if ((*bx-u)*(u-*cx) > 0.0) {            d=SIGN(tol1,xm-x); 
       fu=(*func)(u);        } 
     } else if ((*cx-u)*(u-ulim) > 0.0) {      } else { 
       fu=(*func)(u);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       if (fu < *fc) {      } 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
           SHFT(*fb,*fc,fu,(*func)(u))      fu=(*f)(u); 
           }      if (fu <= fx) { 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        if (u >= x) a=x; else b=x; 
       u=ulim;        SHFT(v,w,x,u) 
       fu=(*func)(u);          SHFT(fv,fw,fx,fu) 
     } else {          } else { 
       u=(*cx)+GOLD*(*cx-*bx);            if (u < x) a=u; else b=u; 
       fu=(*func)(u);            if (fu <= fw || w == x) { 
     }              v=w; 
     SHFT(*ax,*bx,*cx,u)              w=u; 
       SHFT(*fa,*fb,*fc,fu)              fv=fw; 
       }              fw=fu; 
 }            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 /*************** linmin ************************/              fv=fu; 
             } 
 int ncom;          } 
 double *pcom,*xicom;    } 
 double (*nrfunc)(double []);    nrerror("Too many iterations in brent"); 
      *xmin=x; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    return fx; 
 {  } 
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  /****************** mnbrak ***********************/
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double *fc, double (*func)(double));              double (*func)(double)) 
   int j;  { 
   double xx,xmin,bx,ax;    double ulim,u,r,q, dum;
   double fx,fb,fa;    double fu; 
     
   ncom=n;    *fa=(*func)(*ax); 
   pcom=vector(1,n);    *fb=(*func)(*bx); 
   xicom=vector(1,n);    if (*fb > *fa) { 
   nrfunc=func;      SHFT(dum,*ax,*bx,dum) 
   for (j=1;j<=n;j++) {        SHFT(dum,*fb,*fa,dum) 
     pcom[j]=p[j];        } 
     xicom[j]=xi[j];    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   ax=0.0;    while (*fb > *fc) { 
   xx=1.0;      r=(*bx-*ax)*(*fb-*fc); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      q=(*bx-*cx)*(*fb-*fa); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 #ifdef DEBUG        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 #endif      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (j=1;j<=n;j++) {        fu=(*func)(u); 
     xi[j] *= xmin;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     p[j] += xi[j];        fu=(*func)(u); 
   }        if (fu < *fc) { 
   free_vector(xicom,1,n);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   free_vector(pcom,1,n);            SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 /*************** powell ************************/        u=ulim; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        fu=(*func)(u); 
             double (*func)(double []))      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   void linmin(double p[], double xi[], int n, double *fret,        fu=(*func)(u); 
               double (*func)(double []));      } 
   int i,ibig,j;      SHFT(*ax,*bx,*cx,u) 
   double del,t,*pt,*ptt,*xit;        SHFT(*fa,*fb,*fc,fu) 
   double fp,fptt;        } 
   double *xits;  } 
   pt=vector(1,n);  
   ptt=vector(1,n);  /*************** linmin ************************/
   xit=vector(1,n);  
   xits=vector(1,n);  int ncom; 
   *fret=(*func)(p);  double *pcom,*xicom;
   for (j=1;j<=n;j++) pt[j]=p[j];  double (*nrfunc)(double []); 
   for (*iter=1;;++(*iter)) {   
     fp=(*fret);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     ibig=0;  { 
     del=0.0;    double brent(double ax, double bx, double cx, 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);                 double (*f)(double), double tol, double *xmin); 
     for (i=1;i<=n;i++)    double f1dim(double x); 
       printf(" %d %.12f",i, p[i]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     printf("\n");                double *fc, double (*func)(double)); 
     for (i=1;i<=n;i++) {    int j; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double xx,xmin,bx,ax; 
       fptt=(*fret);    double fx,fb,fa;
 #ifdef DEBUG   
       printf("fret=%lf \n",*fret);    ncom=n; 
 #endif    pcom=vector(1,n); 
       printf("%d",i);fflush(stdout);    xicom=vector(1,n); 
       linmin(p,xit,n,fret,func);    nrfunc=func; 
       if (fabs(fptt-(*fret)) > del) {    for (j=1;j<=n;j++) { 
         del=fabs(fptt-(*fret));      pcom[j]=p[j]; 
         ibig=i;      xicom[j]=xi[j]; 
       }    } 
 #ifdef DEBUG    ax=0.0; 
       printf("%d %.12e",i,(*fret));    xx=1.0; 
       for (j=1;j<=n;j++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         printf(" x(%d)=%.12e",j,xit[j]);  #ifdef DEBUG
       }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for(j=1;j<=n;j++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         printf(" p=%.12e",p[j]);  #endif
       printf("\n");    for (j=1;j<=n;j++) { 
 #endif      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    } 
 #ifdef DEBUG    free_vector(xicom,1,n); 
       int k[2],l;    free_vector(pcom,1,n); 
       k[0]=1;  } 
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /*************** powell ************************/
       for (j=1;j<=n;j++)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         printf(" %.12e",p[j]);              double (*func)(double [])) 
       printf("\n");  { 
       for(l=0;l<=1;l++) {    void linmin(double p[], double xi[], int n, double *fret, 
         for (j=1;j<=n;j++) {                double (*func)(double [])); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    int i,ibig,j; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double del,t,*pt,*ptt,*xit;
         }    double fp,fptt;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double *xits;
       }    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
     xit=vector(1,n); 
     xits=vector(1,n); 
       free_vector(xit,1,n);    *fret=(*func)(p); 
       free_vector(xits,1,n);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       free_vector(ptt,1,n);    for (*iter=1;;++(*iter)) { 
       free_vector(pt,1,n);      fp=(*fret); 
       return;      ibig=0; 
     }      del=0.0; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for (j=1;j<=n;j++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       ptt[j]=2.0*p[j]-pt[j];      for (i=1;i<=n;i++) 
       xit[j]=p[j]-pt[j];        printf(" %d %.12f",i, p[i]);
       pt[j]=p[j];      fprintf(ficlog," %d %.12f",i, p[i]);
     }      printf("\n");
     fptt=(*func)(ptt);      fprintf(ficlog,"\n");
     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);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       if (t < 0.0) {        fptt=(*fret); 
         linmin(p,xit,n,fret,func);  #ifdef DEBUG
         for (j=1;j<=n;j++) {        printf("fret=%lf \n",*fret);
           xi[j][ibig]=xi[j][n];        fprintf(ficlog,"fret=%lf \n",*fret);
           xi[j][n]=xit[j];  #endif
         }        printf("%d",i);fflush(stdout);
 #ifdef DEBUG        fprintf(ficlog,"%d",i);fflush(ficlog);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        linmin(p,xit,n,fret,func); 
         for(j=1;j<=n;j++)        if (fabs(fptt-(*fret)) > del) { 
           printf(" %.12e",xit[j]);          del=fabs(fptt-(*fret)); 
         printf("\n");          ibig=i; 
 #endif        } 
       }  #ifdef DEBUG
     }        printf("%d %.12e",i,(*fret));
   }        fprintf(ficlog,"%d %.12e",i,(*fret));
 }        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 /**** Prevalence limit ****************/          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        }
 {        for(j=1;j<=n;j++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          printf(" p=%.12e",p[j]);
      matrix by transitions matrix until convergence is reached */          fprintf(ficlog," p=%.12e",p[j]);
         }
   int i, ii,j,k;        printf("\n");
   double min, max, maxmin, maxmax,sumnew=0.;        fprintf(ficlog,"\n");
   double **matprod2();  #endif
   double **out, cov[NCOVMAX], **pmij();      } 
   double **newm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double agefin, delaymax=50 ; /* Max number of years to converge */  #ifdef DEBUG
         int k[2],l;
   for (ii=1;ii<=nlstate+ndeath;ii++)        k[0]=1;
     for (j=1;j<=nlstate+ndeath;j++){        k[1]=-1;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        for (j=1;j<=n;j++) {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){          printf(" %.12e",p[j]);
     newm=savm;          fprintf(ficlog," %.12e",p[j]);
     /* Covariates have to be included here again */        }
     cov[1]=1.;        printf("\n");
     cov[2]=agefin;        fprintf(ficlog,"\n");
     if (cptcovn>0){        for(l=0;l<=1;l++) {
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*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];
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     savm=oldm;          }
     oldm=newm;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     maxmax=0.;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=1;j<=nlstate;j++){        }
       min=1.;  #endif
       max=0.;  
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;        free_vector(xit,1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        free_vector(xits,1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);        free_vector(ptt,1,n); 
         max=FMAX(max,prlim[i][j]);        free_vector(pt,1,n); 
         min=FMIN(min,prlim[i][j]);        return; 
       }      } 
       maxmin=max-min;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       maxmax=FMAX(maxmax,maxmin);      for (j=1;j<=n;j++) { 
     }        ptt[j]=2.0*p[j]-pt[j]; 
     if(maxmax < ftolpl){        xit[j]=p[j]-pt[j]; 
       return prlim;        pt[j]=p[j]; 
     }      } 
   }      fptt=(*func)(ptt); 
 }      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 /*************** transition probabilities **********/        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          for (j=1;j<=n;j++) { 
 {            xi[j][ibig]=xi[j][n]; 
   double s1, s2;            xi[j][n]=xit[j]; 
   /*double t34;*/          }
   int i,j,j1, nc, ii, jj;  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(i=1; i<= nlstate; i++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=1; j<i;j++){          for(j=1;j<=n;j++){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            printf(" %.12e",xit[j]);
         /*s2 += param[i][j][nc]*cov[nc];*/            fprintf(ficlog," %.12e",xit[j]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          printf("\n");
       }          fprintf(ficlog,"\n");
       ps[i][j]=s2;  #endif
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        }
     }      } 
     for(j=i+1; j<=nlstate+ndeath;j++){    } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /**** Prevalence limit (stable prevalence)  ****************/
       }  
       ps[i][j]=s2;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     }  {
   }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(i=1; i<= nlstate; i++){       matrix by transitions matrix until convergence is reached */
      s1=0;  
     for(j=1; j<i; j++)    int i, ii,j,k;
       s1+=exp(ps[i][j]);    double min, max, maxmin, maxmax,sumnew=0.;
     for(j=i+1; j<=nlstate+ndeath; j++)    double **matprod2();
       s1+=exp(ps[i][j]);    double **out, cov[NCOVMAX], **pmij();
     ps[i][i]=1./(s1+1.);    double **newm;
     for(j=1; j<i; j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (j=1;j<=nlstate+ndeath;j++){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* end i */      }
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){     cov[1]=1.;
     for(jj=1; jj<= nlstate+ndeath; jj++){   
       ps[ii][jj]=0;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       ps[ii][ii]=1;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     }      newm=savm;
   }      /* Covariates have to be included here again */
        cov[2]=agefin;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (k=1; k<=cptcovn;k++) {
      printf("%lf ",ps[ii][jj]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
    }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     printf("\n ");        }
     }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     printf("\n ");printf("%lf ",cov[2]);*/        for (k=1; k<=cptcovprod;k++)
 /*          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     return ps;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 /**************** Product of 2 matrices ******************/  
       savm=oldm;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      oldm=newm;
 {      maxmax=0.;
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      for(j=1;j<=nlstate;j++){
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        min=1.;
   /* in, b, out are matrice of pointers which should have been initialized        max=0.;
      before: only the contents of out is modified. The function returns        for(i=1; i<=nlstate; i++) {
      a pointer to pointers identical to out */          sumnew=0;
   long i, j, k;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for(i=nrl; i<= nrh; i++)          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(k=ncolol; k<=ncoloh; k++)          max=FMAX(max,prlim[i][j]);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          min=FMIN(min,prlim[i][j]);
         out[i][k] +=in[i][j]*b[j][k];        }
         maxmin=max-min;
   return out;        maxmax=FMAX(maxmax,maxmin);
 }      }
       if(maxmax < ftolpl){
         return prlim;
 /************* Higher Matrix Product ***************/      }
     }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*************** transition probabilities ***************/ 
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  {
      (typically every 2 years instead of every month which is too big).    double s1, s2;
      Model is determined by parameters x and covariates have to be    /*double t34;*/
      included manually here.    int i,j,j1, nc, ii, jj;
   
      */      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
   int i, j, d, h, k;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double **out, cov[NCOVMAX];          /*s2 += param[i][j][nc]*cov[nc];*/
   double **newm;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   /* Hstepm could be zero and should return the unit matrix */        }
   for (i=1;i<=nlstate+ndeath;i++)        ps[i][j]=s2;
     for (j=1;j<=nlstate+ndeath;j++){        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       oldm[i][j]=(i==j ? 1.0 : 0.0);      }
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for(j=i+1; j<=nlstate+ndeath;j++){
     }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for(h=1; h <=nhstepm; h++){          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     for(d=1; d <=hstepm; d++){        }
       newm=savm;        ps[i][j]=s2;
       /* Covariates have to be included here again */      }
       cov[1]=1.;    }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      /*ps[3][2]=1;*/
       if (cptcovn>0){  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];    for(i=1; i<= nlstate; i++){
     }       s1=0;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      for(j=1; j<i; j++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        s1+=exp(ps[i][j]);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      for(j=i+1; j<=nlstate+ndeath; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        s1+=exp(ps[i][j]);
       savm=oldm;      ps[i][i]=1./(s1+1.);
       oldm=newm;      for(j=1; j<i; j++)
     }        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for(i=1; i<=nlstate+ndeath; i++)      for(j=i+1; j<=nlstate+ndeath; j++)
       for(j=1;j<=nlstate+ndeath;j++) {        ps[i][j]= exp(ps[i][j])*ps[i][i];
         po[i][j][h]=newm[i][j];      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    } /* end i */
          */  
       }    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   } /* end h */      for(jj=1; jj<= nlstate+ndeath; jj++){
   return po;        ps[ii][jj]=0;
 }        ps[ii][ii]=1;
       }
     }
 /*************** log-likelihood *************/  
 double func( double *x)  
 {    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   int i, ii, j, k, mi, d;      for(jj=1; jj<= nlstate+ndeath; jj++){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       printf("%lf ",ps[ii][jj]);
   double **out;     }
   double sw; /* Sum of weights */      printf("\n ");
   double lli; /* Individual log likelihood */      }
   long ipmx;      printf("\n ");printf("%lf ",cov[2]);*/
   /*extern weight */  /*
   /* We are differentiating ll according to initial status */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    goto end;*/
   /*for(i=1;i<imx;i++)      return ps;
 printf(" %d\n",s[4][i]);  }
   */  
   /**************** Product of 2 matrices ******************/
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
        for(mi=1; mi<= wav[i]-1; mi++){  {
       for (ii=1;ii<=nlstate+ndeath;ii++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
             for(d=0; d<dh[mi][i]; d++){    /* in, b, out are matrice of pointers which should have been initialized 
         newm=savm;       before: only the contents of out is modified. The function returns
           cov[1]=1.;       a pointer to pointers identical to out */
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    long i, j, k;
           if (cptcovn>0){    for(i=nrl; i<= nrh; i++)
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];      for(k=ncolol; k<=ncoloh; k++)
             }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out[i][k] +=in[i][j]*b[j][k];
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;    return out;
           oldm=newm;  }
   
   
       } /* end mult */  /************* Higher Matrix Product ***************/
      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  {
       ipmx +=1;    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
       sw += weight[i];       duration (i.e. until
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
     } /* end of wave */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   } /* end of individual */       (typically every 2 years instead of every month which is too big).
        Model is determined by parameters x and covariates have to be 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];       included manually here. 
   /* 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 */       */
   return -l;  
 }    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
     double **newm;
 /*********** Maximum Likelihood Estimation ***************/  
     /* Hstepm could be zero and should return the unit matrix */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for (i=1;i<=nlstate+ndeath;i++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   int i,j, iter;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   double **xi,*delti;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double fret;      }
   xi=matrix(1,npar,1,npar);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (i=1;i<=npar;i++)    for(h=1; h <=nhstepm; h++){
     for (j=1;j<=npar;j++)      for(d=1; d <=hstepm; d++){
       xi[i][j]=(i==j ? 1.0 : 0.0);        newm=savm;
   printf("Powell\n");        /* Covariates have to be included here again */
   powell(p,xi,npar,ftol,&iter,&fret,func);        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 }        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double  **a,**y,*x,pd;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double **hess;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   int i, j,jk;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int *indx;        savm=oldm;
         oldm=newm;
   double hessii(double p[], double delta, int theta, double delti[]);      }
   double hessij(double p[], double delti[], int i, int j);      for(i=1; i<=nlstate+ndeath; i++)
   void lubksb(double **a, int npar, int *indx, double b[]) ;        for(j=1;j<=nlstate+ndeath;j++) {
   void ludcmp(double **a, int npar, int *indx, double *d) ;          po[i][j][h]=newm[i][j];
           /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
   hess=matrix(1,npar,1,npar);        }
     } /* end h */
   printf("\nCalculation of the hessian matrix. Wait...\n");    return po;
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /*************** log-likelihood *************/
   }  double func( double *x)
   {
   for (i=1;i<=npar;i++) {    int i, ii, j, k, mi, d, kk;
     for (j=1;j<=npar;j++)  {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       if (j>i) {    double **out;
         printf(".%d%d",i,j);fflush(stdout);    double sw; /* Sum of weights */
         hess[i][j]=hessij(p,delti,i,j);    double lli; /* Individual log likelihood */
         hess[j][i]=hess[i][j];    long ipmx;
       }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
   }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   printf("\n");    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    */
      cov[1]=1.;
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   x=vector(1,npar);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   indx=ivector(1,npar);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (i=1;i<=npar;i++)      for(mi=1; mi<= wav[i]-1; mi++){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for (ii=1;ii<=nlstate+ndeath;ii++)
   ludcmp(a,npar,indx,&pd);          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(d=0; d<dh[mi][i]; d++){
   for (j=1;j<=npar;j++) {          newm=savm;
     for (i=1;i<=npar;i++) x[i]=0;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     x[j]=1;          for (kk=1; kk<=cptcovage;kk++) {
     lubksb(a,npar,indx,x);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=1;i<=npar;i++){          }
       matcov[i][j]=x[i];          
     }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   printf("\n#Hessian matrix#\n");          oldm=newm;
   for (i=1;i<=npar;i++) {          
     for (j=1;j<=npar;j++) {          
       printf("%.3e ",hess[i][j]);        } /* end mult */
     }        
     printf("\n");        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;
   /* Recompute Inverse */        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++) a[i][j]=matcov[i][j];      } /* end of wave */
   ludcmp(a,npar,indx,&pd);    } /* end of individual */
   
   /*  printf("\n#Hessian matrix recomputed#\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (j=1;j<=npar;j++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for (i=1;i<=npar;i++) x[i]=0;    return -l;
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /*********** Maximum Likelihood Estimation ***************/
       printf("%.3e ",y[i][j]);  
     }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     printf("\n");  {
   }    int i,j, iter;
   */    double **xi,*delti;
     double fret;
   free_matrix(a,1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   free_matrix(y,1,npar,1,npar);    for (i=1;i<=npar;i++)
   free_vector(x,1,npar);      for (j=1;j<=npar;j++)
   free_ivector(indx,1,npar);        xi[i][j]=(i==j ? 1.0 : 0.0);
   free_matrix(hess,1,npar,1,npar);    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));
     fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 /*************** hessian matrix ****************/    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 double hessii( double x[], double delta, int theta, double delti[])  
 {  }
   int i;  
   int l=1, lmax=20;  /**** Computes Hessian and covariance matrix ***/
   double k1,k2;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double p2[NPARMAX+1];  {
   double res;    double  **a,**y,*x,pd;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double **hess;
   double fx;    int i, j,jk;
   int k=0,kmax=10;    int *indx;
   double l1;  
     double hessii(double p[], double delta, int theta, double delti[]);
   fx=func(x);    double hessij(double p[], double delti[], int i, int j);
   for (i=1;i<=npar;i++) p2[i]=x[i];    void lubksb(double **a, int npar, int *indx, double b[]) ;
   for(l=0 ; l <=lmax; l++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
     l1=pow(10,l);  
     delts=delt;    hess=matrix(1,npar,1,npar);
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);    printf("\nCalculation of the hessian matrix. Wait...\n");
       p2[theta]=x[theta] +delt;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       k1=func(p2)-fx;    for (i=1;i<=npar;i++){
       p2[theta]=x[theta]-delt;      printf("%d",i);fflush(stdout);
       k2=func(p2)-fx;      fprintf(ficlog,"%d",i);fflush(ficlog);
       /*res= (k1-2.0*fx+k2)/delt/delt; */      hess[i][i]=hessii(p,ftolhess,i,delti);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      /*printf(" %f ",p[i]);*/
            /*printf(" %lf ",hess[i][i]);*/
 #ifdef DEBUG    }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    
 #endif    for (i=1;i<=npar;i++) {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      for (j=1;j<=npar;j++)  {
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        if (j>i) { 
         k=kmax;          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          hess[i][j]=hessij(p,delti,i,j);
         k=kmax; l=lmax*10.;          hess[j][i]=hess[i][j];    
       }          /*printf(" %lf ",hess[i][j]);*/
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        }
         delts=delt;      }
       }    }
     }    printf("\n");
   }    fprintf(ficlog,"\n");
   delti[theta]=delts;  
   return res;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 }    
     a=matrix(1,npar,1,npar);
 double hessij( double x[], double delti[], int thetai,int thetaj)    y=matrix(1,npar,1,npar);
 {    x=vector(1,npar);
   int i;    indx=ivector(1,npar);
   int l=1, l1, lmax=20;    for (i=1;i<=npar;i++)
   double k1,k2,k3,k4,res,fx;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double p2[NPARMAX+1];    ludcmp(a,npar,indx,&pd);
   int k;  
     for (j=1;j<=npar;j++) {
   fx=func(x);      for (i=1;i<=npar;i++) x[i]=0;
   for (k=1; k<=2; k++) {      x[j]=1;
     for (i=1;i<=npar;i++) p2[i]=x[i];      lubksb(a,npar,indx,x);
     p2[thetai]=x[thetai]+delti[thetai]/k;      for (i=1;i<=npar;i++){ 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        matcov[i][j]=x[i];
     k1=func(p2)-fx;      }
      }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    printf("\n#Hessian matrix#\n");
     k2=func(p2)-fx;    fprintf(ficlog,"\n#Hessian matrix#\n");
      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]);
     k3=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");
     k4=func(p2)-fx;    }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG    /* Recompute Inverse */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    for (i=1;i<=npar;i++)
 #endif      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   }    ludcmp(a,npar,indx,&pd);
   return res;  
 }    /*  printf("\n#Hessian matrix recomputed#\n");
   
 /************** Inverse of matrix **************/    for (j=1;j<=npar;j++) {
 void ludcmp(double **a, int n, int *indx, double *d)      for (i=1;i<=npar;i++) x[i]=0;
 {      x[j]=1;
   int i,imax,j,k;      lubksb(a,npar,indx,x);
   double big,dum,sum,temp;      for (i=1;i<=npar;i++){ 
   double *vv;        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   vv=vector(1,n);        fprintf(ficlog,"%.3e ",y[i][j]);
   *d=1.0;      }
   for (i=1;i<=n;i++) {      printf("\n");
     big=0.0;      fprintf(ficlog,"\n");
     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;    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
   for (j=1;j<=n;j++) {    free_vector(x,1,npar);
     for (i=1;i<j;i++) {    free_ivector(indx,1,npar);
       sum=a[i][j];    free_matrix(hess,1,npar,1,npar);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  /*************** hessian matrix ****************/
       sum=a[i][j];  double hessii( double x[], double delta, int theta, double delti[])
       for (k=1;k<j;k++)  {
         sum -= a[i][k]*a[k][j];    int i;
       a[i][j]=sum;    int l=1, lmax=20;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    double k1,k2;
         big=dum;    double p2[NPARMAX+1];
         imax=i;    double res;
       }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     }    double fx;
     if (j != imax) {    int k=0,kmax=10;
       for (k=1;k<=n;k++) {    double l1;
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    fx=func(x);
         a[j][k]=dum;    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
       *d = -(*d);      l1=pow(10,l);
       vv[imax]=vv[j];      delts=delt;
     }      for(k=1 ; k <kmax; k=k+1){
     indx[j]=imax;        delt = delta*(l1*k);
     if (a[j][j] == 0.0) a[j][j]=TINY;        p2[theta]=x[theta] +delt;
     if (j != n) {        k1=func(p2)-fx;
       dum=1.0/(a[j][j]);        p2[theta]=x[theta]-delt;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        k2=func(p2)-fx;
     }        /*res= (k1-2.0*fx+k2)/delt/delt; */
   }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   free_vector(vv,1,n);  /* Doesn't work */        
 ;  #ifdef DEBUG
 }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         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);
 void lubksb(double **a, int n, int *indx, double b[])  #endif
 {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   int i,ii=0,ip,j;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   double sum;          k=kmax;
          }
   for (i=1;i<=n;i++) {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     ip=indx[i];          k=kmax; l=lmax*10.;
     sum=b[ip];        }
     b[ip]=b[i];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     if (ii)          delts=delt;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        }
     else if (sum) ii=i;      }
     b[i]=sum;    }
   }    delti[theta]=delts;
   for (i=n;i>=1;i--) {    return res; 
     sum=b[i];    
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  }
     b[i]=sum/a[i][i];  
   }  double hessij( double x[], double delti[], int thetai,int thetaj)
 }  {
     int i;
 /************ Frequencies ********************/    int l=1, l1, lmax=20;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)    double k1,k2,k3,k4,res,fx;
 {  /* Some frequencies */    double p2[NPARMAX+1];
      int k;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    fx=func(x);
   double *pp;    for (k=1; k<=2; k++) {
   double pos;      for (i=1;i<=npar;i++) p2[i]=x[i];
   FILE *ficresp;      p2[thetai]=x[thetai]+delti[thetai]/k;
   char fileresp[FILENAMELENGTH];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=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);      k2=func(p2)-fx;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    
     printf("Problem with prevalence resultfile: %s\n", fileresp);      p2[thetai]=x[thetai]-delti[thetai]/k;
     exit(0);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k3=func(p2)-fx;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    
   j1=0;      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   j=cptcovn;      k4=func(p2)-fx;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
   for(k1=1; k1<=j;k1++){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
    for(i1=1; i1<=ncodemax[k1];i1++){      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);
        j1++;  #endif
     }
         for (i=-1; i<=nlstate+ndeath; i++)      return res;
          for (jk=-1; jk<=nlstate+ndeath; jk++)    }
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  /************** Inverse of matrix **************/
          void ludcmp(double **a, int n, int *indx, double *d) 
        for (i=1; i<=imx; i++) {  { 
          bool=1;    int i,imax,j,k; 
          if  (cptcovn>0) {    double big,dum,sum,temp; 
            for (z1=1; z1<=cptcovn; z1++)    double *vv; 
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;   
          }    vv=vector(1,n); 
           if (bool==1) {    *d=1.0; 
            for(m=firstpass; m<=lastpass-1; m++){    for (i=1;i<=n;i++) { 
              if(agev[m][i]==0) agev[m][i]=agemax+1;      big=0.0; 
              if(agev[m][i]==1) agev[m][i]=agemax+2;      for (j=1;j<=n;j++) 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        if ((temp=fabs(a[i][j])) > big) big=temp; 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
            }      vv[i]=1.0/big; 
          }    } 
        }    for (j=1;j<=n;j++) { 
         if  (cptcovn>0) {      for (i=1;i<j;i++) { 
          fprintf(ficresp, "\n#Variable");        sum=a[i][j]; 
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
        }        a[i][j]=sum; 
        fprintf(ficresp, "\n#");      } 
        for(i=1; i<=nlstate;i++)      big=0.0; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for (i=j;i<=n;i++) { 
        fprintf(ficresp, "\n");        sum=a[i][j]; 
                for (k=1;k<j;k++) 
   for(i=(int)agemin; i <= (int)agemax+3; i++){          sum -= a[i][k]*a[k][j]; 
     if(i==(int)agemax+3)        a[i][j]=sum; 
       printf("Total");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     else          big=dum; 
       printf("Age %d", i);          imax=i; 
     for(jk=1; jk <=nlstate ; jk++){        } 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } 
         pp[jk] += freq[jk][m][i];      if (j != imax) { 
     }        for (k=1;k<=n;k++) { 
     for(jk=1; jk <=nlstate ; jk++){          dum=a[imax][k]; 
       for(m=-1, pos=0; m <=0 ; m++)          a[imax][k]=a[j][k]; 
         pos += freq[jk][m][i];          a[j][k]=dum; 
       if(pp[jk]>=1.e-10)        } 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        *d = -(*d); 
       else        vv[imax]=vv[j]; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      } 
     }      indx[j]=imax; 
     for(jk=1; jk <=nlstate ; jk++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      if (j != n) { 
         pp[jk] += freq[jk][m][i];        dum=1.0/(a[j][j]); 
     }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)      } 
       pos += pp[jk];    } 
     for(jk=1; jk <=nlstate ; jk++){    free_vector(vv,1,n);  /* Doesn't work */
       if(pos>=1.e-5)  ;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  } 
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  void lubksb(double **a, int n, int *indx, double b[]) 
       if( i <= (int) agemax){  { 
         if(pos>=1.e-5)    int i,ii=0,ip,j; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    double sum; 
       else   
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    for (i=1;i<=n;i++) { 
       }      ip=indx[i]; 
     }      sum=b[ip]; 
     for(jk=-1; jk <=nlstate+ndeath; jk++)      b[ip]=b[i]; 
       for(m=-1; m <=nlstate+ndeath; m++)      if (ii) 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     if(i <= (int) agemax)      else if (sum) ii=i; 
       fprintf(ficresp,"\n");      b[i]=sum; 
     printf("\n");    } 
     }    for (i=n;i>=1;i--) { 
     }      sum=b[i]; 
  }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
   fclose(ficresp);    } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  } 
   free_vector(pp,1,nlstate);  
   /************ Frequencies ********************/
 }  /* End of Freq */  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 */
 /************* Waves Concatenation ***************/    
     int i, m, jk, k1,i1, j1, bool, z1,z2,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)    int first;
 {    double ***freq; /* Frequencies */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    double *pp;
      Death is a valid wave (if date is known).    double pos, k2, dateintsum=0,k2cpt=0;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    FILE *ficresp;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    char fileresp[FILENAMELENGTH];
      and mw[mi+1][i]. dh depends on stepm.    
      */    pp=vector(1,nlstate);
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   int i, mi, m;    strcpy(fileresp,"p");
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    strcat(fileresp,fileres);
 float sum=0.;    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   for(i=1; i<=imx; i++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     mi=0;      exit(0);
     m=firstpass;    }
     while(s[m][i] <= nlstate){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
       if(s[m][i]>=1)    j1=0;
         mw[++mi][i]=m;    
       if(m >=lastpass)    j=cptcoveff;
         break;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       else  
         m++;    first=1;
     }/* end while */  
     if (s[m][i] > nlstate){    for(k1=1; k1<=j;k1++){
       mi++;     /* Death is another wave */      for(i1=1; i1<=ncodemax[k1];i1++){
       /* if(mi==0)  never been interviewed correctly before death */        j1++;
          /* Only death is a correct wave */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       mw[mi][i]=m;          scanf("%d", i);*/
     }        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     wav[i]=mi;            for(m=agemin; m <= agemax+3; m++)
     if(mi==0)              freq[i][jk][m]=0;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        
   }        dateintsum=0;
         k2cpt=0;
   for(i=1; i<=imx; i++){        for (i=1; i<=imx; i++) {
     for(mi=1; mi<wav[i];mi++){          bool=1;
       if (stepm <=0)          if  (cptcovn>0) {
         dh[mi][i]=1;            for (z1=1; z1<=cptcoveff; z1++) 
       else{              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         if (s[mw[mi+1][i]][i] > nlstate) {                bool=0;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          }
           if(j=0) j=1;  /* Survives at least one month after exam */          if (bool==1) {
         }            for(m=firstpass; m<=lastpass; m++){
         else{              k2=anint[m][i]+(mint[m][i]/12.);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           k=k+1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
           if (j >= jmax) jmax=j;                if(agev[m][i]==1) agev[m][i]=agemax+2;
           else if (j <= jmin)jmin=j;                if (m<lastpass) {
           sum=sum+j;                  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];
         jk= j/stepm;                }
         jl= j -jk*stepm;                
         ju= j -(jk+1)*stepm;                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
         if(jl <= -ju)                  dateintsum=dateintsum+k2;
           dh[mi][i]=jk;                  k2cpt++;
         else                }
           dh[mi][i]=jk+1;              }
         if(dh[mi][i]==0)            }
           dh[mi][i]=1; /* At least one step */          }
       }        }
     }         
   }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);  
 }        if  (cptcovn>0) {
 /*********** Tricode ****************************/          fprintf(ficresp, "\n#********** Variable "); 
 void tricode(int *Tvar, int **nbcode, int imx)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 {          fprintf(ficresp, "**********\n#");
   int Ndum[80],ij, k, j, i;        }
   int cptcode=0;        for(i=1; i<=nlstate;i++) 
   for (k=0; k<79; k++) Ndum[k]=0;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   for (k=1; k<=7; k++) ncodemax[k]=0;        fprintf(ficresp, "\n");
          
   for (j=1; j<=cptcovn; j++) {        for(i=(int)agemin; i <= (int)agemax+3; i++){
     for (i=1; i<=imx; i++) {          if(i==(int)agemax+3){
       ij=(int)(covar[Tvar[j]][i]);            fprintf(ficlog,"Total");
       Ndum[ij]++;          }else{
       if (ij > cptcode) cptcode=ij;            if(first==1){
     }              first=0;
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/              printf("See log file for details...\n");
     for (i=0; i<=cptcode; i++) {            }
       if(Ndum[i]!=0) ncodemax[j]++;            fprintf(ficlog,"Age %d", i);
     }          }
            for(jk=1; jk <=nlstate ; jk++){
     ij=1;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for (i=1; i<=ncodemax[j]; i++) {              pp[jk] += freq[jk][m][i]; 
       for (k=0; k<=79; k++) {          }
         if (Ndum[k] != 0) {          for(jk=1; jk <=nlstate ; jk++){
           nbcode[Tvar[j]][ij]=k;            for(m=-1, pos=0; m <=0 ; m++)
           ij++;              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
         if (ij > ncodemax[j]) break;              if(first==1){
       }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }              }
   }                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
   }              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /*********** Health Expectancies ****************/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          }
 {  
   /* Health expectancies */          for(jk=1; jk <=nlstate ; jk++){
   int i, j, nhstepm, hstepm, h;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double age, agelim,hf;              pp[jk] += freq[jk][m][i];
   double ***p3mat;          }
    
   fprintf(ficreseij,"# Health expectancies\n");          for(jk=1,pos=0; jk <=nlstate ; jk++)
   fprintf(ficreseij,"# Age");            pos += pp[jk];
   for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j<=nlstate;j++)            if(pos>=1.e-5){
       fprintf(ficreseij," %1d-%1d",i,j);              if(first==1)
   fprintf(ficreseij,"\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   hstepm=1*YEARM; /*  Every j years of age (in month) */            }else{
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   agelim=AGESUP;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     /* nhstepm age range expressed in number of stepm */            if( i <= (int) agemax){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);              if(pos>=1.e-5){
     /* Typically if 20 years = 20*12/6=40 stepm */                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
     if (stepm >= YEARM) hstepm=1;                probs[i][jk][j1]= pp[jk]/pos;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              else
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              }
           }
           
     for(i=1; i<=nlstate;i++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
       for(j=1; j<=nlstate;j++)            for(m=-1; m <=nlstate+ndeath; m++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){              if(freq[jk][m][i] !=0 ) {
           eij[i][j][(int)age] +=p3mat[i][j][h];              if(first==1)
         }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                    fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     hf=1;              }
     if (stepm >= YEARM) hf=stepm/YEARM;          if(i <= (int) agemax)
     fprintf(ficreseij,"%.0f",age );            fprintf(ficresp,"\n");
     for(i=1; i<=nlstate;i++)          if(first==1)
       for(j=1; j<=nlstate;j++){            printf("Others in log...\n");
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          fprintf(ficlog,"\n");
       }        }
     fprintf(ficreseij,"\n");      }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
   }    dateintmean=dateintsum/k2cpt; 
 }   
     fclose(ficresp);
 /************ Variance ******************/    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
 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)    free_vector(pp,1,nlstate);
 {    
   /* Variance of health expectancies */    /* End of Freq */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  }
   double **newm;  
   double **dnewm,**doldm;  /************ Prevalence ********************/
   int i, j, nhstepm, hstepm, h;  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)
   int k, cptcode;  {  /* Some frequencies */
    double *xp;   
   double **gp, **gm;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   double ***gradg, ***trgradg;    double ***freq; /* Frequencies */
   double ***p3mat;    double *pp;
   double age,agelim;    double pos, k2;
   int theta;  
     pp=vector(1,nlstate);
    fprintf(ficresvij,"# Covariances of life expectancies\n");    
   fprintf(ficresvij,"# Age");    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   for(i=1; i<=nlstate;i++)    j1=0;
     for(j=1; j<=nlstate;j++)    
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    j=cptcoveff;
   fprintf(ficresvij,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   xp=vector(1,npar);    for(k1=1; k1<=j;k1++){
   dnewm=matrix(1,nlstate,1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
   doldm=matrix(1,nlstate,1,nlstate);        j1++;
          
   hstepm=1*YEARM; /* Every year of age */        for (i=-1; i<=nlstate+ndeath; i++)  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   agelim = AGESUP;            for(m=agemin; m <= agemax+3; m++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              freq[i][jk][m]=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       
     if (stepm >= YEARM) hstepm=1;        for (i=1; i<=imx; i++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          bool=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if  (cptcovn>0) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            for (z1=1; z1<=cptcoveff; z1++) 
     gp=matrix(0,nhstepm,1,nlstate);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     gm=matrix(0,nhstepm,1,nlstate);                bool=0;
           } 
     for(theta=1; theta <=npar; theta++){          if (bool==1) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */            for(m=firstpass; m<=lastpass; m++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              k2=anint[m][i]+(mint[m][i]/12.);
       }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  if(agev[m][i]==0) agev[m][i]=agemax+1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                if(agev[m][i]==1) agev[m][i]=agemax+2;
       for(j=1; j<= nlstate; j++){                if (m<lastpass) {
         for(h=0; h<=nhstepm; h++){                  if (calagedate>0) 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                  else
         }                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       }                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
                    }
       for(i=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);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(j=1; j<= nlstate; j++){        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
         for(h=0; h<=nhstepm; h++){          for(jk=1; jk <=nlstate ; jk++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              pp[jk] += freq[jk][m][i]; 
         }          }
       }          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<= nlstate; j++)            for(m=-1, pos=0; m <=0 ; m++)
         for(h=0; h<=nhstepm; h++){              pos += freq[jk][m][i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          }
         }          
     } /* End theta */          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              pp[jk] += freq[jk][m][i];
           }
     for(h=0; h<=nhstepm; h++)          
       for(j=1; j<=nlstate;j++)          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
         for(theta=1; theta <=npar; theta++)          
           trgradg[h][j][theta]=gradg[h][theta][j];          for(jk=1; jk <=nlstate ; jk++){    
             if( i <= (int) agemax){
     for(i=1;i<=nlstate;i++)              if(pos>=1.e-5){
       for(j=1;j<=nlstate;j++)                probs[i][jk][j1]= pp[jk]/pos;
         vareij[i][j][(int)age] =0.;              }
     for(h=0;h<=nhstepm;h++){            }
       for(k=0;k<=nhstepm;k++){          }/* end jk */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        }/* end i */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      } /* end i1 */
         for(i=1;i<=nlstate;i++)    } /* end k1 */
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];    
       }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     }    free_vector(pp,1,nlstate);
     h=1;    
     if (stepm >= YEARM) h=stepm/YEARM;  }  /* End of Freq */
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /************* Waves Concatenation ***************/
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       }  {
     fprintf(ficresvij,"\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     free_matrix(gp,0,nhstepm,1,nlstate);       Death is a valid wave (if date is known).
     free_matrix(gm,0,nhstepm,1,nlstate);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);       dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);       and mw[mi+1][i]. dh depends on stepm.
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       */
   } /* End age */  
      int i, mi, m;
   free_vector(xp,1,npar);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   free_matrix(doldm,1,nlstate,1,npar);       double sum=0., jmean=0.;*/
   free_matrix(dnewm,1,nlstate,1,nlstate);    int first;
     int j, k=0,jk, ju, jl;
 }    double sum=0.;
     first=0;
 /************ Variance of prevlim ******************/    jmin=1e+5;
 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)    jmax=-1;
 {    jmean=0.;
   /* Variance of prevalence limit */    for(i=1; i<=imx; i++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      mi=0;
   double **newm;      m=firstpass;
   double **dnewm,**doldm;      while(s[m][i] <= nlstate){
   int i, j, nhstepm, hstepm;        if(s[m][i]>=1)
   int k, cptcode;          mw[++mi][i]=m;
   double *xp;        if(m >=lastpass)
   double *gp, *gm;          break;
   double **gradg, **trgradg;        else
   double age,agelim;          m++;
   int theta;      }/* end while */
          if (s[m][i] > nlstate){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        mi++;     /* Death is another wave */
   fprintf(ficresvpl,"# Age");        /* if(mi==0)  never been interviewed correctly before death */
   for(i=1; i<=nlstate;i++)           /* Only death is a correct wave */
       fprintf(ficresvpl," %1d-%1d",i,i);        mw[mi][i]=m;
   fprintf(ficresvpl,"\n");      }
   
   xp=vector(1,npar);      wav[i]=mi;
   dnewm=matrix(1,nlstate,1,npar);      if(mi==0){
   doldm=matrix(1,nlstate,1,nlstate);        if(first==0){
            printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
   hstepm=1*YEARM; /* Every year of age */          first=1;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        }
   agelim = AGESUP;        if(first==1){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;      } /* end mi==0 */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    for(i=1; i<=imx; i++){
     gm=vector(1,nlstate);      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
     for(theta=1; theta <=npar; theta++){          dh[mi][i]=1;
       for(i=1; i<=npar; i++){ /* Computes gradient */        else{
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          if (s[mw[mi+1][i]][i] > nlstate) {
       }            if (agedc[i] < 2*AGESUP) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       for(i=1;i<=nlstate;i++)            if(j==0) j=1;  /* Survives at least one month after exam */
         gp[i] = prlim[i][i];            k=k+1;
                if (j >= jmax) jmax=j;
       for(i=1; i<=npar; i++) /* Computes gradient */            if (j <= jmin) jmin=j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            sum=sum+j;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            /*if (j<0) printf("j=%d num=%d \n",j,i); */
       for(i=1;i<=nlstate;i++)            }
         gm[i] = prlim[i][i];          }
           else{
       for(i=1;i<=nlstate;i++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            k=k+1;
     } /* End theta */            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
     trgradg =matrix(1,nlstate,1,npar);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             sum=sum+j;
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          jk= j/stepm;
         trgradg[j][theta]=gradg[theta][j];          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
     for(i=1;i<=nlstate;i++)          if(jl <= -ju)
       varpl[i][(int)age] =0.;            dh[mi][i]=jk;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          else
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            dh[mi][i]=jk+1;
     for(i=1;i<=nlstate;i++)          if(dh[mi][i]==0)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            dh[mi][i]=1; /* At least one step */
         }
     fprintf(ficresvpl,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    jmean=sum/k;
     fprintf(ficresvpl,"\n");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     free_vector(gp,1,nlstate);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     free_vector(gm,1,nlstate);   }
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  /*********** Tricode ****************************/
   } /* End age */  void tricode(int *Tvar, int **nbcode, int imx)
   {
   free_vector(xp,1,npar);    int Ndum[20],ij=1, k, j, i;
   free_matrix(doldm,1,nlstate,1,npar);    int cptcode=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);    cptcoveff=0; 
    
 }    for (k=0; k<19; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 /***********************************************/      for (i=1; i<=imx; i++) {
 /**************** Main Program *****************/        ij=(int)(covar[Tvar[j]][i]);
 /***********************************************/        Ndum[ij]++; 
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 /*int main(int argc, char *argv[])*/        if (ij > cptcode) cptcode=ij; 
 int main()      }
 {  
       for (i=0; i<=cptcode; i++) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;        if(Ndum[i]!=0) ncodemax[j]++;
   double agedeb, agefin,hf;      }
   double agemin=1.e20, agemax=-1.e20;      ij=1; 
   
   double fret;  
   double **xi,tmp,delta;      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<=19; k++) {
   double dum; /* Dummy variable */          if (Ndum[k] != 0) {
   double ***p3mat;            nbcode[Tvar[j]][ij]=k; 
   int *indx;            
   char line[MAXLINE], linepar[MAXLINE];            ij++;
   char title[MAXLINE];          }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          if (ij > ncodemax[j]) break; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];        }  
   char filerest[FILENAMELENGTH];      } 
   char fileregp[FILENAMELENGTH];    }  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;   for (k=0; k<19; k++) Ndum[k]=0;
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;   for (i=1; i<=ncovmodel-2; i++) {
   int ju,jl, mi;     ij=Tvar[i];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;     Ndum[ij]++; 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;   }
    
   int hstepm, nhstepm;   ij=1;
   double bage, fage, age, agelim, agebase;   for (i=1; i<=10; i++) {
   double ftolpl=FTOL;     if((Ndum[i]!=0) && (i<=ncovcol)){
   double **prlim;       Tvaraff[ij]=i; 
   double *severity;       ij++;
   double ***param; /* Matrix of parameters */     }
   double  *p;   }
   double **matcov; /* Matrix of covariance */   
   double ***delti3; /* Scale */   cptcoveff=ij-1;
   double *delti; /* Scale */  }
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  /*********** Health Expectancies ****************/
   double *epj, vepp;  
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";  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 )
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   {
   char z[1]="c", occ;    /* Health expectancies */
 #include <sys/time.h>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
 #include <time.h>    double age, agelim, hf;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double ***p3mat,***varhe;
   /* long total_usecs;    double **dnewm,**doldm;
   struct timeval start_time, end_time;    double *xp;
      double **gp, **gm;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double ***gradg, ***trgradg;
     int theta;
   
   printf("\nIMACH, Version 0.64a");    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   printf("\nEnter the parameter file name: ");    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*2,1,npar);
 #ifdef windows    doldm=matrix(1,nlstate*2,1,nlstate*2);
   scanf("%s",pathtot);    
   getcwd(pathcd, size);    fprintf(ficreseij,"# Health expectancies\n");
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficreseij,"# Age");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for(i=1; i<=nlstate;i++)
   /* cutv(path,optionfile,pathtot,'\\');*/      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
 split(pathtot, path,optionfile);    fprintf(ficreseij,"\n");
   chdir(path);  
   replace(pathc,path);    if(estepm < stepm){
 #endif      printf ("Problem %d lower than %d\n",estepm, stepm);
 #ifdef unix    }
   scanf("%s",optionfile);    else  hstepm=estepm;   
 #endif    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 /*-------- arguments in the command line --------*/     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
   strcpy(fileres,"r");     * progression inbetween and thus overestimating or underestimating according
   strcat(fileres, optionfile);     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   /*---------arguments file --------*/     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     * curvature will be obtained if estepm is as small as stepm. */
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   strcpy(filereso,"o");       nstepm is the number of stepm from age to agelin. 
   strcat(filereso,fileres);       Look at hpijx to understand the reason of that which relies in memory size
   if((ficparo=fopen(filereso,"w"))==NULL) {       and note for a fixed period like estepm months */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   /* Reads comments: lines beginning with '#' */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   while((c=getc(ficpar))=='#' && c!= EOF){       results. So we changed our mind and took the option of the best precision.
     ungetc(c,ficpar);    */
     fgets(line, MAXLINE, ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     puts(line);  
     fputs(line,ficparo);    agelim=AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   ungetc(c,ficpar);      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   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);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   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);      /* if (stepm >= YEARM) hstepm=1;*/
   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);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   covar=matrix(1,NCOVMAX,1,n);          gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   if (strlen(model)<=1) cptcovn=0;      gp=matrix(0,nhstepm,1,nlstate*2);
   else {      gm=matrix(0,nhstepm,1,nlstate*2);
     j=0;  
     j=nbocc(model,'+');      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     cptcovn=j+1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   /* Read guess parameters */      /* Computing Variances of health expectancies */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){       for(theta=1; theta <=npar; theta++){
     ungetc(c,ficpar);        for(i=1; i<=npar; i++){ 
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     puts(line);        }
     fputs(line,ficparo);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }    
   ungetc(c,ficpar);        cptj=0;
          for(j=1; j<= nlstate; j++){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for(i=1; i<=nlstate; i++){
     for(i=1; i <=nlstate; i++)            cptj=cptj+1;
     for(j=1; j <=nlstate+ndeath-1; j++){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       fprintf(ficparo,"%1d%1d",i1,j1);            }
       printf("%1d%1d",i,j);          }
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);       
         printf(" %lf",param[i][j][k]);       
         fprintf(ficparo," %lf",param[i][j][k]);        for(i=1; i<=npar; i++) 
       }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fscanf(ficpar,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       printf("\n");        
       fprintf(ficparo,"\n");        cptj=0;
     }        for(j=1; j<= nlstate; j++){
            for(i=1;i<=nlstate;i++){
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            cptj=cptj+1;
   p=param[1][1];            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        for(j=1; j<= nlstate*2; j++)
     puts(line);          for(h=0; h<=nhstepm-1; h++){
     fputs(line,ficparo);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   ungetc(c,ficpar);       } 
      
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  /* End theta */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);       for(h=0; h<=nhstepm-1; h++)
       printf("%1d%1d",i,j);        for(j=1; j<=nlstate*2;j++)
       fprintf(ficparo,"%1d%1d",i1,j1);          for(theta=1; theta <=npar; theta++)
       for(k=1; k<=ncovmodel;k++){            trgradg[h][j][theta]=gradg[h][theta][j];
         fscanf(ficpar,"%le",&delti3[i][j][k]);       
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);       for(i=1;i<=nlstate*2;i++)
       }        for(j=1;j<=nlstate*2;j++)
       fscanf(ficpar,"\n");          varhe[i][j][(int)age] =0.;
       printf("\n");  
       fprintf(ficparo,"\n");       printf("%d|",(int)age);fflush(stdout);
     }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }       for(h=0;h<=nhstepm-1;h++){
   delti=delti3[1][1];        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
   /* Reads comments: lines beginning with '#' */          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1;i<=nlstate*2;i++)
     ungetc(c,ficpar);            for(j=1;j<=nlstate*2;j++)
     fgets(line, MAXLINE, ficpar);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     puts(line);        }
     fputs(line,ficparo);      }
   }      /* Computing expectancies */
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   matcov=matrix(1,npar,1,npar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   for(i=1; i <=npar; i++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fscanf(ficpar,"%s",&str);            
     printf("%s",str);  /* 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]);*/
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);      fprintf(ficreseij,"%3.0f",age );
       fprintf(ficparo," %.5le",matcov[i][j]);      cptj=0;
     }      for(i=1; i<=nlstate;i++)
     fscanf(ficpar,"\n");        for(j=1; j<=nlstate;j++){
     printf("\n");          cptj++;
     fprintf(ficparo,"\n");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
   for(i=1; i <=npar; i++)      fprintf(ficreseij,"\n");
     for(j=i+1;j<=npar;j++)     
       matcov[i][j]=matcov[j][i];      free_matrix(gm,0,nhstepm,1,nlstate*2);
          free_matrix(gp,0,nhstepm,1,nlstate*2);
   printf("\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
       free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    if(mle==1){    }
     /*-------- data file ----------*/    printf("\n");
     if((ficres =fopen(fileres,"w"))==NULL) {    fprintf(ficlog,"\n");
       printf("Problem with resultfile: %s\n", fileres);goto end;  
     }    free_vector(xp,1,npar);
     fprintf(ficres,"#%s\n",version);    free_matrix(dnewm,1,nlstate*2,1,npar);
        free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     if((fic=fopen(datafile,"r"))==NULL)    {    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
       printf("Problem with datafile: %s\n", datafile);goto end;  }
     }  
   /************ Variance ******************/
     n= lastobs;  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)
     severity = vector(1,maxwav);  {
     outcome=imatrix(1,maxwav+1,1,n);    /* Variance of health expectancies */
     num=ivector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     moisnais=vector(1,n);    /* double **newm;*/
     annais=vector(1,n);    double **dnewm,**doldm;
     moisdc=vector(1,n);    double **dnewmp,**doldmp;
     andc=vector(1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     agedc=vector(1,n);    int k, cptcode;
     cod=ivector(1,n);    double *xp;
     weight=vector(1,n);    double **gp, **gm;  /* for var eij */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double ***gradg, ***trgradg; /*for var eij */
     mint=matrix(1,maxwav,1,n);    double **gradgp, **trgradgp; /* for var p point j */
     anint=matrix(1,maxwav,1,n);    double *gpp, *gmp; /* for var p point j */
     s=imatrix(1,maxwav+1,1,n);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     adl=imatrix(1,maxwav+1,1,n);        double ***p3mat;
     tab=ivector(1,NCOVMAX);    double age,agelim, hf;
     ncodemax=ivector(1,8);    double ***mobaverage;
     int theta;
     i=1;    char digit[4];
     while (fgets(line, MAXLINE, fic) != NULL)    {    char digitp[25];
       if ((i >= firstobs) && (i <=lastobs)) {  
            char fileresprobmorprev[FILENAMELENGTH];
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    if(popbased==1){
           strcpy(line,stra);      if(mobilav==1)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        strcpy(digitp,"-populbased-mobilav-");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      else strcpy(digitp,"-populbased-nomobil-");
         }    }
            else 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      strcpy(digitp,"-stablbased-");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
     if (mobilav!=0) {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         for (j=ncov;j>=1;j--){      }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    }
         }  
         num[i]=atol(stra);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
         /*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("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
         i=i+1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       }    strcat(fileresprobmorprev,fileres);
     }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
     /*scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   imx=i-1; /* Number of individuals */    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /* Calculation of the number of parameter from char model*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   Tvar=ivector(1,8);        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);
   if (strlen(model) >1){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     j=0;      fprintf(ficresprobmorprev," p.%-d SE",j);
     j=nbocc(model,'+');      for(i=1; i<=nlstate;i++)
     cptcovn=j+1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
        }  
     strcpy(modelsav,model);    fprintf(ficresprobmorprev,"\n");
     if (j==0) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     else {      exit(0);
       for(i=j; i>=1;i--){    }
         cutv(stra,strb,modelsav,'+');    else{
         if (strchr(strb,'*')) {      fprintf(ficgp,"\n# Routine varevsij");
           cutv(strd,strc,strb,'*');    }
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           cutv(strb,strc,strd,'V');      printf("Problem with html file: %s\n", optionfilehtm);
           for (k=1; k<=lastobs;k++)      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      exit(0);
         }    }
         else {cutv(strd,strc,strb,'V');    else{
         Tvar[i+1]=atoi(strc);      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");
         }      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
         strcpy(modelsav,stra);      }
       }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       cutv(strd,strc,stra,'V');  
       Tvar[1]=atoi(strc);    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");
     }    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   /*printf("tvar=%d ",Tvar[1]);      for(j=1; j<=nlstate;j++)
   scanf("%d ",i);*/        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fclose(fic);    fprintf(ficresvij,"\n");
   
     if (weightopt != 1) { /* Maximisation without weights*/    xp=vector(1,npar);
       for(i=1;i<=n;i++) weight[i]=1.0;    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     /*-calculation of age at interview from date of interview and age at death -*/    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     agev=matrix(1,maxwav,1,imx);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      
     for (i=1; i<=imx; i++)  {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    gpp=vector(nlstate+1,nlstate+ndeath);
       for(m=1; (m<= maxwav); m++){    gmp=vector(nlstate+1,nlstate+ndeath);
         if(s[m][i] >0){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           if (s[m][i] == nlstate+1) {    
             if(agedc[i]>0)    if(estepm < stepm){
               if(moisdc[i]!=99 && andc[i]!=9999)      printf ("Problem %d lower than %d\n",estepm, stepm);
               agev[m][i]=agedc[i];    }
             else{    else  hstepm=estepm;   
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /* For example we decided to compute the life expectancy with the smallest unit */
               agev[m][i]=-1;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             }       nhstepm is the number of hstepm from age to agelim 
           }       nstepm is the number of stepm from age to agelin. 
           else if(s[m][i] !=9){ /* Should no more exist */       Look at hpijx to understand the reason of that which relies in memory size
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       and note for a fixed period like k years */
             if(mint[m][i]==99 || anint[m][i]==9999)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               agev[m][i]=1;       survival function given by stepm (the optimization length). Unfortunately it
             else if(agev[m][i] <agemin){       means that if the survival funtion is printed only each two years of age and if
               agemin=agev[m][i];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       results. So we changed our mind and took the option of the best precision.
             }    */
             else if(agev[m][i] >agemax){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               agemax=agev[m][i];    agelim = AGESUP;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             /*agev[m][i]=anint[m][i]-annais[i];*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             /*   agev[m][i] = age[i]+2*m;*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           else { /* =9 */      gp=matrix(0,nhstepm,1,nlstate);
             agev[m][i]=1;      gm=matrix(0,nhstepm,1,nlstate);
             s[m][i]=-1;  
           }  
         }      for(theta=1; theta <=npar; theta++){
         else /*= 0 Unknown */        for(i=1; i<=npar; i++){ /* Computes gradient */
           agev[m][i]=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){        if (popbased==1) {
         if (s[m][i] > (nlstate+ndeath)) {          if(mobilav ==0){
           printf("Error: Wrong value in nlstate or ndeath\n");              for(i=1; i<=nlstate;i++)
           goto end;              prlim[i][i]=probs[(int)age][i][ij];
         }          }else{ /* mobilav */ 
       }            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
     
     free_vector(severity,1,maxwav);        for(j=1; j<= nlstate; j++){
     free_imatrix(outcome,1,maxwav+1,1,n);          for(h=0; h<=nhstepm; h++){
     free_vector(moisnais,1,n);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     free_vector(annais,1,n);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     free_matrix(mint,1,maxwav,1,n);          }
     free_matrix(anint,1,maxwav,1,n);        }
     free_vector(moisdc,1,n);        /* This for computing forces of mortality (h=1)as a weighted average */
     free_vector(andc,1,n);        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
           for(i=1; i<= nlstate; i++)
                gpp[j] += prlim[i][i]*p3mat[i][j][1];
     wav=ivector(1,imx);        }    
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        /* end force of mortality */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
            for(i=1; i<=npar; i++) /* Computes gradient */
     /* Concatenates waves */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
 Tcode=ivector(1,100);        if (popbased==1) {
    nbcode=imatrix(1,nvar,1,8);            if(mobilav ==0){
    ncodemax[1]=1;            for(i=1; i<=nlstate;i++)
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
    codtab=imatrix(1,100,1,10);            for(i=1; i<=nlstate;i++)
    h=0;              prlim[i][i]=mobaverage[(int)age][i][ij];
    m=pow(2,cptcovn);          }
          }
    for(k=1;k<=cptcovn; k++){  
      for(i=1; i <=(m/pow(2,k));i++){        for(j=1; j<= nlstate; j++){
        for(j=1; j <= ncodemax[k]; j++){          for(h=0; h<=nhstepm; h++){
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
            h++;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            if (h>m) h=1;codtab[h][k]=j;          }
          }        }
        }        /* 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++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
    /*for(i=1; i <=m ;i++){        }    
      for(k=1; k <=cptcovn; k++){        /* end force of mortality */
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);  
      }        for(j=1; j<= nlstate; j++) /* vareij */
      printf("\n");          for(h=0; h<=nhstepm; h++){
    }*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
    /*scanf("%d",i);*/          }
            for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    /* Calculates basic frequencies. Computes observed prevalence at single age          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        and prints on file fileres'p'. */        }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);  
       } /* End theta */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(h=0; h<=nhstepm; h++) /* veij */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     /* For Powell, parameters are in a vector p[] starting at p[1]            trgradg[h][j][theta]=gradg[h][theta][j];
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
            for(theta=1; theta <=npar; theta++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          trgradgp[j][theta]=gradgp[theta][j];
   
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     /*--------- results files --------------*/      for(i=1;i<=nlstate;i++)
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);        for(j=1;j<=nlstate;j++)
              vareij[i][j][(int)age] =0.;
    jk=1;  
    fprintf(ficres,"# Parameters\n");      for(h=0;h<=nhstepm;h++){
    printf("# Parameters\n");        for(k=0;k<=nhstepm;k++){
    for(i=1,jk=1; i <=nlstate; i++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      for(k=1; k <=(nlstate+ndeath); k++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
        if (k != i)          for(i=1;i<=nlstate;i++)
          {            for(j=1;j<=nlstate;j++)
            printf("%d%d ",i,k);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
            fprintf(ficres,"%1d%1d ",i,k);        }
            for(j=1; j <=ncovmodel; j++){      }
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);      /* pptj */
              jk++;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
            printf("\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
            fprintf(ficres,"\n");        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);
     /* Computing hessian and covariance matrix */   
     ftolhess=ftol; /* Usually correct */      if (popbased==1) {
     hesscov(matcov, p, npar, delti, ftolhess, func);        if(mobilav ==0){
     fprintf(ficres,"# Scales\n");          for(i=1; i<=nlstate;i++)
     printf("# Scales\n");            prlim[i][i]=probs[(int)age][i][ij];
      for(i=1,jk=1; i <=nlstate; i++){        }else{ /* mobilav */ 
       for(j=1; j <=nlstate+ndeath; j++){          for(i=1; i<=nlstate;i++)
         if (j!=i) {            prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficres,"%1d%1d",i,j);        }
           printf("%1d%1d",i,j);      }
           for(k=1; k<=ncovmodel;k++){      
             printf(" %.5e",delti[jk]);      /* This for computing force of mortality (h=1)as a weighted average */
             fprintf(ficres," %.5e",delti[jk]);      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
             jk++;        for(i=1; i<= nlstate; i++)
           }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           printf("\n");      }    
           fprintf(ficres,"\n");      /* end force of mortality */
         }  
       }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     k=1;        for(i=1; i<=nlstate;i++){
     fprintf(ficres,"# Covariance\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     printf("# Covariance\n");        }
     for(i=1;i<=npar;i++){      } 
       /*  if (k>nlstate) k=1;      fprintf(ficresprobmorprev,"\n");
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      fprintf(ficresvij,"%.0f ",age );
       printf("%s%d%d",alph[k],i1,tab[i]);*/      for(i=1; i<=nlstate;i++)
       fprintf(ficres,"%3d",i);        for(j=1; j<=nlstate;j++){
       printf("%3d",i);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       for(j=1; j<=i;j++){        }
         fprintf(ficres," %.5e",matcov[i][j]);      fprintf(ficresvij,"\n");
         printf(" %.5e",matcov[i][j]);      free_matrix(gp,0,nhstepm,1,nlstate);
       }      free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficres,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       printf("\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       k++;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
     while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(gmp,nlstate+1,nlstate+ndeath);
       ungetc(c,ficpar);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       fgets(line, MAXLINE, ficpar);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       puts(line);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fputs(line,ficparo);    /* 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)\";");
     ungetc(c,ficpar);    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);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     if (fage <= 2) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
       bage = agemin;    /*  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);
       fage = agemax;  */
     }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    free_vector(xp,1,npar);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    free_matrix(doldm,1,nlstate,1,nlstate);
 /*------------ gnuplot -------------*/    free_matrix(dnewm,1,nlstate,1,npar);
 chdir(pathcd);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     printf("Problem with file graph.gp");goto end;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #ifdef windows    fclose(ficresprobmorprev);
   fprintf(ficgp,"cd \"%s\" \n",pathc);    fclose(ficgp);
 #endif    fclose(fichtm);
 m=pow(2,cptcovn);  }
    
  /* 1eme*/  /************ Variance of prevlim ******************/
   for (cpt=1; cpt<= nlstate ; cpt ++) {  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
    for (k1=1; k1<= m ; k1 ++) {  {
     /* Variance of prevalence limit */
 #ifdef windows    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     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);    double **newm;
 #endif    double **dnewm,**doldm;
 #ifdef unix    int i, j, nhstepm, hstepm;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    int k, cptcode;
 #endif    double *xp;
     double *gp, *gm;
 for (i=1; i<= nlstate ; i ++) {    double **gradg, **trgradg;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double age,agelim;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int theta;
 }     
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     for (i=1; i<= nlstate ; i ++) {    fprintf(ficresvpl,"# Age");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresvpl," %1d-%1d",i,i);
 }    fprintf(ficresvpl,"\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {    xp=vector(1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    dnewm=matrix(1,nlstate,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    doldm=matrix(1,nlstate,1,nlstate);
 }      
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    hstepm=1*YEARM; /* Every year of age */
 #ifdef unix    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 fprintf(ficgp,"\nset ter gif small size 400,300");    agelim = AGESUP;
 #endif    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    }      if (stepm >= YEARM) hstepm=1;
   }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   /*2 eme*/      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {      gm=vector(1,nlstate);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
          for(theta=1; theta <=npar; theta++){
     for (i=1; i<= nlstate+1 ; i ++) {        for(i=1; i<=npar; i++){ /* Computes gradient */
       k=2*i;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1;i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          gp[i] = prlim[i][i];
 }        
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(i=1; i<=npar; i++) /* Computes gradient */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1;i<=nlstate;i++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          gm[i] = prlim[i][i];
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(i=1;i<=nlstate;i++)
       fprintf(ficgp,"\" t\"\" w l 0,");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      } /* End theta */
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      trgradg =matrix(1,nlstate,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        for(j=1; j<=nlstate;j++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(theta=1; theta <=npar; theta++)
       else fprintf(ficgp,"\" t\"\" w l 0,");          trgradg[j][theta]=gradg[theta][j];
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /*3eme*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(cpt-1);      fprintf(ficresvpl,"%.0f ",age );
       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++)
       for (i=1; i< nlstate ; i ++) {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      fprintf(ficresvpl,"\n");
       }      free_vector(gp,1,nlstate);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      free_vector(gm,1,nlstate);
     }      free_matrix(gradg,1,npar,1,nlstate);
   }      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {    free_vector(xp,1,npar);
     for (cpt=1; cpt<nlstate ; cpt ++) {    free_matrix(doldm,1,nlstate,1,npar);
       k=3;    free_matrix(dnewm,1,nlstate,1,nlstate);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)  }
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  /************ 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)
       l=3+(nlstate+ndeath)*cpt;  {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    int i, j=0,  i1, k1, l1, t, tj;
       for (i=1; i< nlstate ; i ++) {    int k2, l2, j1,  z1;
         l=3+(nlstate+ndeath)*cpt;    int k=0,l, cptcode;
         fprintf(ficgp,"+$%d",l+i+1);    int first=1, first1;
       }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      double **dnewm,**doldm;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double *xp;
     }    double *gp, *gm;
   }    double **gradg, **trgradg;
     double **mu;
   /* proba elementaires */    double age,agelim, cov[NCOVMAX];
    for(i=1,jk=1; i <=nlstate; i++){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     for(k=1; k <=(nlstate+ndeath); k++){    int theta;
       if (k != i) {    char fileresprob[FILENAMELENGTH];
         for(j=1; j <=ncovmodel; j++){    char fileresprobcov[FILENAMELENGTH];
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    char fileresprobcor[FILENAMELENGTH];
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    double ***varpij;
           jk++;  
           fprintf(ficgp,"\n");    strcpy(fileresprob,"prob"); 
         }    strcat(fileresprob,fileres);
       }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprob);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   for(jk=1; jk <=m; jk++) {    strcpy(fileresprobcov,"probcov"); 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    strcat(fileresprobcov,fileres);
    i=1;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
    for(k2=1; k2<=nlstate; k2++) {      printf("Problem with resultfile: %s\n", fileresprobcov);
      k3=i;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      for(k=1; k<=(nlstate+ndeath); k++) {    }
        if (k != k2){    strcpy(fileresprobcor,"probcor"); 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         for(j=3; j <=ncovmodel; j++)      printf("Problem with resultfile: %s\n", fileresprobcor);
           fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficgp,")/(1");    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         for(k1=1; k1 <=nlstate+1; k1=k1+2){      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             fprintf(ficgp,"+exp(p%d+p%d*x",k1+k3-1,k1+k3);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             for(j=3; j <=ncovmodel; j++)    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
               fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
             fprintf(ficgp,")");    
         }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    fprintf(ficresprob,"# Age");
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     i=i+ncovmodel;    fprintf(ficresprobcov,"# Age");
        }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      }    fprintf(ficresprobcov,"# Age");
    }  
   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }    for(i=1; i<=nlstate;i++)
          for(j=1; j<=(nlstate+ndeath);j++){
   fclose(ficgp);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
            fprintf(ficresprobcov," p%1d-%1d ",i,j);
 chdir(path);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     free_matrix(agev,1,maxwav,1,imx);      }  
     free_ivector(wav,1,imx);    fprintf(ficresprob,"\n");
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fprintf(ficresprobcov,"\n");
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    fprintf(ficresprobcor,"\n");
        xp=vector(1,npar);
     free_imatrix(s,1,maxwav+1,1,n);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     free_ivector(num,1,n);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     free_vector(agedc,1,n);    first=1;
     free_vector(weight,1,n);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
     fclose(ficparo);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     fclose(ficres);      exit(0);
    }    }
        else{
    /*________fin mle=1_________*/      fprintf(ficgp,"\n# Routine varprob");
        }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        printf("Problem with html file: %s\n", optionfilehtm);
     /* No more information from the sample is required now */      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   /* Reads comments: lines beginning with '#' */      exit(0);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else{
     fgets(line, MAXLINE, ficpar);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     puts(line);      fprintf(fichtm,"\n");
     fputs(line,ficparo);  
   }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   ungetc(c,ficpar);      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
        fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   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);    }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/   
     cov[1]=1;
   if((fichtm=fopen("index.htm","w"))==NULL)    {    tj=cptcoveff;
     printf("Problem with index.htm \n");goto end;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   }    j1=0;
     for(t=1; t<=tj;t++){
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n      for(i1=1; i1<=ncodemax[t];i1++){ 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        j1++;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        if  (cptcovn>0) {
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          fprintf(ficresprob, "\n#********** Variable "); 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          fprintf(ficresprob, "**********\n#");
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          fprintf(ficresprobcov, "\n#********** Variable "); 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         - 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);          fprintf(ficresprobcov, "**********\n#");
           
  fprintf(fichtm," <li>Graphs</li>\n<p>");          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  m=cptcovn;          fprintf(ficgp, "**********\n#");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          
           
  j1=0;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
  for(k1=1; k1<=m;k1++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
        j1++;          
        if (cptcovn > 0) {          fprintf(ficresprobcor, "\n#********** Variable ");    
          fprintf(fichtm,"<hr>************ Results for covariates");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          for (cpt=1; cpt<=cptcovn;cpt++)          fprintf(ficgp, "**********\n#");    
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);        }
          fprintf(fichtm," ************\n<hr>");        
        }        for (age=bage; age<=fage; age ++){ 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          cov[2]=age;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              for (k=1; k<=cptcovn;k++) {
        for(cpt=1; cpt<nlstate;cpt++){            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        }          for (k=1; k<=cptcovprod;k++)
     for(cpt=1; cpt<=nlstate;cpt++) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          
 interval) in state (%d): v%s%d%d.gif <br>          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      }          gp=vector(1,(nlstate)*(nlstate+ndeath));
      for(cpt=1; cpt<=nlstate;cpt++) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(theta=1; theta <=npar; theta++){
      }            for(i=1; i<=npar; i++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              xp[i] = x[i] + (i==theta ?delti[theta]:0);
 health expectancies in states (1) and (2): e%s%d.gif<br>            
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
 fprintf(fichtm,"\n</body>");            
    }            k=0;
  }            for(i=1; i<= (nlstate); i++){
 fclose(fichtm);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   /*--------------- Prevalence limit --------------*/                gp[k]=pmmij[i][j];
                }
   strcpy(filerespl,"pl");            }
   strcat(filerespl,fileres);            
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            for(i=1; i<=npar; i++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }      
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   fprintf(ficrespl,"#Prevalence limit\n");            k=0;
   fprintf(ficrespl,"#Age ");            for(i=1; i<=(nlstate); i++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficrespl,"\n");                k=k+1;
                  gm[k]=pmmij[i][j];
   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 */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
   k=0;  
   agebase=agemin;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   agelim=agemax;            for(theta=1; theta <=npar; theta++)
   ftolpl=1.e-10;              trgradg[j][theta]=gradg[theta][j];
   i1=cptcovn;          
   if (cptcovn < 1){i1=1;}          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   for(cptcov=1;cptcov<=i1;cptcov++){          
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
         k=k+1;          
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          k=0;
         fprintf(ficrespl,"\n#****** ");          for(i=1; i<=(nlstate); i++){
         for(j=1;j<=cptcovn;j++)            for(j=1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);              k=k+1;
         fprintf(ficrespl,"******\n");              mu[k][(int) age]=pmmij[i][j];
                    }
         for (age=agebase; age<=agelim; age++){          }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           fprintf(ficrespl,"%.0f",age );            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           for(i=1; i<=nlstate;i++)              varpij[i][j][(int)age] = doldm[i][j];
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");          /*printf("\n%d ",(int)age);
         }       for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       }         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(ficrespl);       }*/
   /*------------- h Pij x at various ages ------------*/  
            fprintf(ficresprob,"\n%d ",(int)age);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficresprobcov,"\n%d ",(int)age);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          fprintf(ficresprobcor,"\n%d ",(int)age);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   printf("Computing pij: result on file '%s' \n", filerespij);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if (stepm<=24) stepsize=2;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   agelim=AGESUP;          i=0;
   hstepm=stepsize*YEARM; /* Every year of age */          for (k=1; k<=(nlstate);k++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
   k=0;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   for(cptcov=1;cptcov<=i1;cptcov++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              for (j=1; j<=i;j++){
       k=k+1;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         fprintf(ficrespij,"\n#****** ");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         for(j=1;j<=cptcovn;j++)              }
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            }
         fprintf(ficrespij,"******\n");          }/* end of loop for state */
                } /* end of loop for age */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /* Confidence intervalle of pij  */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /*
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,"\nset noparametric;unset label");
           oldm=oldms;savm=savms;        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(ficrespij,"# Age");        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);
           for(i=1; i<=nlstate;i++)        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           fprintf(ficrespij,"\n");        */
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             for(i=1; i<=nlstate;i++)        first1=1;
               for(j=1; j<=nlstate+ndeath;j++)        for (k2=1; k2<=(nlstate);k2++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             fprintf(ficrespij,"\n");            if(l2==k2) continue;
           }            j=(k2-1)*(nlstate+ndeath)+l2;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (k1=1; k1<=(nlstate);k1++){
           fprintf(ficrespij,"\n");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         }                if(l1==k1) continue;
     }                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   fclose(ficrespij);                  if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   /*---------- Health expectancies and variances ------------*/                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   strcpy(filerest,"t");                    mu1=mu[i][(int) age]/stepm*YEARM ;
   strcat(filerest,fileres);                    mu2=mu[j][(int) age]/stepm*YEARM;
   if((ficrest=fopen(filerest,"w"))==NULL) {                    c12=cv12/sqrt(v1*v2);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                    /* Computing eigen value of matrix of covariance */
   }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   strcpy(filerese,"e");                    /*v21=sqrt(1.-v11*v11); *//* error */
   strcat(filerese,fileres);                    v21=(lc1-v1)/cv12*v11;
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    v12=-v21;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    v22=v11;
   }                    tnalp=v21/v11;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                    if(first1==1){
                       first1=0;
  strcpy(fileresv,"v");                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   strcat(fileresv,fileres);                    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                    /*printf(fignu*/
   }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   k=0;                      first=0;
   for(cptcov=1;cptcov<=i1;cptcov++){                      fprintf(ficgp,"\nset parametric;unset label");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      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);
       k=k+1;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(ficrest,"\n#****** ");                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
       for(j=1;j<=cptcovn;j++)                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       fprintf(ficrest,"******\n");                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       fprintf(ficreseij,"\n#****** ");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       for(j=1;j<=cptcovn;j++)                      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",\
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       fprintf(ficreseij,"******\n");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
       fprintf(ficresvij,"\n#****** ");                      first=0;
       for(j=1;j<=cptcovn;j++)                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       fprintf(ficresvij,"******\n");                      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",\
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       oldm=oldms;savm=savms;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                      }/* if first */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  } /* age mod 5 */
       oldm=oldms;savm=savms;                } /* end loop age */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                      first=1;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              } /*l12 */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            } /* k12 */
       fprintf(ficrest,"\n");          } /*l1 */
                }/* k1 */
       hf=1;      } /* loop covariates */
       if (stepm >= YEARM) hf=stepm/YEARM;      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       epj=vector(1,nlstate+1);      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       for(age=bage; age <=fage ;age++){      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         fprintf(ficrest," %.0f",age);      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    free_vector(xp,1,npar);
           }    fclose(ficresprob);
           epj[nlstate+1] +=epj[j];    fclose(ficresprobcov);
         }    fclose(ficresprobcor);
         for(i=1, vepp=0.;i <=nlstate;i++)    fclose(ficgp);
           for(j=1;j <=nlstate;j++)    fclose(fichtm);
             vepp += vareij[i][j][(int)age];  }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  /******************* Printing html file ***********/
         }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         fprintf(ficrest,"\n");                    int lastpass, int stepm, int weightopt, char model[],\
       }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     }                    int popforecast, int estepm ,\
   }                    double jprev1, double mprev1,double anprev1, \
                            double jprev2, double mprev2,double anprev2){
  fclose(ficreseij);    int jj1, k1, i1, cpt;
  fclose(ficresvij);    /*char optionfilehtm[FILENAMELENGTH];*/
   fclose(ficrest);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   fclose(ficpar);      printf("Problem with %s \n",optionfilehtm), exit(0);
   free_vector(epj,1,nlstate+1);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   /*  scanf("%d ",i); */    }
   
   /*------- Variance limit prevalence------*/       fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
 strcpy(fileresvpl,"vpl");   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   strcat(fileresvpl,fileres);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   - Life expectancies by age and initial health status (estepm=%2d months): 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     exit(0);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
  k=0;   m=cptcoveff;
  for(cptcov=1;cptcov<=i1;cptcov++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;   jj1=0;
      fprintf(ficresvpl,"\n#****** ");   for(k1=1; k1<=m;k1++){
      for(j=1;j<=cptcovn;j++)     for(i1=1; i1<=ncodemax[k1];i1++){
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);       jj1++;
      fprintf(ficresvpl,"******\n");       if (cptcovn > 0) {
               fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      varpl=matrix(1,nlstate,(int) bage, (int) fage);         for (cpt=1; cpt<=cptcoveff;cpt++) 
      oldm=oldms;savm=savms;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
    }       }
  }       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
   fclose(ficresvpl);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
   /*---------- End : free ----------------*/       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>
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           /* Stable prevalence in each health state */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         for(cpt=1; cpt<nlstate;cpt++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
    <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       for(cpt=1; cpt<=nlstate;cpt++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and
   free_matrix(matcov,1,npar,1,npar);  health expectancies in states (1) and (2): e%s%d.png<br>
   free_vector(delti,1,npar);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
       } /* end i1 */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);   }/* End k1 */
    fprintf(fichtm,"</ul>");
   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
     fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   /* 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);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
   /*printf("Total time was %d uSec.\n", total_usecs);*/   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   /*------ End -----------*/   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
  end:   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
 #ifdef windows   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
  chdir(pathcd);   - 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);
 #endif  
  system("wgnuplot graph.plt");   if(popforecast==1) fprintf(fichtm,"\n
    - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
 #ifdef windows   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   while (z[0] != 'q') {          <br>",fileres,fileres,fileres,fileres);
     chdir(pathcd);   else 
     printf("\nType e to edit output files, c to start again, and q for exiting: ");     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);
     scanf("%s",z);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {   m=cptcoveff;
       chdir(path);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       system("index.htm");  
     }   jj1=0;
     else if (z[0] == 'q') exit(0);   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
 #endif       jj1++;
 }       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+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\"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.1.5  
changed lines
  Added in v.1.57


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