Diff for /imach/src/imach.c between versions 1.42 and 1.56

version 1.42, 2002/05/21 18:44:41 version 1.56, 2002/07/24 17:28:25
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    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    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month or quarter trimester,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is model as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  double jmean; /* Mean space between 2 waves */
   char fileresv[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
  FILE  *ficresvpl;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   char fileresvpl[FILENAMELENGTH];  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog;
 #define NR_END 1  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define FREE_ARG char*  FILE *ficresprobmorprev;
 #define FTOL 1.0e-10  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 #define NRANSI  char filerese[FILENAMELENGTH];
 #define ITMAX 200  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 #define CGOLD 0.3819660  char title[MAXLINE];
 #define ZEPS 1.0e-10  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 #define GOLD 1.618034  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define GLIMIT 100.0  char filelog[FILENAMELENGTH]; /* Log file */
 #define TINY 1.0e-20  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 static double maxarg1,maxarg2;  char popfile[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define NR_END 1
 #define rint(a) floor(a+0.5)  #define FREE_ARG char*
   #define FTOL 1.0e-10
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define NRANSI 
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define ITMAX 200 
   
 int imx;  #define TOL 2.0e-4 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 int estepm;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
   #define GOLD 1.618034 
 int m,nb;  #define GLIMIT 100.0 
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define TINY 1.0e-20 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  static double maxarg1,maxarg2;
 double dateintmean=0;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double *weight;    
 int **s; /* Status */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double *agedc, **covar, idx;  #define rint(a) floor(a+0.5)
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   static double sqrarg;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 double ftolhess; /* Tolerance for computing hessian */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 /**************** split *************************/  int imx; 
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int stepm;
 {  /* Stepm, step in month: minimum step interpolation*/
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int m,nb;
 #ifdef windows  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    s = strrchr( path, '\\' );           /* find last / */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #else  double **pmmij, ***probs;
    s = strrchr( path, '/' );            /* find last / */  double dateintmean=0;
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  double *weight;
 #if     defined(__bsd__)                /* get current working directory */  int **s; /* Status */
       extern char       *getwd( );  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if ( getwd( dirc ) == NULL ) {  
 #else  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       extern char       *getcwd( );  double ftolhess; /* Tolerance for computing hessian */
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /**************** split *************************/
 #endif  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
          return( GLOCK_ERROR_GETCWD );  {
       }     char *s;                             /* pointer */
       strcpy( name, path );             /* we've got it */     int  l1, l2;                         /* length counters */
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */     l1 = strlen( path );                 /* length of path */
       l2 = strlen( s );                 /* length of filename */     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );     s= strrchr( path, DIRSEPARATOR );            /* find last / */
       strcpy( name, s );                /* save file name */     if ( s == NULL ) {                   /* no directory, so use current */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       dirc[l1-l2] = 0;                  /* add zero */         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
    }  #if     defined(__bsd__)                /* get current working directory */
    l1 = strlen( dirc );                 /* length of directory */        extern char       *getwd( );
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }        if ( getwd( dirc ) == NULL ) {
 #else  #else
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }        extern char       *getcwd( );
 #endif  
    s = strrchr( name, '.' );            /* find last / */        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    s++;  #endif
    strcpy(ext,s);                       /* save extension */           return( GLOCK_ERROR_GETCWD );
    l1= strlen( name);        }
    l2= strlen( s)+1;        strcpy( name, path );             /* we've got it */
    strncpy( finame, name, l1-l2);     } else {                             /* strip direcotry from path */
    finame[l1-l2]= 0;        s++;                              /* after this, the filename */
    return( 0 );                         /* we're done */        l2 = strlen( s );                 /* length of filename */
 }        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         strcpy( name, s );                /* save file name */
         strncpy( dirc, path, l1 - l2 );   /* now the directory */
 /******************************************/        dirc[l1-l2] = 0;                  /* add zero */
      }
 void replace(char *s, char*t)     l1 = strlen( dirc );                 /* length of directory */
 {  #ifdef windows
   int i;     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   int lg=20;  #else
   i=0;     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   lg=strlen(t);  #endif
   for(i=0; i<= lg; i++) {     s = strrchr( name, '.' );            /* find last / */
     (s[i] = t[i]);     s++;
     if (t[i]== '\\') s[i]='/';     strcpy(ext,s);                       /* save extension */
   }     l1= strlen( name);
 }     l2= strlen( s)+1;
      strncpy( finame, name, l1-l2);
 int nbocc(char *s, char occ)     finame[l1-l2]= 0;
 {     return( 0 );                         /* we're done */
   int i,j=0;  }
   int lg=20;  
   i=0;  
   lg=strlen(s);  /******************************************/
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  void replace(char *s, char*t)
   }  {
   return j;    int i;
 }    int lg=20;
     i=0;
 void cutv(char *u,char *v, char*t, char occ)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   int i,lg,j,p=0;      (s[i] = t[i]);
   i=0;      if (t[i]== '\\') s[i]='/';
   for(j=0; j<=strlen(t)-1; j++) {    }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  }
   }  
   int nbocc(char *s, char occ)
   lg=strlen(t);  {
   for(j=0; j<p; j++) {    int i,j=0;
     (u[j] = t[j]);    int lg=20;
   }    i=0;
      u[p]='\0';    lg=strlen(s);
     for(i=0; i<= lg; i++) {
    for(j=0; j<= lg; j++) {    if  (s[i] == occ ) j++;
     if (j>=(p+1))(v[j-p-1] = t[j]);    }
   }    return j;
 }  }
   
 /********************** nrerror ********************/  void cutv(char *u,char *v, char*t, char occ)
   {
 void nrerror(char error_text[])    /* 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)
   fprintf(stderr,"ERREUR ...\n");       gives u="abcedf" and v="ghi2j" */
   fprintf(stderr,"%s\n",error_text);    int i,lg,j,p=0;
   exit(1);    i=0;
 }    for(j=0; j<=strlen(t)-1; j++) {
 /*********************** vector *******************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 double *vector(int nl, int nh)    }
 {  
   double *v;    lg=strlen(t);
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    for(j=0; j<p; j++) {
   if (!v) nrerror("allocation failure in vector");      (u[j] = t[j]);
   return v-nl+NR_END;    }
 }       u[p]='\0';
   
 /************************ free vector ******************/     for(j=0; j<= lg; j++) {
 void free_vector(double*v, int nl, int nh)      if (j>=(p+1))(v[j-p-1] = t[j]);
 {    }
   free((FREE_ARG)(v+nl-NR_END));  }
 }  
   /********************** nrerror ********************/
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  void nrerror(char error_text[])
 {  {
   int *v;    fprintf(stderr,"ERREUR ...\n");
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    fprintf(stderr,"%s\n",error_text);
   if (!v) nrerror("allocation failure in ivector");    exit(1);
   return v-nl+NR_END;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /******************free ivector **************************/  {
 void free_ivector(int *v, long nl, long nh)    double *v;
 {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free((FREE_ARG)(v+nl-NR_END));    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /************************ free vector ******************/
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  void free_vector(double*v, int nl, int nh)
 {  {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    free((FREE_ARG)(v+nl-NR_END));
   int **m;  }
    
   /* allocate pointers to rows */  /************************ivector *******************************/
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int *ivector(long nl,long nh)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int *v;
   m -= nrl;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
   /* allocate rows and set pointers to them */  }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /******************free ivector **************************/
   m[nrl] += NR_END;  void free_ivector(int *v, long nl, long nh)
   m[nrl] -= ncl;  {
      free((FREE_ARG)(v+nl-NR_END));
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  }
    
   /* return pointer to array of pointers to rows */  /******************* imatrix *******************************/
   return m;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
 /****************** free_imatrix *************************/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 void free_imatrix(m,nrl,nrh,ncl,nch)    int **m; 
       int **m;    
       long nch,ncl,nrh,nrl;    /* allocate pointers to rows */ 
      /* free an int matrix allocated by imatrix() */    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; 
 }    
     
 /******************* matrix *******************************/    /* allocate rows and set pointers to them */ 
 double **matrix(long nrl, long nrh, long ncl, long nch)    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+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() */ 
   return m;  { 
 }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
 /*************************free matrix ************************/  } 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  /******************* matrix *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double **matrix(long nrl, long nrh, long ncl, long nch)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m += NR_END;
   double ***m;    m -= nrl;
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   if (!m) nrerror("allocation failure 1 in matrix()");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   m += NR_END;    m[nrl] += NR_END;
   m -= nrl;    m[nrl] -= ncl;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return m;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /*************************free matrix ************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   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++)  /******************* ma3x *******************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
   for (i=nrl+1; i<=nrh; i++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+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;
 }  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 /***************** f1dim *************************/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 extern int ncom;    m[nrl][ncl] += NR_END;
 extern double *pcom,*xicom;    m[nrl][ncl] -= nll;
 extern double (*nrfunc)(double []);    for (j=ncl+1; j<=nch; j++) 
        m[nrl][j]=m[nrl][j-1]+nlay;
 double f1dim(double x)    
 {    for (i=nrl+1; i<=nrh; i++) {
   int j;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double f;      for (j=ncl+1; j<=nch; j++) 
   double *xt;        m[i][j]=m[i][j-1]+nlay;
      }
   xt=vector(1,ncom);    return m;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  }
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  /*************************free ma3x ************************/
   return f;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 /*****************brent *************************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   int iter;  
   double a,b,d,etemp;  /***************** f1dim *************************/
   double fu,fv,fw,fx;  extern int ncom; 
   double ftemp;  extern double *pcom,*xicom;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern double (*nrfunc)(double []); 
   double e=0.0;   
    double f1dim(double x) 
   a=(ax < cx ? ax : cx);  { 
   b=(ax > cx ? ax : cx);    int j; 
   x=w=v=bx;    double f;
   fw=fv=fx=(*f)(x);    double *xt; 
   for (iter=1;iter<=ITMAX;iter++) {   
     xm=0.5*(a+b);    xt=vector(1,ncom); 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    f=(*nrfunc)(xt); 
     printf(".");fflush(stdout);    free_vector(xt,1,ncom); 
 #ifdef DEBUG    return f; 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  } 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  /*****************brent *************************/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       *xmin=x;  { 
       return fx;    int iter; 
     }    double a,b,d,etemp;
     ftemp=fu;    double fu,fv,fw,fx;
     if (fabs(e) > tol1) {    double ftemp;
       r=(x-w)*(fx-fv);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       q=(x-v)*(fx-fw);    double e=0.0; 
       p=(x-v)*q-(x-w)*r;   
       q=2.0*(q-r);    a=(ax < cx ? ax : cx); 
       if (q > 0.0) p = -p;    b=(ax > cx ? ax : cx); 
       q=fabs(q);    x=w=v=bx; 
       etemp=e;    fw=fv=fx=(*f)(x); 
       e=d;    for (iter=1;iter<=ITMAX;iter++) { 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      xm=0.5*(a+b); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       else {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         d=p/q;      printf(".");fflush(stdout);
         u=x+d;      fprintf(ficlog,".");fflush(ficlog);
         if (u-a < tol2 || b-u < tol2)  #ifdef DEBUG
           d=SIGN(tol1,xm-x);      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);
     } else {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        *xmin=x; 
     fu=(*f)(u);        return fx; 
     if (fu <= fx) {      } 
       if (u >= x) a=x; else b=x;      ftemp=fu;
       SHFT(v,w,x,u)      if (fabs(e) > tol1) { 
         SHFT(fv,fw,fx,fu)        r=(x-w)*(fx-fv); 
         } else {        q=(x-v)*(fx-fw); 
           if (u < x) a=u; else b=u;        p=(x-v)*q-(x-w)*r; 
           if (fu <= fw || w == x) {        q=2.0*(q-r); 
             v=w;        if (q > 0.0) p = -p; 
             w=u;        q=fabs(q); 
             fv=fw;        etemp=e; 
             fw=fu;        e=d; 
           } else if (fu <= fv || v == x || v == w) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
             v=u;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             fv=fu;        else { 
           }          d=p/q; 
         }          u=x+d; 
   }          if (u-a < tol2 || b-u < tol2) 
   nrerror("Too many iterations in brent");            d=SIGN(tol1,xm-x); 
   *xmin=x;        } 
   return fx;      } else { 
 }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 /****************** mnbrak ***********************/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      if (fu <= fx) { 
             double (*func)(double))        if (u >= x) a=x; else b=x; 
 {        SHFT(v,w,x,u) 
   double ulim,u,r,q, dum;          SHFT(fv,fw,fx,fu) 
   double fu;          } else { 
              if (u < x) a=u; else b=u; 
   *fa=(*func)(*ax);            if (fu <= fw || w == x) { 
   *fb=(*func)(*bx);              v=w; 
   if (*fb > *fa) {              w=u; 
     SHFT(dum,*ax,*bx,dum)              fv=fw; 
       SHFT(dum,*fb,*fa,dum)              fw=fu; 
       }            } else if (fu <= fv || v == x || v == w) { 
   *cx=(*bx)+GOLD*(*bx-*ax);              v=u; 
   *fc=(*func)(*cx);              fv=fu; 
   while (*fb > *fc) {            } 
     r=(*bx-*ax)*(*fb-*fc);          } 
     q=(*bx-*cx)*(*fb-*fa);    } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    nrerror("Too many iterations in brent"); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    *xmin=x; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    return fx; 
     if ((*bx-u)*(u-*cx) > 0.0) {  } 
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  /****************** mnbrak ***********************/
       fu=(*func)(u);  
       if (fu < *fc) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))              double (*func)(double)) 
           SHFT(*fb,*fc,fu,(*func)(u))  { 
           }    double ulim,u,r,q, dum;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    double fu; 
       u=ulim;   
       fu=(*func)(u);    *fa=(*func)(*ax); 
     } else {    *fb=(*func)(*bx); 
       u=(*cx)+GOLD*(*cx-*bx);    if (*fb > *fa) { 
       fu=(*func)(u);      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
     SHFT(*ax,*bx,*cx,u)        } 
       SHFT(*fa,*fb,*fc,fu)    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
 }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 /*************** linmin ************************/      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 int ncom;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 double *pcom,*xicom;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 double (*nrfunc)(double []);      if ((*bx-u)*(u-*cx) > 0.0) { 
          fu=(*func)(u); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 {        fu=(*func)(u); 
   double brent(double ax, double bx, double cx,        if (fu < *fc) { 
                double (*f)(double), double tol, double *xmin);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double f1dim(double x);            SHFT(*fb,*fc,fu,(*func)(u)) 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,            } 
               double *fc, double (*func)(double));      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int j;        u=ulim; 
   double xx,xmin,bx,ax;        fu=(*func)(u); 
   double fx,fb,fa;      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
   ncom=n;        fu=(*func)(u); 
   pcom=vector(1,n);      } 
   xicom=vector(1,n);      SHFT(*ax,*bx,*cx,u) 
   nrfunc=func;        SHFT(*fa,*fb,*fc,fu) 
   for (j=1;j<=n;j++) {        } 
     pcom[j]=p[j];  } 
     xicom[j]=xi[j];  
   }  /*************** linmin ************************/
   ax=0.0;  
   xx=1.0;  int ncom; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  double *pcom,*xicom;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double (*nrfunc)(double []); 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 #endif  { 
   for (j=1;j<=n;j++) {    double brent(double ax, double bx, double cx, 
     xi[j] *= xmin;                 double (*f)(double), double tol, double *xmin); 
     p[j] += xi[j];    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   free_vector(xicom,1,n);                double *fc, double (*func)(double)); 
   free_vector(pcom,1,n);    int j; 
 }    double xx,xmin,bx,ax; 
     double fx,fb,fa;
 /*************** powell ************************/   
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    ncom=n; 
             double (*func)(double []))    pcom=vector(1,n); 
 {    xicom=vector(1,n); 
   void linmin(double p[], double xi[], int n, double *fret,    nrfunc=func; 
               double (*func)(double []));    for (j=1;j<=n;j++) { 
   int i,ibig,j;      pcom[j]=p[j]; 
   double del,t,*pt,*ptt,*xit;      xicom[j]=xi[j]; 
   double fp,fptt;    } 
   double *xits;    ax=0.0; 
   pt=vector(1,n);    xx=1.0; 
   ptt=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   xit=vector(1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   xits=vector(1,n);  #ifdef DEBUG
   *fret=(*func)(p);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (j=1;j<=n;j++) pt[j]=p[j];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (*iter=1;;++(*iter)) {  #endif
     fp=(*fret);    for (j=1;j<=n;j++) { 
     ibig=0;      xi[j] *= xmin; 
     del=0.0;      p[j] += xi[j]; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    } 
     for (i=1;i<=n;i++)    free_vector(xicom,1,n); 
       printf(" %d %.12f",i, p[i]);    free_vector(pcom,1,n); 
     printf("\n");  } 
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /*************** powell ************************/
       fptt=(*fret);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 #ifdef DEBUG              double (*func)(double [])) 
       printf("fret=%lf \n",*fret);  { 
 #endif    void linmin(double p[], double xi[], int n, double *fret, 
       printf("%d",i);fflush(stdout);                double (*func)(double [])); 
       linmin(p,xit,n,fret,func);    int i,ibig,j; 
       if (fabs(fptt-(*fret)) > del) {    double del,t,*pt,*ptt,*xit;
         del=fabs(fptt-(*fret));    double fp,fptt;
         ibig=i;    double *xits;
       }    pt=vector(1,n); 
 #ifdef DEBUG    ptt=vector(1,n); 
       printf("%d %.12e",i,(*fret));    xit=vector(1,n); 
       for (j=1;j<=n;j++) {    xits=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    *fret=(*func)(p); 
         printf(" x(%d)=%.12e",j,xit[j]);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       }    for (*iter=1;;++(*iter)) { 
       for(j=1;j<=n;j++)      fp=(*fret); 
         printf(" p=%.12e",p[j]);      ibig=0; 
       printf("\n");      del=0.0; 
 #endif      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      for (i=1;i<=n;i++) 
 #ifdef DEBUG        printf(" %d %.12f",i, p[i]);
       int k[2],l;      fprintf(ficlog," %d %.12f",i, p[i]);
       k[0]=1;      printf("\n");
       k[1]=-1;      fprintf(ficlog,"\n");
       printf("Max: %.12e",(*func)(p));      for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         printf(" %.12e",p[j]);        fptt=(*fret); 
       printf("\n");  #ifdef DEBUG
       for(l=0;l<=1;l++) {        printf("fret=%lf \n",*fret);
         for (j=1;j<=n;j++) {        fprintf(ficlog,"fret=%lf \n",*fret);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #endif
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        printf("%d",i);fflush(stdout);
         }        fprintf(ficlog,"%d",i);fflush(ficlog);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        linmin(p,xit,n,fret,func); 
       }        if (fabs(fptt-(*fret)) > del) { 
 #endif          del=fabs(fptt-(*fret)); 
           ibig=i; 
         } 
       free_vector(xit,1,n);  #ifdef DEBUG
       free_vector(xits,1,n);        printf("%d %.12e",i,(*fret));
       free_vector(ptt,1,n);        fprintf(ficlog,"%d %.12e",i,(*fret));
       free_vector(pt,1,n);        for (j=1;j<=n;j++) {
       return;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }          printf(" x(%d)=%.12e",j,xit[j]);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=n;j++) {        }
       ptt[j]=2.0*p[j]-pt[j];        for(j=1;j<=n;j++) {
       xit[j]=p[j]-pt[j];          printf(" p=%.12e",p[j]);
       pt[j]=p[j];          fprintf(ficlog," p=%.12e",p[j]);
     }        }
     fptt=(*func)(ptt);        printf("\n");
     if (fptt < fp) {        fprintf(ficlog,"\n");
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #endif
       if (t < 0.0) {      } 
         linmin(p,xit,n,fret,func);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           xi[j][ibig]=xi[j][n];        int k[2],l;
           xi[j][n]=xit[j];        k[0]=1;
         }        k[1]=-1;
 #ifdef DEBUG        printf("Max: %.12e",(*func)(p));
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for(j=1;j<=n;j++)        for (j=1;j<=n;j++) {
           printf(" %.12e",xit[j]);          printf(" %.12e",p[j]);
         printf("\n");          fprintf(ficlog," %.12e",p[j]);
 #endif        }
       }        printf("\n");
     }        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
 }          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 /**** Prevalence limit ****************/            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]);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)          }
 {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      matrix by transitions matrix until convergence is reached */        }
   #endif
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();        free_vector(xit,1,n); 
   double **out, cov[NCOVMAX], **pmij();        free_vector(xits,1,n); 
   double **newm;        free_vector(ptt,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(pt,1,n); 
         return; 
   for (ii=1;ii<=nlstate+ndeath;ii++)      } 
     for (j=1;j<=nlstate+ndeath;j++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for (j=1;j<=n;j++) { 
     }        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
    cov[1]=1.;        pt[j]=p[j]; 
        } 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fptt=(*func)(ptt); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      if (fptt < fp) { 
     newm=savm;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     /* Covariates have to be included here again */        if (t < 0.0) { 
      cov[2]=agefin;          linmin(p,xit,n,fret,func); 
            for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovn;k++) {            xi[j][ibig]=xi[j][n]; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            xi[j][n]=xit[j]; 
         /*      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]]);*/          }
       }  #ifdef DEBUG
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (k=1; k<=cptcovprod;k++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/            fprintf(ficlog," %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          }
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          printf("\n");
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          fprintf(ficlog,"\n");
   #endif
     savm=oldm;        }
     oldm=newm;      } 
     maxmax=0.;    } 
     for(j=1;j<=nlstate;j++){  } 
       min=1.;  
       max=0.;  /**** Prevalence limit (stable prevalence)  ****************/
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  {
         prlim[i][j]= newm[i][j]/(1-sumnew);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         max=FMAX(max,prlim[i][j]);       matrix by transitions matrix until convergence is reached */
         min=FMIN(min,prlim[i][j]);  
       }    int i, ii,j,k;
       maxmin=max-min;    double min, max, maxmin, maxmax,sumnew=0.;
       maxmax=FMAX(maxmax,maxmin);    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
     if(maxmax < ftolpl){    double **newm;
       return prlim;    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
 }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /*************** transition probabilities ***************/      }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )     cov[1]=1.;
 {   
   double s1, s2;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /*double t34;*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   int i,j,j1, nc, ii, jj;      newm=savm;
       /* Covariates have to be included here again */
     for(i=1; i<= nlstate; i++){       cov[2]=agefin;
     for(j=1; j<i;j++){    
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for (k=1; k<=cptcovn;k++) {
         /*s2 += param[i][j][nc]*cov[nc];*/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          /*      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("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        }
       }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ps[i][j]=s2;        for (k=1; k<=cptcovprod;k++)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       }  
       ps[i][j]=s2;      savm=oldm;
     }      oldm=newm;
   }      maxmax=0.;
     /*ps[3][2]=1;*/      for(j=1;j<=nlstate;j++){
         min=1.;
   for(i=1; i<= nlstate; i++){        max=0.;
      s1=0;        for(i=1; i<=nlstate; i++) {
     for(j=1; j<i; j++)          sumnew=0;
       s1+=exp(ps[i][j]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(j=i+1; j<=nlstate+ndeath; j++)          prlim[i][j]= newm[i][j]/(1-sumnew);
       s1+=exp(ps[i][j]);          max=FMAX(max,prlim[i][j]);
     ps[i][i]=1./(s1+1.);          min=FMIN(min,prlim[i][j]);
     for(j=1; j<i; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmin=max-min;
     for(j=i+1; j<=nlstate+ndeath; j++)        maxmax=FMAX(maxmax,maxmin);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      if(maxmax < ftolpl){
   } /* end i */        return prlim;
       }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){  }
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  /*************** transition probabilities ***************/ 
     }  
   }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
     double s1, s2;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    /*double t34;*/
     for(jj=1; jj<= nlstate+ndeath; jj++){    int i,j,j1, nc, ii, jj;
      printf("%lf ",ps[ii][jj]);  
    }      for(i=1; i<= nlstate; i++){
     printf("\n ");      for(j=1; j<i;j++){
     }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     printf("\n ");printf("%lf ",cov[2]);*/          /*s2 += param[i][j][nc]*cov[nc];*/
 /*          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   goto end;*/        }
     return ps;        ps[i][j]=s2;
 }        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
 /**************** Product of 2 matrices ******************/      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          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);*/
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        ps[i][j]=s2;
   /* in, b, out are matrice of pointers which should have been initialized      }
      before: only the contents of out is modified. The function returns    }
      a pointer to pointers identical to out */      /*ps[3][2]=1;*/
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)    for(i=1; i<= nlstate; i++){
     for(k=ncolol; k<=ncoloh; k++)       s1=0;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      for(j=1; j<i; j++)
         out[i][k] +=in[i][j]*b[j][k];        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
   return out;        s1+=exp(ps[i][j]);
 }      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 /************* Higher Matrix Product ***************/      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {    } /* end i */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      for(jj=1; jj<= nlstate+ndeath; jj++){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        ps[ii][jj]=0;
      (typically every 2 years instead of every month which is too big).        ps[ii][ii]=1;
      Model is determined by parameters x and covariates have to be      }
      included manually here.    }
   
      */  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   int i, j, d, h, k;      for(jj=1; jj<= nlstate+ndeath; jj++){
   double **out, cov[NCOVMAX];       printf("%lf ",ps[ii][jj]);
   double **newm;     }
       printf("\n ");
   /* Hstepm could be zero and should return the unit matrix */      }
   for (i=1;i<=nlstate+ndeath;i++)      printf("\n ");printf("%lf ",cov[2]);*/
     for (j=1;j<=nlstate+ndeath;j++){  /*
       oldm[i][j]=(i==j ? 1.0 : 0.0);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    goto end;*/
     }      return ps;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /**************** Product of 2 matrices ******************/
       newm=savm;  
       /* Covariates have to be included here again */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       cov[1]=1.;  {
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (k=1; k<=cptcovage;k++)    /* in, b, out are matrice of pointers which should have been initialized 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       before: only the contents of out is modified. The function returns
       for (k=1; k<=cptcovprod;k++)       a pointer to pointers identical to out */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    long i, j, k;
     for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          out[i][k] +=in[i][j]*b[j][k];
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    return out;
       savm=oldm;  }
       oldm=newm;  
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /************* Higher Matrix Product ***************/
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
       }       duration (i.e. until
   } /* end h */       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
   return po;       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).
        Model is determined by parameters x and covariates have to be 
        included manually here. 
 /*************** log-likelihood *************/  
 double func( double *x)       */
 {  
   int i, ii, j, k, mi, d, kk;    int i, j, d, h, k;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double **out, cov[NCOVMAX];
   double **out;    double **newm;
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    /* Hstepm could be zero and should return the unit matrix */
   long ipmx;    for (i=1;i<=nlstate+ndeath;i++)
   /*extern weight */      for (j=1;j<=nlstate+ndeath;j++){
   /* We are differentiating ll according to initial status */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /*for(i=1;i<imx;i++)      }
     printf(" %d\n",s[4][i]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   */    for(h=1; h <=nhstepm; h++){
   cov[1]=1.;      for(d=1; d <=hstepm; d++){
         newm=savm;
   for(k=1; k<=nlstate; k++) ll[k]=0.;        /* Covariates have to be included here again */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        cov[1]=1.;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for(mi=1; mi<= wav[i]-1; mi++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (k=1; k<=cptcovage;k++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for(d=0; d<dh[mi][i]; d++){        for (k=1; k<=cptcovprod;k++)
         newm=savm;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        savm=oldm;
         savm=oldm;        oldm=newm;
         oldm=newm;      }
              for(i=1; i<=nlstate+ndeath; i++)
                for(j=1;j<=nlstate+ndeath;j++) {
       } /* end mult */          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]);
       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;    } /* end h */
       sw += weight[i];    return po;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  }
     } /* end of wave */  
   } /* end of individual */  
   /*************** log-likelihood *************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  double func( double *x)
   /* 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 */    int i, ii, j, k, mi, d, kk;
   return -l;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 }    double **out;
     double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 /*********** Maximum Likelihood Estimation ***************/    long ipmx;
     /*extern weight */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /* We are differentiating ll according to initial status */
 {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int i,j, iter;    /*for(i=1;i<imx;i++) 
   double **xi,*delti;      printf(" %d\n",s[4][i]);
   double fret;    */
   xi=matrix(1,npar,1,npar);    cov[1]=1.;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       xi[i][j]=(i==j ? 1.0 : 0.0);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   printf("Powell\n");      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   powell(p,xi,npar,ftol,&iter,&fret,func);      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
 }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 /**** Computes Hessian and covariance matrix ***/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          }
 {          
   double  **a,**y,*x,pd;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **hess;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i, j,jk;          savm=oldm;
   int *indx;          oldm=newm;
           
   double hessii(double p[], double delta, int theta, double delti[]);          
   double hessij(double p[], double delti[], int i, int j);        } /* end mult */
   void lubksb(double **a, int npar, int *indx, double b[]) ;        
   void ludcmp(double **a, int npar, int *indx, double *d) ;        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]]);*/
   hess=matrix(1,npar,1,npar);        ipmx +=1;
         sw += weight[i];
   printf("\nCalculation of the hessian matrix. Wait...\n");        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (i=1;i<=npar;i++){      } /* end of wave */
     printf("%d",i);fflush(stdout);    } /* end of individual */
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /*printf(" %lf ",hess[i][i]);*/    /* 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;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  /*********** Maximum Likelihood Estimation ***************/
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         /*printf(" %lf ",hess[i][j]);*/  {
       }    int i,j, iter;
     }    double **xi,*delti;
   }    double fret;
   printf("\n");    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
   a=matrix(1,npar,1,npar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   y=matrix(1,npar,1,npar);    powell(p,xi,npar,ftol,&iter,&fret,func);
   x=vector(1,npar);  
   indx=ivector(1,npar);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (i=1;i<=npar;i++)    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   ludcmp(a,npar,indx,&pd);  
   }
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /**** Computes Hessian and covariance matrix ***/
     x[j]=1;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    double  **a,**y,*x,pd;
       matcov[i][j]=x[i];    double **hess;
     }    int i, j,jk;
   }    int *indx;
   
   printf("\n#Hessian matrix#\n");    double hessii(double p[], double delta, int theta, double delti[]);
   for (i=1;i<=npar;i++) {    double hessij(double p[], double delti[], int i, int j);
     for (j=1;j<=npar;j++) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
       printf("%.3e ",hess[i][j]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     }  
     printf("\n");    hess=matrix(1,npar,1,npar);
   }  
     printf("\nCalculation of the hessian matrix. Wait...\n");
   /* Recompute Inverse */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++){
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      printf("%d",i);fflush(stdout);
   ludcmp(a,npar,indx,&pd);      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
   /*  printf("\n#Hessian matrix recomputed#\n");      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
   for (j=1;j<=npar;j++) {    }
     for (i=1;i<=npar;i++) x[i]=0;    
     x[j]=1;    for (i=1;i<=npar;i++) {
     lubksb(a,npar,indx,x);      for (j=1;j<=npar;j++)  {
     for (i=1;i<=npar;i++){        if (j>i) { 
       y[i][j]=x[i];          printf(".%d%d",i,j);fflush(stdout);
       printf("%.3e ",y[i][j]);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     }          hess[i][j]=hessij(p,delti,i,j);
     printf("\n");          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
   */        }
       }
   free_matrix(a,1,npar,1,npar);    }
   free_matrix(y,1,npar,1,npar);    printf("\n");
   free_vector(x,1,npar);    fprintf(ficlog,"\n");
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);    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);
     y=matrix(1,npar,1,npar);
 /*************** hessian matrix ****************/    x=vector(1,npar);
 double hessii( double x[], double delta, int theta, double delti[])    indx=ivector(1,npar);
 {    for (i=1;i<=npar;i++)
   int i;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   int l=1, lmax=20;    ludcmp(a,npar,indx,&pd);
   double k1,k2;  
   double p2[NPARMAX+1];    for (j=1;j<=npar;j++) {
   double res;      for (i=1;i<=npar;i++) x[i]=0;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      x[j]=1;
   double fx;      lubksb(a,npar,indx,x);
   int k=0,kmax=10;      for (i=1;i<=npar;i++){ 
   double l1;        matcov[i][j]=x[i];
       }
   fx=func(x);    }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){    printf("\n#Hessian matrix#\n");
     l1=pow(10,l);    fprintf(ficlog,"\n#Hessian matrix#\n");
     delts=delt;    for (i=1;i<=npar;i++) { 
     for(k=1 ; k <kmax; k=k+1){      for (j=1;j<=npar;j++) { 
       delt = delta*(l1*k);        printf("%.3e ",hess[i][j]);
       p2[theta]=x[theta] +delt;        fprintf(ficlog,"%.3e ",hess[i][j]);
       k1=func(p2)-fx;      }
       p2[theta]=x[theta]-delt;      printf("\n");
       k2=func(p2)-fx;      fprintf(ficlog,"\n");
       /*res= (k1-2.0*fx+k2)/delt/delt; */    }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          /* Recompute Inverse */
 #ifdef DEBUG    for (i=1;i<=npar;i++)
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 #endif    ludcmp(a,npar,indx,&pd);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /*  printf("\n#Hessian matrix recomputed#\n");
         k=kmax;  
       }    for (j=1;j<=npar;j++) {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for (i=1;i<=npar;i++) x[i]=0;
         k=kmax; l=lmax*10.;      x[j]=1;
       }      lubksb(a,npar,indx,x);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (i=1;i<=npar;i++){ 
         delts=delt;        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
     }        fprintf(ficlog,"%.3e ",y[i][j]);
   }      }
   delti[theta]=delts;      printf("\n");
   return res;      fprintf(ficlog,"\n");
      }
 }    */
   
 double hessij( double x[], double delti[], int thetai,int thetaj)    free_matrix(a,1,npar,1,npar);
 {    free_matrix(y,1,npar,1,npar);
   int i;    free_vector(x,1,npar);
   int l=1, l1, lmax=20;    free_ivector(indx,1,npar);
   double k1,k2,k3,k4,res,fx;    free_matrix(hess,1,npar,1,npar);
   double p2[NPARMAX+1];  
   int k;  
   }
   fx=func(x);  
   for (k=1; k<=2; k++) {  /*************** hessian matrix ****************/
     for (i=1;i<=npar;i++) p2[i]=x[i];  double hessii( double x[], double delta, int theta, double delti[])
     p2[thetai]=x[thetai]+delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    int i;
     k1=func(p2)-fx;    int l=1, lmax=20;
      double k1,k2;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double p2[NPARMAX+1];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double res;
     k2=func(p2)-fx;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      double fx;
     p2[thetai]=x[thetai]-delti[thetai]/k;    int k=0,kmax=10;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double l1;
     k3=func(p2)-fx;  
      fx=func(x);
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (i=1;i<=npar;i++) p2[i]=x[i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for(l=0 ; l <=lmax; l++){
     k4=func(p2)-fx;      l1=pow(10,l);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      delts=delt;
 #ifdef DEBUG      for(k=1 ; k <kmax; k=k+1){
     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);        delt = delta*(l1*k);
 #endif        p2[theta]=x[theta] +delt;
   }        k1=func(p2)-fx;
   return res;        p2[theta]=x[theta]-delt;
 }        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 /************** Inverse of matrix **************/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 void ludcmp(double **a, int n, int *indx, double *d)        
 {  #ifdef DEBUG
   int i,imax,j,k;        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);
   double big,dum,sum,temp;        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);
   double *vv;  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   vv=vector(1,n);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   *d=1.0;          k=kmax;
   for (i=1;i<=n;i++) {        }
     big=0.0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     for (j=1;j<=n;j++)          k=kmax; l=lmax*10.;
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     vv[i]=1.0/big;          delts=delt;
   }        }
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {    }
       sum=a[i][j];    delti[theta]=delts;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    return res; 
       a[i][j]=sum;    
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  double hessij( double x[], double delti[], int thetai,int thetaj)
       sum=a[i][j];  {
       for (k=1;k<j;k++)    int i;
         sum -= a[i][k]*a[k][j];    int l=1, l1, lmax=20;
       a[i][j]=sum;    double k1,k2,k3,k4,res,fx;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    double p2[NPARMAX+1];
         big=dum;    int k;
         imax=i;  
       }    fx=func(x);
     }    for (k=1; k<=2; k++) {
     if (j != imax) {      for (i=1;i<=npar;i++) p2[i]=x[i];
       for (k=1;k<=n;k++) {      p2[thetai]=x[thetai]+delti[thetai]/k;
         dum=a[imax][k];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         a[imax][k]=a[j][k];      k1=func(p2)-fx;
         a[j][k]=dum;    
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
       *d = -(*d);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       vv[imax]=vv[j];      k2=func(p2)-fx;
     }    
     indx[j]=imax;      p2[thetai]=x[thetai]-delti[thetai]/k;
     if (a[j][j] == 0.0) a[j][j]=TINY;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     if (j != n) {      k3=func(p2)-fx;
       dum=1.0/(a[j][j]);    
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k4=func(p2)-fx;
   free_vector(vv,1,n);  /* Doesn't work */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 ;  #ifdef DEBUG
 }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       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);
 void lubksb(double **a, int n, int *indx, double b[])  #endif
 {    }
   int i,ii=0,ip,j;    return res;
   double sum;  }
    
   for (i=1;i<=n;i++) {  /************** Inverse of matrix **************/
     ip=indx[i];  void ludcmp(double **a, int n, int *indx, double *d) 
     sum=b[ip];  { 
     b[ip]=b[i];    int i,imax,j,k; 
     if (ii)    double big,dum,sum,temp; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    double *vv; 
     else if (sum) ii=i;   
     b[i]=sum;    vv=vector(1,n); 
   }    *d=1.0; 
   for (i=n;i>=1;i--) {    for (i=1;i<=n;i++) { 
     sum=b[i];      big=0.0; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for (j=1;j<=n;j++) 
     b[i]=sum/a[i][i];        if ((temp=fabs(a[i][j])) > big) big=temp; 
   }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 }      vv[i]=1.0/big; 
     } 
 /************ Frequencies ********************/    for (j=1;j<=n;j++) { 
 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)      for (i=1;i<j;i++) { 
 {  /* Some frequencies */        sum=a[i][j]; 
          for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        a[i][j]=sum; 
   double ***freq; /* Frequencies */      } 
   double *pp;      big=0.0; 
   double pos, k2, dateintsum=0,k2cpt=0;      for (i=j;i<=n;i++) { 
   FILE *ficresp;        sum=a[i][j]; 
   char fileresp[FILENAMELENGTH];        for (k=1;k<j;k++) 
            sum -= a[i][k]*a[k][j]; 
   pp=vector(1,nlstate);        a[i][j]=sum; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   strcpy(fileresp,"p");          big=dum; 
   strcat(fileresp,fileres);          imax=i; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        } 
     printf("Problem with prevalence resultfile: %s\n", fileresp);      } 
     exit(0);      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          dum=a[imax][k]; 
   j1=0;          a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
   j=cptcoveff;        } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        *d = -(*d); 
          vv[imax]=vv[j]; 
   for(k1=1; k1<=j;k1++){      } 
     for(i1=1; i1<=ncodemax[k1];i1++){      indx[j]=imax; 
       j1++;      if (a[j][j] == 0.0) a[j][j]=TINY; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      if (j != n) { 
         scanf("%d", i);*/        dum=1.0/(a[j][j]); 
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        } 
           for(m=agemin; m <= agemax+3; m++)    } 
             freq[i][jk][m]=0;    free_vector(vv,1,n);  /* Doesn't work */
        ;
       dateintsum=0;  } 
       k2cpt=0;  
       for (i=1; i<=imx; i++) {  void lubksb(double **a, int n, int *indx, double b[]) 
         bool=1;  { 
         if  (cptcovn>0) {    int i,ii=0,ip,j; 
           for (z1=1; z1<=cptcoveff; z1++)    double sum; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])   
               bool=0;    for (i=1;i<=n;i++) { 
         }      ip=indx[i]; 
         if (bool==1) {      sum=b[ip]; 
           for(m=firstpass; m<=lastpass; m++){      b[ip]=b[i]; 
             k2=anint[m][i]+(mint[m][i]/12.);      if (ii) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      else if (sum) ii=i; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      b[i]=sum; 
               if (m<lastpass) {    } 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for (i=n;i>=1;i--) { 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      sum=b[i]; 
               }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                    b[i]=sum/a[i][i]; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    } 
                 dateintsum=dateintsum+k2;  } 
                 k2cpt++;  
               }  /************ Frequencies ********************/
             }  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
           }  {  /* Some frequencies */
         }    
       }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
            int first;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double ***freq; /* Frequencies */
     double *pp;
       if  (cptcovn>0) {    double pos, k2, dateintsum=0,k2cpt=0;
         fprintf(ficresp, "\n#********** Variable ");    FILE *ficresp;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    char fileresp[FILENAMELENGTH];
         fprintf(ficresp, "**********\n#");    
       }    pp=vector(1,nlstate);
       for(i=1; i<=nlstate;i++)    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    strcpy(fileresp,"p");
       fprintf(ficresp, "\n");    strcat(fileresp,fileres);
          if((ficresp=fopen(fileresp,"w"))==NULL) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
         if(i==(int)agemax+3)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           printf("Total");      exit(0);
         else    }
           printf("Age %d", i);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         for(jk=1; jk <=nlstate ; jk++){    j1=0;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    
             pp[jk] += freq[jk][m][i];    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)    first=1;
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10)    for(k1=1; k1<=j;k1++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      for(i1=1; i1<=ncodemax[k1];i1++){
           else        j1++;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
         for(jk=1; jk <=nlstate ; jk++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for(m=agemin; m <= agemax+3; m++)
             pp[jk] += freq[jk][m][i];              freq[i][jk][m]=0;
         }        
         dateintsum=0;
         for(jk=1,pos=0; jk <=nlstate ; jk++)        k2cpt=0;
           pos += pp[jk];        for (i=1; i<=imx; i++) {
         for(jk=1; jk <=nlstate ; jk++){          bool=1;
           if(pos>=1.e-5)          if  (cptcovn>0) {
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            for (z1=1; z1<=cptcoveff; z1++) 
           else              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                bool=0;
           if( i <= (int) agemax){          }
             if(pos>=1.e-5){          if (bool==1) {
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for(m=firstpass; m<=lastpass; m++){
               probs[i][jk][j1]= pp[jk]/pos;              k2=anint[m][i]+(mint[m][i]/12.);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              if ((k2>=dateprev1) && (k2<=dateprev2)) {
             }                if(agev[m][i]==0) agev[m][i]=agemax+1;
             else                if(agev[m][i]==1) agev[m][i]=agemax+2;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);                if (m<lastpass) {
           }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         }                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
                        }
         for(jk=-1; jk <=nlstate+ndeath; jk++)                
           for(m=-1; m <=nlstate+ndeath; m++)                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                  dateintsum=dateintsum+k2;
         if(i <= (int) agemax)                  k2cpt++;
           fprintf(ficresp,"\n");                }
         printf("\n");              }
       }            }
     }          }
   }        }
   dateintmean=dateintsum/k2cpt;         
          fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if  (cptcovn>0) {
   free_vector(pp,1,nlstate);          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* End of Freq */          fprintf(ficresp, "**********\n#");
 }        }
         for(i=1; i<=nlstate;i++) 
 /************ Prevalence ********************/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 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)        fprintf(ficresp, "\n");
 {  /* Some frequencies */        
          for(i=(int)agemin; i <= (int)agemax+3; i++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          if(i==(int)agemax+3){
   double ***freq; /* Frequencies */            fprintf(ficlog,"Total");
   double *pp;          }else{
   double pos, k2;            if(first==1){
               first=0;
   pp=vector(1,nlstate);              printf("See log file for details...\n");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
              fprintf(ficlog,"Age %d", i);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }
   j1=0;          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   j=cptcoveff;              pp[jk] += freq[jk][m][i]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          }
            for(jk=1; jk <=nlstate ; jk++){
   for(k1=1; k1<=j;k1++){            for(m=-1, pos=0; m <=0 ; m++)
     for(i1=1; i1<=ncodemax[k1];i1++){              pos += freq[jk][m][i];
       j1++;            if(pp[jk]>=1.e-10){
                    if(first==1){
       for (i=-1; i<=nlstate+ndeath; i++)                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)                }
           for(m=agemin; m <= agemax+3; m++)              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             freq[i][jk][m]=0;            }else{
                    if(first==1)
       for (i=1; i<=imx; i++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         bool=1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         if  (cptcovn>0) {            }
           for (z1=1; z1<=cptcoveff; z1++)          }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         if (bool==1) {              pp[jk] += freq[jk][m][i];
           for(m=firstpass; m<=lastpass; m++){          }
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          for(jk=1,pos=0; jk <=nlstate ; jk++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;            pos += pp[jk];
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for(jk=1; jk <=nlstate ; jk++){
               if (m<lastpass) {            if(pos>=1.e-5){
                 if (calagedate>0)              if(first==1)
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                 else              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            }else{
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];              if(first==1)
               }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
         }            if( i <= (int) agemax){
       }              if(pos>=1.e-5){
       for(i=(int)agemin; i <= (int)agemax+3; i++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
         for(jk=1; jk <=nlstate ; jk++){                probs[i][jk][j1]= pp[jk]/pos;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             pp[jk] += freq[jk][m][i];              }
         }              else
         for(jk=1; jk <=nlstate ; jk++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
           for(m=-1, pos=0; m <=0 ; m++)            }
             pos += freq[jk][m][i];          }
         }          
                  for(jk=-1; jk <=nlstate+ndeath; jk++)
         for(jk=1; jk <=nlstate ; jk++){            for(m=-1; m <=nlstate+ndeath; m++)
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              if(freq[jk][m][i] !=0 ) {
             pp[jk] += freq[jk][m][i];              if(first==1)
         }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                        fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];              }
                  if(i <= (int) agemax)
         for(jk=1; jk <=nlstate ; jk++){                fprintf(ficresp,"\n");
           if( i <= (int) agemax){          if(first==1)
             if(pos>=1.e-5){            printf("Others in log...\n");
               probs[i][jk][j1]= pp[jk]/pos;          fprintf(ficlog,"\n");
             }        }
           }      }
         }    }
            dateintmean=dateintsum/k2cpt; 
       }   
     }    fclose(ficresp);
   }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     free_vector(pp,1,nlstate);
      
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* End of Freq */
   free_vector(pp,1,nlstate);  }
    
 }  /* End of Freq */  /************ Prevalence ********************/
   void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
 /************* Waves Concatenation ***************/  {  /* Some frequencies */
    
 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 i, m, jk, k1, i1, j1, bool, z1,z2,j;
 {    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;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    pp=vector(1,nlstate);
      and mw[mi+1][i]. dh depends on stepm.    
      */    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
     j1=0;
   int i, mi, m;    
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    j=cptcoveff;
      double sum=0., jmean=0.;*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   int j, k=0,jk, ju, jl;    for(k1=1; k1<=j;k1++){
   double sum=0.;      for(i1=1; i1<=ncodemax[k1];i1++){
   jmin=1e+5;        j1++;
   jmax=-1;        
   jmean=0.;        for (i=-1; i<=nlstate+ndeath; i++)  
   for(i=1; i<=imx; i++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     mi=0;            for(m=agemin; m <= agemax+3; m++)
     m=firstpass;              freq[i][jk][m]=0;
     while(s[m][i] <= nlstate){       
       if(s[m][i]>=1)        for (i=1; i<=imx; i++) {
         mw[++mi][i]=m;          bool=1;
       if(m >=lastpass)          if  (cptcovn>0) {
         break;            for (z1=1; z1<=cptcoveff; z1++) 
       else              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         m++;                bool=0;
     }/* end while */          } 
     if (s[m][i] > nlstate){          if (bool==1) { 
       mi++;     /* Death is another wave */            for(m=firstpass; m<=lastpass; m++){
       /* if(mi==0)  never been interviewed correctly before death */              k2=anint[m][i]+(mint[m][i]/12.);
          /* Only death is a correct wave */              if ((k2>=dateprev1) && (k2<=dateprev2)) {
       mw[mi][i]=m;                if(agev[m][i]==0) agev[m][i]=agemax+1;
     }                if(agev[m][i]==1) agev[m][i]=agemax+2;
                 if (m<lastpass) {
     wav[i]=mi;                  if (calagedate>0) 
     if(mi==0)                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);                  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<=imx; i++){                }
     for(mi=1; mi<wav[i];mi++){              }
       if (stepm <=0)            }
         dh[mi][i]=1;          }
       else{        }
         if (s[mw[mi+1][i]][i] > nlstate) {        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
           if (agedc[i] < 2*AGESUP) {          for(jk=1; jk <=nlstate ; jk++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           if(j==0) j=1;  /* Survives at least one month after exam */              pp[jk] += freq[jk][m][i]; 
           k=k+1;          }
           if (j >= jmax) jmax=j;          for(jk=1; jk <=nlstate ; jk++){
           if (j <= jmin) jmin=j;            for(m=-1, pos=0; m <=0 ; m++)
           sum=sum+j;              pos += freq[jk][m][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          }
           }          
         }          for(jk=1; jk <=nlstate ; jk++){
         else{            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              pp[jk] += freq[jk][m][i];
           k=k+1;          }
           if (j >= jmax) jmax=j;          
           else if (j <= jmin)jmin=j;          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          
           sum=sum+j;          for(jk=1; jk <=nlstate ; jk++){    
         }            if( i <= (int) agemax){
         jk= j/stepm;              if(pos>=1.e-5){
         jl= j -jk*stepm;                probs[i][jk][j1]= pp[jk]/pos;
         ju= j -(jk+1)*stepm;              }
         if(jl <= -ju)            }
           dh[mi][i]=jk;          }/* end jk */
         else        }/* end i */
           dh[mi][i]=jk+1;      } /* end i1 */
         if(dh[mi][i]==0)    } /* end k1 */
           dh[mi][i]=1; /* At least one step */  
       }    
     }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   }    free_vector(pp,1,nlstate);
   jmean=sum/k;    
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  }  /* End of Freq */
  }  
 /*********** Tricode ****************************/  /************* Waves Concatenation ***************/
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  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 Ndum[20],ij=1, k, j, i;  {
   int cptcode=0;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   cptcoveff=0;       Death is a valid wave (if date is known).
         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   for (k=0; k<19; k++) Ndum[k]=0;       dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
   for (k=1; k<=7; k++) ncodemax[k]=0;       and mw[mi+1][i]. dh depends on stepm.
        */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {    int i, mi, m;
       ij=(int)(covar[Tvar[j]][i]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       Ndum[ij]++;       double sum=0., jmean=0.;*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    int first;
       if (ij > cptcode) cptcode=ij;    int j, k=0,jk, ju, jl;
     }    double sum=0.;
     first=0;
     for (i=0; i<=cptcode; i++) {    jmin=1e+5;
       if(Ndum[i]!=0) ncodemax[j]++;    jmax=-1;
     }    jmean=0.;
     ij=1;    for(i=1; i<=imx; i++){
       mi=0;
       m=firstpass;
     for (i=1; i<=ncodemax[j]; i++) {      while(s[m][i] <= nlstate){
       for (k=0; k<=19; k++) {        if(s[m][i]>=1)
         if (Ndum[k] != 0) {          mw[++mi][i]=m;
           nbcode[Tvar[j]][ij]=k;        if(m >=lastpass)
                    break;
           ij++;        else
         }          m++;
         if (ij > ncodemax[j]) break;      }/* end while */
       }        if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
   }          /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
  for (k=0; k<19; k++) Ndum[k]=0;        mw[mi][i]=m;
       }
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];      wav[i]=mi;
       Ndum[ij]++;      if(mi==0){
     }        if(first==0){
           printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
  ij=1;          first=1;
  for (i=1; i<=10; i++) {        }
    if((Ndum[i]!=0) && (i<=ncovcol)){        if(first==1){
      Tvaraff[ij]=i;          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
      ij++;        }
    }      } /* end mi==0 */
  }    }
    
     cptcoveff=ij-1;    for(i=1; i<=imx; i++){
 }      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
 /*********** Health Expectancies ****************/          dh[mi][i]=1;
         else{
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
 {            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   /* Health expectancies */            if(j==0) j=1;  /* Survives at least one month after exam */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;            k=k+1;
   double age, agelim, hf;            if (j >= jmax) jmax=j;
   double ***p3mat,***varhe;            if (j <= jmin) jmin=j;
   double **dnewm,**doldm;            sum=sum+j;
   double *xp;            /*if (j<0) printf("j=%d num=%d \n",j,i); */
   double **gp, **gm;            }
   double ***gradg, ***trgradg;          }
   int theta;          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            k=k+1;
   xp=vector(1,npar);            if (j >= jmax) jmax=j;
   dnewm=matrix(1,nlstate*2,1,npar);            else if (j <= jmin)jmin=j;
   doldm=matrix(1,nlstate*2,1,nlstate*2);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
              sum=sum+j;
   fprintf(ficreseij,"# Health expectancies\n");          }
   fprintf(ficreseij,"# Age");          jk= j/stepm;
   for(i=1; i<=nlstate;i++)          jl= j -jk*stepm;
     for(j=1; j<=nlstate;j++)          ju= j -(jk+1)*stepm;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          if(jl <= -ju)
   fprintf(ficreseij,"\n");            dh[mi][i]=jk;
           else
   if(estepm < stepm){            dh[mi][i]=jk+1;
     printf ("Problem %d lower than %d\n",estepm, stepm);          if(dh[mi][i]==0)
   }            dh[mi][i]=1; /* At least one step */
   else  hstepm=estepm;          }
   /* We compute the life expectancy from trapezoids spaced every estepm months      }
    * This is mainly to measure the difference between two models: for example    }
    * if stepm=24 months pijx are given only every 2 years and by summing them    jmean=sum/k;
    * we are calculating an estimate of the Life Expectancy assuming a linear    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    * progression inbetween and thus overestimating or underestimating according    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    * 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  
    * to compare the new estimate of Life expectancy with the same linear  /*********** Tricode ****************************/
    * hypothesis. A more precise result, taking into account a more precise  void tricode(int *Tvar, int **nbcode, int imx)
    * curvature will be obtained if estepm is as small as stepm. */  {
     int Ndum[20],ij=1, k, j, i;
   /* For example we decided to compute the life expectancy with the smallest unit */    int cptcode=0;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    cptcoveff=0; 
      nhstepm is the number of hstepm from age to agelim   
      nstepm is the number of stepm from age to agelin.    for (k=0; k<19; k++) Ndum[k]=0;
      Look at hpijx to understand the reason of that which relies in memory size    for (k=1; k<=7; k++) ncodemax[k]=0;
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      survival function given by stepm (the optimization length). Unfortunately it      for (i=1; i<=imx; i++) {
      means that if the survival funtion is printed only each two years of age and if        ij=(int)(covar[Tvar[j]][i]);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        Ndum[ij]++; 
      results. So we changed our mind and took the option of the best precision.        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   */        if (ij > cptcode) cptcode=ij; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      }
   
   agelim=AGESUP;      for (i=0; i<=cptcode; i++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if(Ndum[i]!=0) ncodemax[j]++;
     /* nhstepm age range expressed in number of stepm */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      ij=1; 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */  
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1; i<=ncodemax[j]; i++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=0; k<=19; k++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          if (Ndum[k] != 0) {
     gp=matrix(0,nhstepm,1,nlstate*2);            nbcode[Tvar[j]][ij]=k; 
     gm=matrix(0,nhstepm,1,nlstate*2);            
             ij++;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          if (ij > ncodemax[j]) break; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }  
        } 
     }  
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
    for (k=0; k<19; k++) Ndum[k]=0;
     /* Computing Variances of health expectancies */  
    for (i=1; i<=ncovmodel-2; i++) {
      for(theta=1; theta <=npar; theta++){     ij=Tvar[i];
       for(i=1; i<=npar; i++){     Ndum[ij]++; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     ij=1;
     for (i=1; i<=10; i++) {
       cptj=0;     if((Ndum[i]!=0) && (i<=ncovcol)){
       for(j=1; j<= nlstate; j++){       Tvaraff[ij]=i; 
         for(i=1; i<=nlstate; i++){       ij++;
           cptj=cptj+1;     }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){   }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;   
           }   cptcoveff=ij-1;
         }  }
       }  
        /*********** Health Expectancies ****************/
        
       for(i=1; i<=npar; i++)  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
          /* Health expectancies */
       cptj=0;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for(j=1; j<= nlstate; j++){    double age, agelim, hf;
         for(i=1;i<=nlstate;i++){    double ***p3mat,***varhe;
           cptj=cptj+1;    double **dnewm,**doldm;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    double *xp;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double **gp, **gm;
           }    double ***gradg, ***trgradg;
         }    int theta;
       }  
          varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
        xp=vector(1,npar);
     dnewm=matrix(1,nlstate*2,1,npar);
       for(j=1; j<= nlstate*2; j++)    doldm=matrix(1,nlstate*2,1,nlstate*2);
         for(h=0; h<=nhstepm-1; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficreseij,"# Health expectancies\n");
         }    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
      }      for(j=1; j<=nlstate;j++)
            fprintf(ficreseij," %1d-%1d (SE)",i,j);
 /* End theta */    fprintf(ficreseij,"\n");
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
      for(h=0; h<=nhstepm-1; h++)    }
       for(j=1; j<=nlstate*2;j++)    else  hstepm=estepm;   
         for(theta=1; theta <=npar; theta++)    /* We compute the life expectancy from trapezoids spaced every estepm months
         trgradg[h][j][theta]=gradg[h][theta][j];     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      for(i=1;i<=nlstate*2;i++)     * progression inbetween and thus overestimating or underestimating according
       for(j=1;j<=nlstate*2;j++)     * to the curvature of the survival function. If, for the same date, we 
         varhe[i][j][(int)age] =0.;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      printf("%d||",(int)age);fflush(stdout);     * hypothesis. A more precise result, taking into account a more precise
     for(h=0;h<=nhstepm-1;h++){     * curvature will be obtained if estepm is as small as stepm. */
       for(k=0;k<=nhstepm-1;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    /* For example we decided to compute the life expectancy with the smallest unit */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         for(i=1;i<=nlstate*2;i++)       nhstepm is the number of hstepm from age to agelim 
           for(j=1;j<=nlstate*2;j++)       nstepm is the number of stepm from age to agelin. 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;       Look at hpijx to understand the reason of that which relies in memory size
       }       and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        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
     /* Computing expectancies */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for(i=1; i<=nlstate;i++)       results. So we changed our mind and took the option of the best precision.
       for(j=1; j<=nlstate;j++)    */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
              agelim=AGESUP;
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
         }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fprintf(ficreseij,"%3.0f",age );      /* if (stepm >= YEARM) hstepm=1;*/
     cptj=0;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(i=1; i<=nlstate;i++)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j<=nlstate;j++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
         cptj++;      gp=matrix(0,nhstepm,1,nlstate*2);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      gm=matrix(0,nhstepm,1,nlstate*2);
       }  
     fprintf(ficreseij,"\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     free_matrix(gm,0,nhstepm,1,nlstate*2);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);   
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }      /* Computing Variances of health expectancies */
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);       for(theta=1; theta <=npar; theta++){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        for(i=1; i<=npar; i++){ 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 /************ Variance ******************/    
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)        cptj=0;
 {        for(j=1; j<= nlstate; j++){
   /* Variance of health expectancies */          for(i=1; i<=nlstate; i++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            cptj=cptj+1;
   double **newm;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   double **dnewm,**doldm;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   int i, j, nhstepm, hstepm, h, nstepm ;            }
   int k, cptcode;          }
   double *xp;        }
   double **gp, **gm;       
   double ***gradg, ***trgradg;       
   double ***p3mat;        for(i=1; i<=npar; i++) 
   double age,agelim, hf;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   int theta;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
    fprintf(ficresvij,"# Covariances of life expectancies\n");        cptj=0;
   fprintf(ficresvij,"# Age");        for(j=1; j<= nlstate; j++){
   for(i=1; i<=nlstate;i++)          for(i=1;i<=nlstate;i++){
     for(j=1; j<=nlstate;j++)            cptj=cptj+1;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   fprintf(ficresvij,"\n");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);        for(j=1; j<= nlstate*2; j++)
            for(h=0; h<=nhstepm-1; h++){
   if(estepm < stepm){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     printf ("Problem %d lower than %d\n",estepm, stepm);          }
   }       } 
   else  hstepm=estepm;       
   /* For example we decided to compute the life expectancy with the smallest unit */  /* End theta */
   /* 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       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size       for(h=0; h<=nhstepm-1; h++)
      and note for a fixed period like k years */        for(j=1; j<=nlstate*2;j++)
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(theta=1; theta <=npar; theta++)
      survival function given by stepm (the optimization length). Unfortunately it            trgradg[h][j][theta]=gradg[h][theta][j];
      means that if the survival funtion is printed only each two years of age and if       
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.       for(i=1;i<=nlstate*2;i++)
   */        for(j=1;j<=nlstate*2;j++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          varhe[i][j][(int)age] =0.;
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       printf("%d|",(int)age);fflush(stdout);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */       for(h=0;h<=nhstepm-1;h++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(k=0;k<=nhstepm-1;k++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
     gp=matrix(0,nhstepm,1,nlstate);          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
     gm=matrix(0,nhstepm,1,nlstate);          for(i=1;i<=nlstate*2;i++)
             for(j=1;j<=nlstate*2;j++)
     for(theta=1; theta <=npar; theta++){              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }      /* Computing expectancies */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(i=1; i<=nlstate;i++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       if (popbased==1) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         for(i=1; i<=nlstate;i++)            
           prlim[i][i]=probs[(int)age][i][ij];  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       }  
            }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){      fprintf(ficreseij,"%3.0f",age );
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      cptj=0;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
       }          cptj++;
              fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      fprintf(ficreseij,"\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);       
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      free_matrix(gm,0,nhstepm,1,nlstate*2);
        free_matrix(gp,0,nhstepm,1,nlstate*2);
       if (popbased==1) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
         for(i=1; i<=nlstate;i++)      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
           prlim[i][i]=probs[(int)age][i][ij];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    }
     printf("\n");
       for(j=1; j<= nlstate; j++){    fprintf(ficlog,"\n");
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    free_vector(xp,1,npar);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    free_matrix(dnewm,1,nlstate*2,1,npar);
         }    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
       }    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
   }
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){  /************ Variance ******************/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  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)
         }  {
     } /* End theta */    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* double **newm;*/
     double **dnewm,**doldm;
     for(h=0; h<=nhstepm; h++)    double **dnewmp,**doldmp;
       for(j=1; j<=nlstate;j++)    int i, j, nhstepm, hstepm, h, nstepm ;
         for(theta=1; theta <=npar; theta++)    int k, cptcode;
           trgradg[h][j][theta]=gradg[h][theta][j];    double *xp;
     double **gp, **gm;  /* for var eij */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double ***gradg, ***trgradg; /*for var eij */
     for(i=1;i<=nlstate;i++)    double **gradgp, **trgradgp; /* for var p point j */
       for(j=1;j<=nlstate;j++)    double *gpp, *gmp; /* for var p point j */
         vareij[i][j][(int)age] =0.;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     for(h=0;h<=nhstepm;h++){    double age,agelim, hf;
       for(k=0;k<=nhstepm;k++){    double ***mobaverage;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int theta;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    char digit[4];
         for(i=1;i<=nlstate;i++)    char digitp[25];
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    char fileresprobmorprev[FILENAMELENGTH];
       }  
     }    if(popbased==1){
       if(mobilav==1)
     fprintf(ficresvij,"%.0f ",age );        strcpy(digitp,"-populbased-mobilav-");
     for(i=1; i<=nlstate;i++)      else strcpy(digitp,"-populbased-nomobil-");
       for(j=1; j<=nlstate;j++){    }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    else 
       }      strcpy(digitp,"-stablbased-");
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    if (mobilav!=0) {
     free_matrix(gm,0,nhstepm,1,nlstate);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   } /* End age */      }
      }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    strcpy(fileresprobmorprev,"prmorprev"); 
   free_matrix(dnewm,1,nlstate,1,nlstate);    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 /************ Variance of prevlim ******************/    strcat(fileresprobmorprev,fileres);
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 {      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   /* Variance of prevalence limit */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   double **newm;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double **dnewm,**doldm;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   int i, j, nhstepm, hstepm;    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
   int k, cptcode;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   double *xp;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double *gp, *gm;      fprintf(ficresprobmorprev," p.%-d SE",j);
   double **gradg, **trgradg;      for(i=1; i<=nlstate;i++)
   double age,agelim;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int theta;    }  
        fprintf(ficresprobmorprev,"\n");
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   fprintf(ficresvpl,"# Age");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficresvpl," %1d-%1d",i,i);      exit(0);
   fprintf(ficresvpl,"\n");    }
     else{
   xp=vector(1,npar);      fprintf(ficgp,"\n# Routine varevsij");
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        printf("Problem with html file: %s\n", optionfilehtm);
   hstepm=1*YEARM; /* Every year of age */      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      exit(0);
   agelim = AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    else{
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      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");
     if (stepm >= YEARM) hstepm=1;      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    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(theta=1; theta <=npar; theta++){    for(i=1; i<=nlstate;i++)
       for(i=1; i<=npar; i++){ /* Computes gradient */      for(j=1; j<=nlstate;j++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       }    fprintf(ficresvij,"\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    xp=vector(1,npar);
         gp[i] = prlim[i][i];    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
       for(i=1; i<=npar; i++) /* Computes gradient */    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         gm[i] = prlim[i][i];    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
       for(i=1;i<=nlstate;i++)    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    
     } /* End theta */    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     trgradg =matrix(1,nlstate,1,npar);    }
     else  hstepm=estepm;   
     for(j=1; j<=nlstate;j++)    /* For example we decided to compute the life expectancy with the smallest unit */
       for(theta=1; theta <=npar; theta++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         trgradg[j][theta]=gradg[theta][j];       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
     for(i=1;i<=nlstate;i++)       Look at hpijx to understand the reason of that which relies in memory size
       varpl[i][(int)age] =0.;       and note for a fixed period like k years */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);       survival function given by stepm (the optimization length). Unfortunately it
     for(i=1;i<=nlstate;i++)       means that if the survival funtion is printed only each two years of age and if
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     fprintf(ficresvpl,"%.0f ",age );    */
     for(i=1; i<=nlstate;i++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    agelim = AGESUP;
     fprintf(ficresvpl,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_vector(gp,1,nlstate);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     free_vector(gm,1,nlstate);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     free_matrix(gradg,1,npar,1,nlstate);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_matrix(trgradg,1,nlstate,1,npar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   } /* End age */      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
 }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
 /************ Variance of one-step probabilities  ******************/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 {  
   int i, j, i1, k1, j1, z1;        if (popbased==1) {
   int k=0, cptcode;          if(mobilav ==0){
   double **dnewm,**doldm;            for(i=1; i<=nlstate;i++)
   double *xp;              prlim[i][i]=probs[(int)age][i][ij];
   double *gp, *gm;          }else{ /* mobilav */ 
   double **gradg, **trgradg;            for(i=1; i<=nlstate;i++)
   double age,agelim, cov[NCOVMAX];              prlim[i][i]=mobaverage[(int)age][i][ij];
   int theta;          }
   char fileresprob[FILENAMELENGTH];        }
     
   strcpy(fileresprob,"prob");        for(j=1; j<= nlstate; j++){
   strcat(fileresprob,fileres);          for(h=0; h<=nhstepm; h++){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     printf("Problem with resultfile: %s\n", fileresprob);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        }
          /* This for computing forces of mortality (h=1)as a weighted average */
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
   fprintf(ficresprob,"# Age");          for(i=1; i<= nlstate; i++)
   for(i=1; i<=nlstate;i++)            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     for(j=1; j<=(nlstate+ndeath);j++)        }    
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);        /* end force of mortality */
   
         for(i=1; i<=npar; i++) /* Computes gradient */
   fprintf(ficresprob,"\n");          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);
   xp=vector(1,npar);   
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        if (popbased==1) {
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   cov[1]=1;              prlim[i][i]=probs[(int)age][i][ij];
   j=cptcoveff;          }else{ /* mobilav */ 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for(i=1; i<=nlstate;i++)
   j1=0;              prlim[i][i]=mobaverage[(int)age][i][ij];
   for(k1=1; k1<=1;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){        }
     j1++;  
         for(j=1; j<= nlstate; j++){
     if  (cptcovn>0) {          for(h=0; h<=nhstepm; h++){
       fprintf(ficresprob, "\n#********** Variable ");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficresprob, "**********\n#");          }
     }        }
            /* This for computing force of mortality (h=1)as a weighted average */
       for (age=bage; age<=fage; age ++){        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
         cov[2]=age;          for(i=1; i<= nlstate; i++)
         for (k=1; k<=cptcovn;k++) {            gmp[j] += prlim[i][i]*p3mat[i][j][1];
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        }    
                  /* end force of mortality */
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=1; j<= nlstate; j++) /* vareij */
         for (k=1; k<=cptcovprod;k++)          for(h=0; h<=nhstepm; h++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                  }
         gradg=matrix(1,npar,1,9);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         trgradg=matrix(1,9,1,npar);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
          } /* End theta */
         for(theta=1; theta <=npar; theta++){  
           for(i=1; i<=npar; i++)      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                for(h=0; h<=nhstepm; h++) /* veij */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(j=1; j<=nlstate;j++)
                    for(theta=1; theta <=npar; theta++)
           k=0;            trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<= (nlstate+ndeath); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
               k=k+1;        for(theta=1; theta <=npar; theta++)
               gp[k]=pmmij[i][j];          trgradgp[j][theta]=gradgp[theta][j];
             }  
           }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                for(i=1;i<=nlstate;i++)
           for(i=1; i<=npar; i++)        for(j=1;j<=nlstate;j++)
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          vareij[i][j][(int)age] =0.;
      
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for(h=0;h<=nhstepm;h++){
           k=0;        for(k=0;k<=nhstepm;k++){
           for(i=1; i<=(nlstate+ndeath); i++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
             for(j=1; j<=(nlstate+ndeath);j++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
               k=k+1;          for(i=1;i<=nlstate;i++)
               gm[k]=pmmij[i][j];            for(j=1;j<=nlstate;j++)
             }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           }        }
            }
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        /* pptj */
         }      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);
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           for(theta=1; theta <=npar; theta++)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
             trgradg[j][theta]=gradg[theta][j];          varppt[j][i]=doldmp[j][i];
              /* end ppptj */
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           
         pmij(pmmij,cov,ncovmodel,x,nlstate);      if (popbased==1) {
                if(mobilav ==0){
         k=0;          for(i=1; i<=nlstate;i++)
         for(i=1; i<=(nlstate+ndeath); i++){            prlim[i][i]=probs[(int)age][i][ij];
           for(j=1; j<=(nlstate+ndeath);j++){        }else{ /* mobilav */ 
             k=k+1;          for(i=1; i<=nlstate;i++)
             gm[k]=pmmij[i][j];            prlim[i][i]=mobaverage[(int)age][i][ij];
           }        }
         }      }
            
      /*printf("\n%d ",(int)age);      /* This for computing force of mortality (h=1)as a weighted average */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        for(i=1; i<= nlstate; i++)
      }*/          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
         fprintf(ficresprob,"\n%d ",(int)age);      /* end force of mortality */
   
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       }        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      } 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      fprintf(ficresprobmorprev,"\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }      fprintf(ficresvij,"%.0f ",age );
   free_vector(xp,1,npar);      for(i=1; i<=nlstate;i++)
   fclose(ficresprob);        for(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 }        }
       fprintf(ficresvij,"\n");
 /******************* Printing html file ***********/      free_matrix(gp,0,nhstepm,1,nlstate);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      free_matrix(gm,0,nhstepm,1,nlstate);
  int lastpass, int stepm, int weightopt, char model[],\      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  char version[], int popforecast, int estepm ){    } /* End age */
   int jj1, k1, i1, cpt;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   FILE *fichtm;    free_vector(gmp,nlstate+1,nlstate+ndeath);
   /*char optionfilehtm[FILENAMELENGTH];*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   strcpy(optionfilehtm,optionfile);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   strcat(optionfilehtm,".htm");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     printf("Problem with %s \n",optionfilehtm), exit(0);    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);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
 \n    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
 Total number of observations=%d <br>\n  */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Outputs files<br>\n    free_vector(xp,1,npar);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    free_matrix(doldm,1,nlstate,1,nlstate);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    free_matrix(dnewm,1,nlstate,1,npar);
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
  fprintf(fichtm,"\n    fclose(ficgp);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    fclose(fichtm);
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n  }
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n  /************ Variance of prevlim ******************/
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   {
  if(popforecast==1) fprintf(fichtm,"\n    /* Variance of prevalence limit */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    double **newm;
         <br>",fileres,fileres,fileres,fileres);    double **dnewm,**doldm;
  else    int i, j, nhstepm, hstepm;
    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);    int k, cptcode;
 fprintf(fichtm," <li>Graphs</li><p>");    double *xp;
     double *gp, *gm;
  m=cptcoveff;    double **gradg, **trgradg;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double age,agelim;
     int theta;
  jj1=0;     
  for(k1=1; k1<=m;k1++){    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficresvpl,"# Age");
        jj1++;    for(i=1; i<=nlstate;i++)
        if (cptcovn > 0) {        fprintf(ficresvpl," %1d-%1d",i,i);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficresvpl,"\n");
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    xp=vector(1,npar);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    dnewm=matrix(1,nlstate,1,npar);
        }    doldm=matrix(1,nlstate,1,nlstate);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.png<br>    
 <img src=\"pe%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        hstepm=1*YEARM; /* Every year of age */
        for(cpt=1; cpt<nlstate;cpt++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.png<br>    agelim = AGESUP;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for(cpt=1; cpt<=nlstate;cpt++) {      if (stepm >= YEARM) hstepm=1;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 interval) in state (%d): v%s%d%d.png <br>      gradg=matrix(1,npar,1,nlstate);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        gp=vector(1,nlstate);
      }      gm=vector(1,nlstate);
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      for(theta=1; theta <=npar; theta++){
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i=1; i<=npar; i++){ /* Computes gradient */
      }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        }
 health expectancies in states (1) and (2): e%s%d.png<br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(i=1;i<=nlstate;i++)
 fprintf(fichtm,"\n</body>");          gp[i] = prlim[i][i];
    }      
    }        for(i=1; i<=npar; i++) /* Computes gradient */
 fclose(fichtm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
 /******************* Gnuplot file **************/          gm[i] = prlim[i][i];
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
         for(i=1;i<=nlstate;i++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp.txt");      trgradg =matrix(1,nlstate,1,npar);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);      for(j=1; j<=nlstate;j++)
   }        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);      for(i=1;i<=nlstate;i++)
 #endif        varpl[i][(int)age] =0.;
 m=pow(2,cptcoveff);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
  /* 1eme*/      for(i=1;i<=nlstate;i++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    for (k1=1; k1<= m ; k1 ++) {  
       fprintf(ficresvpl,"%.0f ",age );
 #ifdef windows      for(i=1; i<=nlstate;i++)
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      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);      fprintf(ficresvpl,"\n");
 #endif      free_vector(gp,1,nlstate);
 #ifdef unix      free_vector(gm,1,nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);      free_matrix(gradg,1,npar,1,nlstate);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      free_matrix(trgradg,1,nlstate,1,npar);
 #endif    } /* End age */
   
 for (i=1; i<= nlstate ; i ++) {    free_vector(xp,1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(doldm,1,nlstate,1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(dnewm,1,nlstate,1,nlstate);
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  }
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /************ Variance of one-step probabilities  ******************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 }  {
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    int i, j=0,  i1, k1, l1, t, tj;
      for (i=1; i<= nlstate ; i ++) {    int k2, l2, j1,  z1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int k=0,l, cptcode;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int first=1, first1;
 }      double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double **dnewm,**doldm;
 #ifdef unix    double *xp;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    double *gp, *gm;
 #endif    double **gradg, **trgradg;
    }    double **mu;
   }    double age,agelim, cov[NCOVMAX];
   /*2 eme*/    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   for (k1=1; k1<= m ; k1 ++) {    char fileresprob[FILENAMELENGTH];
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n\n",strtok(optionfile, "."),k1);    char fileresprobcov[FILENAMELENGTH];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    char fileresprobcor[FILENAMELENGTH];
      
     for (i=1; i<= nlstate+1 ; i ++) {    double ***varpij;
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    strcpy(fileresprob,"prob"); 
       for (j=1; j<= nlstate+1 ; j ++) {    strcat(fileresprob,fileres);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf("Problem with resultfile: %s\n", fileresprob);
 }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    strcpy(fileresprobcov,"probcov"); 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    strcat(fileresprobcov,fileres);
       for (j=1; j<= nlstate+1 ; j ++) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with resultfile: %s\n", fileresprobcov);
         else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 }      }
       fprintf(ficgp,"\" t\"\" w l 0,");    strcpy(fileresprobcor,"probcor"); 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    strcat(fileresprobcor,fileres);
       for (j=1; j<= nlstate+1 ; j ++) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with resultfile: %s\n", fileresprobcor);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 }      }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       else fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     }    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);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   /*3eme*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
   for (k1=1; k1<= m ; k1 ++) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {    fprintf(ficresprob,"# Age");
       k=2+nlstate*(2*cpt-2);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresprobcov,"# Age");
       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(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    fprintf(ficresprobcov,"# Age");
  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;i++)
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      for(j=1; j<=(nlstate+ndeath);j++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
 */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       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);    fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
       }    fprintf(ficresprobcor,"\n");
     }    xp=vector(1,npar);
   }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   /* CV preval stat */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     for (k1=1; k1<= m ; k1 ++) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     for (cpt=1; cpt<nlstate ; cpt ++) {    first=1;
       k=3;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       fprintf(ficgp,"set out \"p%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
       for (i=1; i< nlstate ; i ++)    }
         fprintf(ficgp,"+$%d",k+i+1);    else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      fprintf(ficgp,"\n# Routine varprob");
          }
       l=3+(nlstate+ndeath)*cpt;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      printf("Problem with html file: %s\n", optionfilehtm);
       for (i=1; i< nlstate ; i ++) {      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         l=3+(nlstate+ndeath)*cpt;      exit(0);
         fprintf(ficgp,"+$%d",l+i+1);    }
       }    else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     }      fprintf(fichtm,"\n");
   }    
        fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   /* proba elementaires */      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
    for(i=1,jk=1; i <=nlstate; i++){      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");
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    }
         for(j=1; j <=ncovmodel; j++){  
           
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    cov[1]=1;
           jk++;    tj=cptcoveff;
           fprintf(ficgp,"\n");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         }    j1=0;
       }    for(t=1; t<=tj;t++){
     }      for(i1=1; i1<=ncodemax[t];i1++){ 
    }        j1++;
         
    for(jk=1; jk <=m; jk++) {        if  (cptcovn>0) {
      fprintf(ficgp,"\nset out \"pe%s%d.png\" \n\n",strtok(optionfile, "."),jk);          fprintf(ficresprob, "\n#********** Variable "); 
      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      i=1;          fprintf(ficresprob, "**********\n#");
      for(k2=1; k2<=nlstate; k2++) {          fprintf(ficresprobcov, "\n#********** Variable "); 
        k3=i;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficresprobcov, "**********\n#");
          if (k != k2){          
            fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          fprintf(ficgp, "\n#********** Variable "); 
            ij=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            for(j=3; j <=ncovmodel; j++) {          fprintf(ficgp, "**********\n#");
              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++;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
              }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              else          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          
            }          fprintf(ficresprobcor, "\n#********** Variable ");    
            fprintf(ficgp,")/(1");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                      fprintf(ficgp, "**********\n#");    
            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 (age=bage; age<=fage; age ++){ 
              for(j=3; j <=ncovmodel; j++){          cov[2]=age;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for (k=1; k<=cptcovn;k++) {
                  fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                  ij++;          }
                }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                else          for (k=1; k<=cptcovprod;k++)
                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              }          
              fprintf(ficgp,")");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            fprintf(ficgp,") t \"p%d%d\" ", k2,k);          gp=vector(1,(nlstate)*(nlstate+ndeath));
            if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          gm=vector(1,(nlstate)*(nlstate+ndeath));
            i=i+ncovmodel;      
          }          for(theta=1; theta <=npar; theta++){
        }            for(i=1; i<=npar; i++)
      }              xp[i] = x[i] + (i==theta ?delti[theta]:0);
    }            
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
    fclose(ficgp);            
 }  /* end gnuplot */            k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
 /*************** Moving average **************/                k=k+1;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                gp[k]=pmmij[i][j];
               }
   int i, cpt, cptcod;            }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            
       for (i=1; i<=nlstate;i++)            for(i=1; i<=npar; i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              xp[i] = x[i] - (i==theta ?delti[theta]:0);
           mobaverage[(int)agedeb][i][cptcod]=0.;      
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            k=0;
       for (i=1; i<=nlstate;i++){            for(i=1; i<=(nlstate); i++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              for(j=1; j<=(nlstate+ndeath);j++){
           for (cpt=0;cpt<=4;cpt++){                k=k+1;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                gm[k]=pmmij[i][j];
           }              }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            }
         }       
       }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     }              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
              }
 }  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
 /************** Forecasting ******************/              trgradg[j][theta]=gradg[theta][j];
 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){          
            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   int *popage;          
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   double *popeffectif,*popcount;          
   double ***p3mat;          k=0;
   char fileresf[FILENAMELENGTH];          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
  agelim=AGESUP;              k=k+1;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              mu[k][(int) age]=pmmij[i][j];
             }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          }
            for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   strcpy(fileresf,"f");              varpij[i][j][(int)age] = doldm[i][j];
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {          /*printf("\n%d ",(int)age);
     printf("Problem with forecast resultfile: %s\n", fileresf);       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]));
   printf("Computing forecasting: result on file '%s' \n", fileresf);         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        }*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
           fprintf(ficresprob,"\n%d ",(int)age);
   if (mobilav==1) {          fprintf(ficresprobcov,"\n%d ",(int)age);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprobcor,"\n%d ",(int)age);
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   if (stepm<=12) stepsize=1;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
              fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   agelim=AGESUP;          }
            i=0;
   hstepm=1;          for (k=1; k<=(nlstate);k++){
   hstepm=hstepm/stepm;            for (l=1; l<=(nlstate+ndeath);l++){ 
   yp1=modf(dateintmean,&yp);              i=i++;
   anprojmean=yp;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   yp2=modf((yp1*12),&yp);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   mprojmean=yp;              for (j=1; j<=i;j++){
   yp1=modf((yp2*30.5),&yp);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   jprojmean=yp;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   if(jprojmean==0) jprojmean=1;              }
   if(mprojmean==0) jprojmean=1;            }
            }/* end of loop for state */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        } /* end of loop for age */
    
   for(cptcov=1;cptcov<=i2;cptcov++){        /* Confidence intervalle of pij  */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        /*
       k=k+1;        fprintf(ficgp,"\nset noparametric;unset label");
       fprintf(ficresf,"\n#******");        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       for(j=1;j<=cptcoveff;j++) {        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
       }        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       fprintf(ficresf,"******\n");        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficresf,"# StartingAge FinalAge");        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        */
        
              /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        first1=1;
         fprintf(ficresf,"\n");        for (k2=1; k2<=(nlstate);k2++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            j=(k2-1)*(nlstate+ndeath)+l2;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for (k1=1; k1<=(nlstate);k1++){
           nhstepm = nhstepm/hstepm;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                          if(l1==k1) continue;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                i=(k1-1)*(nlstate+ndeath)+l1;
           oldm=oldms;savm=savms;                if(i<=j) continue;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  for (age=bage; age<=fage; age ++){ 
                          if ((int)age %5==0){
           for (h=0; h<=nhstepm; h++){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
             if (h==(int) (calagedate+YEARM*cpt)) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
             }                    mu1=mu[i][(int) age]/stepm*YEARM ;
             for(j=1; j<=nlstate+ndeath;j++) {                    mu2=mu[j][(int) age]/stepm*YEARM;
               kk1=0.;kk2=0;                    c12=cv12/sqrt(v1*v2);
               for(i=1; i<=nlstate;i++) {                                  /* Computing eigen value of matrix of covariance */
                 if (mobilav==1)                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                 else {                    /* Eigen vectors */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                 }                    /*v21=sqrt(1.-v11*v11); *//* error */
                                    v21=(lc1-v1)/cv12*v11;
               }                    v12=-v21;
               if (h==(int)(calagedate+12*cpt)){                    v22=v11;
                 fprintf(ficresf," %.3f", kk1);                    tnalp=v21/v11;
                                            if(first1==1){
               }                      first1=0;
             }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           }                    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         }                    /*printf(fignu*/
       }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   }                    if(first==1){
                              first=0;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   fclose(ficresf);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 }                      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);
 /************** Forecasting ******************/                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
 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){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   int *popage;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                      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",\
   double *popeffectif,*popcount;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double ***p3mat,***tabpop,***tabpopprev;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   char filerespop[FILENAMELENGTH];                    }else{
                       first=0;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   agelim=AGESUP;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }/* if first */
                    } /* age mod 5 */
   strcpy(filerespop,"pop");                } /* end loop age */
   strcat(filerespop,fileres);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {                first=1;
     printf("Problem with forecast resultfile: %s\n", filerespop);              } /*l12 */
   }            } /* k12 */
   printf("Computing forecasting: result on file '%s' \n", filerespop);          } /*l1 */
         }/* k1 */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      } /* loop covariates */
       free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   if (mobilav==1) {      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     movingaverage(agedeb, fage, ageminpar, mobaverage);      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   }      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    }
   if (stepm<=12) stepsize=1;    free_vector(xp,1,npar);
      fclose(ficresprob);
   agelim=AGESUP;    fclose(ficresprobcov);
      fclose(ficresprobcor);
   hstepm=1;    fclose(ficgp);
   hstepm=hstepm/stepm;    fclose(fichtm);
    }
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);  /******************* Printing html file ***********/
     }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     popage=ivector(0,AGESUP);                    int lastpass, int stepm, int weightopt, char model[],\
     popeffectif=vector(0,AGESUP);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     popcount=vector(0,AGESUP);                    int popforecast, int estepm ,\
                        double jprev1, double mprev1,double anprev1, \
     i=1;                      double jprev2, double mprev2,double anprev2){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    int jj1, k1, i1, cpt;
        /*char optionfilehtm[FILENAMELENGTH];*/
     imx=i;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      printf("Problem with %s \n",optionfilehtm), exit(0);
   }      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     }
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
       k=k+1;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
       fprintf(ficrespop,"\n#******");   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       for(j=1;j<=cptcoveff;j++) {   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Life expectancies by age and initial health status (estepm=%2d months): 
       }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
       fprintf(ficrespop,"******\n");    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
         m=cptcoveff;
       for (cpt=0; cpt<=0;cpt++) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
           jj1=0;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   for(k1=1; k1<=m;k1++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     for(i1=1; i1<=ncodemax[k1];i1++){
           nhstepm = nhstepm/hstepm;       jj1++;
                 if (cptcovn > 0) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           oldm=oldms;savm=savms;         for (cpt=1; cpt<=cptcoveff;cpt++) 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                 fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           for (h=0; h<=nhstepm; h++){       }
             if (h==(int) (calagedate+YEARM*cpt)) {       /* Pij */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
             }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
             for(j=1; j<=nlstate+ndeath;j++) {       /* Quasi-incidences */
               kk1=0.;kk2=0;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
               for(i=1; i<=nlstate;i++) {                <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
                 if (mobilav==1)         /* Stable prevalence in each health state */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];         for(cpt=1; cpt<nlstate;cpt++){
                 else {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
                 }         }
               }       for(cpt=1; cpt<=nlstate;cpt++) {
               if (h==(int)(calagedate+12*cpt)){          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
                   /*fprintf(ficrespop," %.3f", kk1);       }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       fprintf(fichtm,"\n<br>- Total life expectancy by age and
               }  health expectancies in states (1) and (2): e%s%d.png<br>
             }  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
             for(i=1; i<=nlstate;i++){     } /* end i1 */
               kk1=0.;   }/* End k1 */
                 for(j=1; j<=nlstate;j++){   fprintf(fichtm,"</ul>");
                   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)];   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
             }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
           }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
         }   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
       }  
     if(popforecast==1) fprintf(fichtm,"\n
   /******/   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          <br>",fileres,fileres,fileres,fileres);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     else 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     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);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           nhstepm = nhstepm/hstepm;  
             m=cptcoveff;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     jj1=0;
           for (h=0; h<=nhstepm; h++){   for(k1=1; k1<=m;k1++){
             if (h==(int) (calagedate+YEARM*cpt)) {     for(i1=1; i1<=ncodemax[k1];i1++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       jj1++;
             }       if (cptcovn > 0) {
             for(j=1; j<=nlstate+ndeath;j++) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               kk1=0.;kk2=0;         for (cpt=1; cpt<=cptcoveff;cpt++) 
               for(i=1; i<=nlstate;i++) {                         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];             fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               }       }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);       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>
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  <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);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   
   if (popforecast==1) {  /******************* Gnuplot file **************/
     free_ivector(popage,0,AGESUP);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   }    int ng;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with file %s",optionfilegnuplot);
   fclose(ficrespop);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
 }    }
   
 /***********************************************/    /*#ifdef windows */
 /**************** Main Program *****************/      fprintf(ficgp,"cd \"%s\" \n",pathc);
 /***********************************************/      /*#endif */
   m=pow(2,cptcoveff);
 int main(int argc, char *argv[])    
 {   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;     for (k1=1; k1<= m ; k1 ++) {
   double agedeb, agefin,hf;       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       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);
   
   double fret;       for (i=1; i<= nlstate ; i ++) {
   double **xi,tmp,delta;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   double dum; /* Dummy variable */       }
   double ***p3mat;       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
   int *indx;       for (i=1; i<= nlstate ; i ++) {
   char line[MAXLINE], linepar[MAXLINE];         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   char title[MAXLINE];         else fprintf(ficgp," \%%*lf (\%%*lf)");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];       } 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
         for (i=1; i<= nlstate ; i ++) {
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   char filerest[FILENAMELENGTH];       }  
   char fileregp[FILENAMELENGTH];       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   char popfile[FILENAMELENGTH];     }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    }
   int firstobs=1, lastobs=10;    /*2 eme*/
   int sdeb, sfin; /* Status at beginning and end */    
   int c,  h , cpt,l;    for (k1=1; k1<= m ; k1 ++) { 
   int ju,jl, mi;      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      
   int mobilav=0,popforecast=0;      for (i=1; i<= nlstate+1 ; i ++) {
   int hstepm, nhstepm;        k=2*i;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
   double bage, fage, age, agelim, agebase;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   double ftolpl=FTOL;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   double **prlim;        }   
   double *severity;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   double ***param; /* Matrix of parameters */        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   double  *p;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
   double **matcov; /* Matrix of covariance */        for (j=1; j<= nlstate+1 ; j ++) {
   double ***delti3; /* Scale */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   double *delti; /* Scale */          else fprintf(ficgp," \%%*lf (\%%*lf)");
   double ***eij, ***vareij;        }   
   double **varpl; /* Variances of prevalence limits by age */        fprintf(ficgp,"\" t\"\" w l 0,");
   double *epj, vepp;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   double kk1, kk2;        for (j=1; j<= nlstate+1 ; j ++) {
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   char *alph[]={"a","a","b","c","d","e"}, str[4];        else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
   char z[1]="c", occ;    
 #include <sys/time.h>    /*3eme*/
 #include <time.h>    
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<= nlstate ; cpt ++) {
   /* long total_usecs;        k=2+nlstate*(2*cpt-2);
   struct timeval start_time, end_time;        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
          fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   getcwd(pathcd, size);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   printf("\n%s",version);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   if(argc <=1){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     printf("\nEnter the parameter file name: ");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     scanf("%s",pathtot);          
   }        */
   else{        for (i=1; i< nlstate ; i ++) {
     strcpy(pathtot,argv[1]);          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
   }          
   /*if(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,'\\');*/    
     /* CV preval stat */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    for (k1=1; k1<= m ; k1 ++) { 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      for (cpt=1; cpt<nlstate ; cpt ++) {
   chdir(path);        k=3;
   replace(pathc,path);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
 /*-------- arguments in the command line --------*/        
         for (i=1; i< nlstate ; i ++)
   strcpy(fileres,"r");          fprintf(ficgp,"+$%d",k+i+1);
   strcat(fileres, optionfilefiname);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   strcat(fileres,".txt");    /* Other files have txt extension */        
         l=3+(nlstate+ndeath)*cpt;
   /*---------arguments file --------*/        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          l=3+(nlstate+ndeath)*cpt;
     printf("Problem with optionfile %s\n",optionfile);          fprintf(ficgp,"+$%d",l+i+1);
     goto end;        }
   }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
   strcpy(filereso,"o");    }  
   strcat(filereso,fileres);    
   if((ficparo=fopen(filereso,"w"))==NULL) {    /* proba elementaires */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    for(i=1,jk=1; i <=nlstate; i++){
   }      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   /* Reads comments: lines beginning with '#' */          for(j=1; j <=ncovmodel; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     ungetc(c,ficpar);            jk++; 
     fgets(line, MAXLINE, ficpar);            fprintf(ficgp,"\n");
     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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   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);       for(jk=1; jk <=m; jk++) {
   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);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
 while((c=getc(ficpar))=='#' && c!= EOF){         if (ng==2)
     ungetc(c,ficpar);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     fgets(line, MAXLINE, ficpar);         else
     puts(line);           fprintf(ficgp,"\nset title \"Probability\"\n");
     fputs(line,ficparo);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   }         i=1;
   ungetc(c,ficpar);         for(k2=1; k2<=nlstate; k2++) {
             k3=i;
               for(k=1; k<=(nlstate+ndeath); k++) {
   covar=matrix(0,NCOVMAX,1,n);             if (k != k2){
   cptcovn=0;               if(ng==2)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
   ncovmodel=2+cptcovn;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */               ij=1;
                 for(j=3; j <=ncovmodel; j++) {
   /* Read guess parameters */                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   /* Reads comments: lines beginning with '#' */                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   while((c=getc(ficpar))=='#' && c!= EOF){                   ij++;
     ungetc(c,ficpar);                 }
     fgets(line, MAXLINE, ficpar);                 else
     puts(line);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     fputs(line,ficparo);               }
   }               fprintf(ficgp,")/(1");
   ungetc(c,ficpar);               
                 for(k1=1; k1 <=nlstate; k1++){   
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     for(i=1; i <=nlstate; i++)                 ij=1;
     for(j=1; j <=nlstate+ndeath-1; j++){                 for(j=3; j <=ncovmodel; j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       fprintf(ficparo,"%1d%1d",i1,j1);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       printf("%1d%1d",i,j);                     ij++;
       for(k=1; k<=ncovmodel;k++){                   }
         fscanf(ficpar," %lf",&param[i][j][k]);                   else
         printf(" %lf",param[i][j][k]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         fprintf(ficparo," %lf",param[i][j][k]);                 }
       }                 fprintf(ficgp,")");
       fscanf(ficpar,"\n");               }
       printf("\n");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       fprintf(ficparo,"\n");               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     }               i=i+ncovmodel;
               }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;           } /* end k */
          } /* end k2 */
   p=param[1][1];       } /* end jk */
       } /* end ng */
   /* Reads comments: lines beginning with '#' */     fclose(ficgp); 
   while((c=getc(ficpar))=='#' && c!= EOF){  }  /* end gnuplot */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /*************** Moving average **************/
     fputs(line,ficparo);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   }  
   ungetc(c,ficpar);    int i, cpt, cptcod;
     int mobilavrange, mob;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double age;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   for(i=1; i <=nlstate; i++){      if(mobilav==1) mobilavrange=5; /* default */
     for(j=1; j <=nlstate+ndeath-1; j++){      else mobilavrange=mobilav;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for (age=bage; age<=fage; age++)
       printf("%1d%1d",i,j);        for (i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);          for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
       for(k=1; k<=ncovmodel;k++){            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
         fscanf(ficpar,"%le",&delti3[i][j][k]);      /* We keep the original values on the extreme ages bage, fage and for 
         printf(" %le",delti3[i][j][k]);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
         fprintf(ficparo," %le",delti3[i][j][k]);         we use a 5 terms etc. until the borders are no more concerned. 
       }      */ 
       fscanf(ficpar,"\n");      for (mob=3;mob <=mobilavrange;mob=mob+2){
       printf("\n");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
       fprintf(ficparo,"\n");          for (i=1; i<=nlstate;i++){
     }            for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   delti=delti3[1][1];                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   /* Reads comments: lines beginning with '#' */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   while((c=getc(ficpar))=='#' && c!= EOF){                }
     ungetc(c,ficpar);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }/* end age */
   }      }/* end mob */
   ungetc(c,ficpar);    }else return -1;
      return 0;
   matcov=matrix(1,npar,1,npar);  }/* End movingaverage */
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);  /************** Forecasting ******************/
     fprintf(ficparo,"%s",str);  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){
     for(j=1; j <=i; j++){    
       fscanf(ficpar," %le",&matcov[i][j]);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       printf(" %.5le",matcov[i][j]);    int *popage;
       fprintf(ficparo," %.5le",matcov[i][j]);    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     }    double *popeffectif,*popcount;
     fscanf(ficpar,"\n");    double ***p3mat;
     printf("\n");    double ***mobaverage;
     fprintf(ficparo,"\n");    char fileresf[FILENAMELENGTH];
   }  
   for(i=1; i <=npar; i++)   agelim=AGESUP;
     for(j=i+1;j<=npar;j++)  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
       matcov[i][j]=matcov[j][i];  
        prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   printf("\n");   
    
     strcpy(fileresf,"f"); 
     /*-------- Rewriting paramater file ----------*/    strcat(fileresf,fileres);
      strcpy(rfileres,"r");    /* "Rparameterfile */    if((ficresf=fopen(fileresf,"w"))==NULL) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      printf("Problem with forecast resultfile: %s\n", fileresf);
      strcat(rfileres,".");    /* */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    }
     if((ficres =fopen(rfileres,"w"))==NULL) {    printf("Computing forecasting: result on file '%s' \n", fileresf);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     }  
     fprintf(ficres,"#%s\n",version);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
      
     /*-------- data file ----------*/    if (mobilav!=0) {
     if((fic=fopen(datafile,"r"))==NULL)    {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       printf("Problem with datafile: %s\n", datafile);goto end;      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);
     n= lastobs;      }
     severity = vector(1,maxwav);    }
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     moisnais=vector(1,n);    if (stepm<=12) stepsize=1;
     annais=vector(1,n);    
     moisdc=vector(1,n);    agelim=AGESUP;
     andc=vector(1,n);    
     agedc=vector(1,n);    hstepm=1;
     cod=ivector(1,n);    hstepm=hstepm/stepm; 
     weight=vector(1,n);    yp1=modf(dateintmean,&yp);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    anprojmean=yp;
     mint=matrix(1,maxwav,1,n);    yp2=modf((yp1*12),&yp);
     anint=matrix(1,maxwav,1,n);    mprojmean=yp;
     s=imatrix(1,maxwav+1,1,n);    yp1=modf((yp2*30.5),&yp);
     adl=imatrix(1,maxwav+1,1,n);        jprojmean=yp;
     tab=ivector(1,NCOVMAX);    if(jprojmean==0) jprojmean=1;
     ncodemax=ivector(1,8);    if(mprojmean==0) jprojmean=1;
     
     i=1;    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     while (fgets(line, MAXLINE, fic) != NULL)    {    
       if ((i >= firstobs) && (i <=lastobs)) {    for(cptcov=1;cptcov<=i2;cptcov++){
              for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         for (j=maxwav;j>=1;j--){        k=k+1;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        fprintf(ficresf,"\n#******");
           strcpy(line,stra);        for(j=1;j<=cptcoveff;j++) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }        fprintf(ficresf,"******\n");
                fprintf(ficresf,"# StartingAge FinalAge");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        
         
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncovcol;j>=1;j--){          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         }            nhstepm = nhstepm/hstepm; 
         num[i]=atol(stra);            
                    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            oldm=oldms;savm=savms;
           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;}*/            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
         i=i+1;            for (h=0; h<=nhstepm; h++){
       }              if (h==(int) (calagedate+YEARM*cpt)) {
     }                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
     /* printf("ii=%d", ij);              } 
        scanf("%d",i);*/              for(j=1; j<=nlstate+ndeath;j++) {
   imx=i-1; /* Number of individuals */                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
   /* for (i=1; i<=imx; i++){                  if (mobilav==1) 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                  else {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     }*/                  }
    /*  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]));}*/                if (h==(int)(calagedate+12*cpt)){
                    fprintf(ficresf," %.3f", kk1);
                            
   /* Calculation of the number of parameter from char model*/                }
   Tvar=ivector(1,15);              }
   Tprod=ivector(1,15);            }
   Tvaraff=ivector(1,15);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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,'+');    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     j1=nbocc(model,'*');  
     cptcovn=j+1;    fclose(ficresf);
     cptcovprod=j1;  }
      /************** Forecasting ******************/
     strcpy(modelsav,model);  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){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    
       printf("Error. Non available option model=%s ",model);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       goto end;    int *popage;
     }    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
        double *popeffectif,*popcount;
     for(i=(j+1); i>=1;i--){    double ***p3mat,***tabpop,***tabpopprev;
       cutv(stra,strb,modelsav,'+');    double ***mobaverage;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    char filerespop[FILENAMELENGTH];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (strchr(strb,'*')) {    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         cutv(strd,strc,strb,'*');    agelim=AGESUP;
         if (strcmp(strc,"age")==0) {    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
           cptcovprod--;    
           cutv(strb,stre,strd,'V');    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
           Tvar[i]=atoi(stre);    
           cptcovage++;    
             Tage[cptcovage]=i;    strcpy(filerespop,"pop"); 
             /*printf("stre=%s ", stre);*/    strcat(filerespop,fileres);
         }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
         else if (strcmp(strd,"age")==0) {      printf("Problem with forecast resultfile: %s\n", filerespop);
           cptcovprod--;      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=atoi(stre);    printf("Computing forecasting: result on file '%s' \n", filerespop);
           cptcovage++;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
           Tage[cptcovage]=i;  
         }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
         else {  
           cutv(strb,stre,strc,'V');    if (mobilav!=0) {
           Tvar[i]=ncovcol+k1;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cutv(strb,strc,strd,'V');      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           Tprod[k1]=i;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           Tvard[k1][1]=atoi(strc);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           Tvard[k1][2]=atoi(stre);      }
           Tvar[cptcovn+k2]=Tvard[k1][1];    }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)    stepsize=(int) (stepm+YEARM-1)/YEARM;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    if (stepm<=12) stepsize=1;
           k1++;    
           k2=k2+2;    agelim=AGESUP;
         }    
       }    hstepm=1;
       else {    hstepm=hstepm/stepm; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    
        /*  scanf("%d",i);*/    if (popforecast==1) {
       cutv(strd,strc,strb,'V');      if((ficpop=fopen(popfile,"r"))==NULL) {
       Tvar[i]=atoi(strc);        printf("Problem with population file : %s\n",popfile);exit(0);
       }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       strcpy(modelsav,stra);        } 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      popage=ivector(0,AGESUP);
         scanf("%d",i);*/      popeffectif=vector(0,AGESUP);
     }      popcount=vector(0,AGESUP);
 }      
        i=1;   
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   printf("cptcovprod=%d ", cptcovprod);     
   scanf("%d ",i);*/      imx=i;
     fclose(fic);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    for(cptcov=1;cptcov<=i2;cptcov++){
       for(i=1;i<=n;i++) weight[i]=1.0;     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     }        k=k+1;
     /*-calculation of age at interview from date of interview and age at death -*/        fprintf(ficrespop,"\n#******");
     agev=matrix(1,maxwav,1,imx);        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     for (i=1; i<=imx; i++) {        }
       for(m=2; (m<= maxwav); m++) {        fprintf(ficrespop,"******\n");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        fprintf(ficrespop,"# Age");
          anint[m][i]=9999;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
          s[m][i]=-1;        if (popforecast==1)  fprintf(ficrespop," [Population]");
        }        
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        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--){ 
     for (i=1; i<=imx; i++)  {            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            nhstepm = nhstepm/hstepm; 
       for(m=1; (m<= maxwav); m++){            
         if(s[m][i] >0){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           if (s[m][i] >= nlstate+1) {            oldm=oldms;savm=savms;
             if(agedc[i]>0)            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
               if(moisdc[i]!=99 && andc[i]!=9999)          
                 agev[m][i]=agedc[i];            for (h=0; h<=nhstepm; h++){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/              if (h==(int) (calagedate+YEARM*cpt)) {
            else {                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               if (andc[i]!=9999){              } 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              for(j=1; j<=nlstate+ndeath;j++) {
               agev[m][i]=-1;                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 if(s[m][i] !=9){ /* Should no more exist */                  else {
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
             if(mint[m][i]==99 || anint[m][i]==9999)                  }
               agev[m][i]=1;                }
             else if(agev[m][i] <agemin){                if (h==(int)(calagedate+12*cpt)){
               agemin=agev[m][i];                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                    /*fprintf(ficrespop," %.3f", kk1);
             }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
             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);*/              for(i=1; i<=nlstate;i++){
             }                kk1=0.;
             /*agev[m][i]=anint[m][i]-annais[i];*/                  for(j=1; j<=nlstate;j++){
             /*   agev[m][i] = age[i]+2*m;*/                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
           }                  }
           else { /* =9 */                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
             agev[m][i]=1;              }
             s[m][i]=-1;  
           }              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
         }                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         else /*= 0 Unknown */            }
           agev[m][i]=1;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }          }
            }
     }   
     for (i=1; i<=imx; i++)  {    /******/
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           goto end;          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);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     free_vector(severity,1,maxwav);            for (h=0; h<=nhstepm; h++){
     free_imatrix(outcome,1,maxwav+1,1,n);              if (h==(int) (calagedate+YEARM*cpt)) {
     free_vector(moisnais,1,n);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     free_vector(annais,1,n);              } 
     /* free_matrix(mint,1,maxwav,1,n);              for(j=1; j<=nlstate+ndeath;j++) {
        free_matrix(anint,1,maxwav,1,n);*/                kk1=0.;kk2=0;
     free_vector(moisdc,1,n);                for(i=1; i<=nlstate;i++) {              
     free_vector(andc,1,n);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                    if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
     wav=ivector(1,imx);              }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              }
     /* Concatenates waves */        }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     } 
     }
    
       Tcode=ivector(1,100);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    if (popforecast==1) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      free_ivector(popage,0,AGESUP);
            free_vector(popeffectif,0,AGESUP);
    codtab=imatrix(1,100,1,10);      free_vector(popcount,0,AGESUP);
    h=0;    }
    m=pow(2,cptcoveff);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for(k=1;k<=cptcoveff; k++){    fclose(ficrespop);
      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++;  /**************** Main Program *****************/
            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]);*/  
          }  int main(int argc, char *argv[])
        }  {
      }  
    }    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    double agedeb, agefin,hf;
       codtab[1][2]=1;codtab[2][2]=2; */    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){    double fret;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    double **xi,tmp,delta;
       }  
       printf("\n");    double dum; /* Dummy variable */
       }    double ***p3mat;
       scanf("%d",i);*/    double ***mobaverage;
        int *indx;
    /* Calculates basic frequencies. Computes observed prevalence at single age    char line[MAXLINE], linepar[MAXLINE];
        and prints on file fileres'p'. */    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;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int ju,jl, mi;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int mobilav=0,popforecast=0;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int hstepm, nhstepm;
          double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
     /* 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] */    double bage, fage, age, agelim, agebase;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    double ftolpl=FTOL;
     double **prlim;
     if(mle==1){    double *severity;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    double ***param; /* Matrix of parameters */
     }    double  *p;
        double **matcov; /* Matrix of covariance */
     /*--------- results files --------------*/    double ***delti3; /* Scale */
     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);    double *delti; /* Scale */
      double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
    jk=1;    double *epj, vepp;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double kk1, kk2;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
    for(i=1,jk=1; i <=nlstate; i++){    
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    char *alph[]={"a","a","b","c","d","e"}, str[4];
          {  
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    char z[1]="c", occ;
            for(j=1; j <=ncovmodel; j++){  #include <sys/time.h>
              printf("%f ",p[jk]);  #include <time.h>
              fprintf(ficres,"%f ",p[jk]);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
              jk++;   
            }    /* long total_usecs;
            printf("\n");    struct timeval start_time, end_time;
            fprintf(ficres,"\n");    
          }    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
      }    getcwd(pathcd, size);
    }  
  if(mle==1){    printf("\n%s",version);
     /* Computing hessian and covariance matrix */    if(argc <=1){
     ftolhess=ftol; /* Usually correct */      printf("\nEnter the parameter file name: ");
     hesscov(matcov, p, npar, delti, ftolhess, func);      scanf("%s",pathtot);
  }    }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    else{
     printf("# Scales (for hessian or gradient estimation)\n");      strcpy(pathtot,argv[1]);
      for(i=1,jk=1; i <=nlstate; i++){    }
       for(j=1; j <=nlstate+ndeath; j++){    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
         if (j!=i) {    /*cygwin_split_path(pathtot,path,optionfile);
           fprintf(ficres,"%1d%1d",i,j);      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
           printf("%1d%1d",i,j);    /* cutv(path,optionfile,pathtot,'\\');*/
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
             fprintf(ficres," %.5e",delti[jk]);     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             jk++;    chdir(path);
           }    replace(pathc,path);
           printf("\n");  
           fprintf(ficres,"\n");  /*-------- arguments in the command line --------*/
         }  
       }    /* Log file */
      }    strcat(filelog, optionfilefiname);
        strcat(filelog,".log");    /* */
     k=1;    if((ficlog=fopen(filelog,"w"))==NULL)    {
     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");      printf("Problem with logfile %s\n",filelog);
     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");      goto end;
     for(i=1;i<=npar;i++){    }
       /*  if (k>nlstate) k=1;    fprintf(ficlog,"Log filename:%s\n",filelog);
       i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficlog,"\n%s",version);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    fprintf(ficlog,"\nEnter the parameter file name: ");
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       fprintf(ficres,"%3d",i);    fflush(ficlog);
       printf("%3d",i);  
       for(j=1; j<=i;j++){    /* */
         fprintf(ficres," %.5e",matcov[i][j]);    strcpy(fileres,"r");
         printf(" %.5e",matcov[i][j]);    strcat(fileres, optionfilefiname);
       }    strcat(fileres,".txt");    /* Other files have txt extension */
       fprintf(ficres,"\n");  
       printf("\n");    /*---------arguments file --------*/
       k++;  
     }    if((ficpar=fopen(optionfile,"r"))==NULL)    {
          printf("Problem with optionfile %s\n",optionfile);
     while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       ungetc(c,ficpar);      goto end;
       fgets(line, MAXLINE, ficpar);    }
       puts(line);  
       fputs(line,ficparo);    strcpy(filereso,"o");
     }    strcat(filereso,fileres);
     ungetc(c,ficpar);    if((ficparo=fopen(filereso,"w"))==NULL) {
     estepm=0;      printf("Problem with Output resultfile: %s\n", filereso);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
     if (estepm==0 || estepm < stepm) estepm=stepm;      goto end;
     if (fage <= 2) {    }
       bage = ageminpar;  
       fage = agemaxpar;    /* Reads comments: lines beginning with '#' */
     }    while((c=getc(ficpar))=='#' && c!= EOF){
          ungetc(c,ficpar);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fgets(line, MAXLINE, ficpar);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      puts(line);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fputs(line,ficparo);
      }
     while((c=getc(ficpar))=='#' && c!= EOF){    ungetc(c,ficpar);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, 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);
     puts(line);    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);
     fputs(line,ficparo);    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);      ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      puts(line);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fputs(line,ficparo);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    }
          ungetc(c,ficpar);
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);     
     fgets(line, MAXLINE, ficpar);    covar=matrix(0,NCOVMAX,1,n); 
     puts(line);    cptcovn=0; 
     fputs(line,ficparo);    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   }  
   ungetc(c,ficpar);    ncovmodel=2+cptcovn;
      nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    /* Read guess parameters */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
   fscanf(ficpar,"pop_based=%d\n",&popbased);      ungetc(c,ficpar);
   fprintf(ficparo,"pop_based=%d\n",popbased);        fgets(line, MAXLINE, ficpar);
   fprintf(ficres,"pop_based=%d\n",popbased);        puts(line);
        fputs(line,ficparo);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);    
     puts(line);    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     fputs(line,ficparo);      for(i=1; i <=nlstate; i++)
   }      for(j=1; j <=nlstate+ndeath-1; j++){
   ungetc(c,ficpar);        fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        if(mle==1)
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          printf("%1d%1d",i,j);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
 while((c=getc(ficpar))=='#' && c!= EOF){          if(mle==1){
     ungetc(c,ficpar);            printf(" %lf",param[i][j][k]);
     fgets(line, MAXLINE, ficpar);            fprintf(ficlog," %lf",param[i][j][k]);
     puts(line);          }
     fputs(line,ficparo);          else
   }            fprintf(ficlog," %lf",param[i][j][k]);
   ungetc(c,ficpar);          fprintf(ficparo," %lf",param[i][j][k]);
         }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        fscanf(ficpar,"\n");
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        if(mle==1)
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          printf("\n");
         fprintf(ficlog,"\n");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficparo,"\n");
       }
 /*------------ gnuplot -------------*/    
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);      npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
    
 /*------------ free_vector  -------------*/    p=param[1][1];
  chdir(path);    
      /* Reads comments: lines beginning with '#' */
  free_ivector(wav,1,imx);    while((c=getc(ficpar))=='#' && c!= EOF){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      ungetc(c,ficpar);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        fgets(line, MAXLINE, ficpar);
  free_ivector(num,1,n);      puts(line);
  free_vector(agedc,1,n);      fputs(line,ficparo);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    }
  fclose(ficparo);    ungetc(c,ficpar);
  fclose(ficres);  
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 /*--------- index.htm --------*/    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
          printf("%1d%1d",i,j);
   /*--------------- Prevalence limit --------------*/        fprintf(ficparo,"%1d%1d",i1,j1);
          for(k=1; k<=ncovmodel;k++){
   strcpy(filerespl,"pl");          fscanf(ficpar,"%le",&delti3[i][j][k]);
   strcat(filerespl,fileres);          printf(" %le",delti3[i][j][k]);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          fprintf(ficparo," %le",delti3[i][j][k]);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        }
   }        fscanf(ficpar,"\n");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        printf("\n");
   fprintf(ficrespl,"#Prevalence limit\n");        fprintf(ficparo,"\n");
   fprintf(ficrespl,"#Age ");      }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    delti=delti3[1][1];
      
   prlim=matrix(1,nlstate,1,nlstate);    /* Reads comments: lines beginning with '#' */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    while((c=getc(ficpar))=='#' && c!= EOF){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      ungetc(c,ficpar);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fgets(line, MAXLINE, ficpar);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      puts(line);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fputs(line,ficparo);
   k=0;    }
   agebase=ageminpar;    ungetc(c,ficpar);
   agelim=agemaxpar;    
   ftolpl=1.e-10;    matcov=matrix(1,npar,1,npar);
   i1=cptcoveff;    for(i=1; i <=npar; i++){
   if (cptcovn < 1){i1=1;}      fscanf(ficpar,"%s",&str);
       if(mle==1)
   for(cptcov=1;cptcov<=i1;cptcov++){        printf("%s",str);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficlog,"%s",str);
         k=k+1;      fprintf(ficparo,"%s",str);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      for(j=1; j <=i; j++){
         fprintf(ficrespl,"\n#******");        fscanf(ficpar," %le",&matcov[i][j]);
         for(j=1;j<=cptcoveff;j++)        if(mle==1){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf(" %.5le",matcov[i][j]);
         fprintf(ficrespl,"******\n");          fprintf(ficlog," %.5le",matcov[i][j]);
                }
         for (age=agebase; age<=agelim; age++){        else
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficrespl,"%.0f",age );        fprintf(ficparo," %.5le",matcov[i][j]);
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);      fscanf(ficpar,"\n");
           fprintf(ficrespl,"\n");      if(mle==1)
         }        printf("\n");
       }      fprintf(ficlog,"\n");
     }      fprintf(ficparo,"\n");
   fclose(ficrespl);    }
     for(i=1; i <=npar; i++)
   /*------------- h Pij x at various ages ------------*/      for(j=i+1;j<=npar;j++)
          matcov[i][j]=matcov[j][i];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);     
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if(mle==1)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      printf("\n");
   }    fprintf(ficlog,"\n");
   printf("Computing pij: result on file '%s' \n", filerespij);  
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;      /*-------- Rewriting paramater file ----------*/
   /*if (stepm<=24) stepsize=2;*/       strcpy(rfileres,"r");    /* "Rparameterfile */
        strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
   agelim=AGESUP;       strcat(rfileres,".");    /* */
   hstepm=stepsize*YEARM; /* Every year of age */       strcat(rfileres,optionfilext);    /* Other files have txt extension */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      if((ficres =fopen(rfileres,"w"))==NULL) {
          printf("Problem writing new parameter file: %s\n", fileres);goto end;
   k=0;        fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficres,"#%s\n",version);
       k=k+1;      
         fprintf(ficrespij,"\n#****** ");      /*-------- data file ----------*/
         for(j=1;j<=cptcoveff;j++)      if((fic=fopen(datafile,"r"))==NULL)    {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        printf("Problem with datafile: %s\n", datafile);goto end;
         fprintf(ficrespij,"******\n");        fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
              }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      n= lastobs;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      severity = vector(1,maxwav);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      outcome=imatrix(1,maxwav+1,1,n);
           oldm=oldms;savm=savms;      num=ivector(1,n);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        moisnais=vector(1,n);
           fprintf(ficrespij,"# Age");      annais=vector(1,n);
           for(i=1; i<=nlstate;i++)      moisdc=vector(1,n);
             for(j=1; j<=nlstate+ndeath;j++)      andc=vector(1,n);
               fprintf(ficrespij," %1d-%1d",i,j);      agedc=vector(1,n);
           fprintf(ficrespij,"\n");      cod=ivector(1,n);
            for (h=0; h<=nhstepm; h++){      weight=vector(1,n);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
             for(i=1; i<=nlstate;i++)      mint=matrix(1,maxwav,1,n);
               for(j=1; j<=nlstate+ndeath;j++)      anint=matrix(1,maxwav,1,n);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      s=imatrix(1,maxwav+1,1,n);
             fprintf(ficrespij,"\n");      adl=imatrix(1,maxwav+1,1,n);    
              }      tab=ivector(1,NCOVMAX);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      ncodemax=ivector(1,8);
           fprintf(ficrespij,"\n");  
         }      i=1;
     }      while (fgets(line, MAXLINE, fic) != NULL)    {
   }        if ((i >= firstobs) && (i <=lastobs)) {
           
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          for (j=maxwav;j>=1;j--){
             cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
   fclose(ficrespij);            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);
   /*---------- Forecasting ------------------*/          }
   if((stepm == 1) && (strcmp(model,".")==0)){          
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   }  
   else{          cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
     erreur=108;          cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
     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);  
   }          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);
   /*---------- Health expectancies and variances ------------*/          } 
           num[i]=atol(stra);
   strcpy(filerest,"t");          
   strcat(filerest,fileres);          /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
   if((ficrest=fopen(filerest,"w"))==NULL) {            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;}*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }          i=i+1;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        }
       } 
       /* printf("ii=%d", ij);
   strcpy(filerese,"e");         scanf("%d",i);*/
   strcat(filerese,fileres);    imx=i-1; /* Number of individuals */
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /* for (i=1; i<=imx; i++){
   }      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      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;
  strcpy(fileresv,"v");      }*/
   strcat(fileresv,fileres);     /*  for (i=1; i<=imx; i++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       if (s[4][i]==9)  s[4][i]=-1; 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
   }    
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   
   calagedate=-1;    /* Calculation of the number of parameter from char model*/
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
   k=0;    Tvaraff=ivector(1,15); 
   for(cptcov=1;cptcov<=i1;cptcov++){    Tvard=imatrix(1,15,1,2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    Tage=ivector(1,15);      
       k=k+1;     
       fprintf(ficrest,"\n#****** ");    if (strlen(model) >1){
       for(j=1;j<=cptcoveff;j++)      j=0, j1=0, k1=1, k2=1;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      j=nbocc(model,'+');
       fprintf(ficrest,"******\n");      j1=nbocc(model,'*');
       cptcovn=j+1;
       fprintf(ficreseij,"\n#****** ");      cptcovprod=j1;
       for(j=1;j<=cptcoveff;j++)      
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      strcpy(modelsav,model); 
       fprintf(ficreseij,"******\n");      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
       fprintf(ficresvij,"\n#****** ");        fprintf(ficlog,"Error. Non available option model=%s ",model);
       for(j=1;j<=cptcoveff;j++)        goto end;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
       fprintf(ficresvij,"******\n");      
       for(i=(j+1); i>=1;i--){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
       oldm=oldms;savm=savms;        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
          /*scanf("%d",i);*/
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        if (strchr(strb,'*')) {  /* Model includes a product */
       oldm=oldms;savm=savms;          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          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*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            cptcovage++;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              Tage[cptcovage]=i;
       fprintf(ficrest,"\n");              /*printf("stre=%s ", stre);*/
           }
       epj=vector(1,nlstate+1);          else if (strcmp(strd,"age")==0) { /* or age*Vn */
       for(age=bage; age <=fage ;age++){            cptcovprod--;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            cutv(strb,stre,strc,'V');
         if (popbased==1) {            Tvar[i]=atoi(stre);
           for(i=1; i<=nlstate;i++)            cptcovage++;
             prlim[i][i]=probs[(int)age][i][k];            Tage[cptcovage]=i;
         }          }
                  else {  /* Age is not in the model */
         fprintf(ficrest," %4.0f",age);            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            Tvar[i]=ncovcol+k1;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];            Tprod[k1]=i;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/            Tvard[k1][1]=atoi(strc); /* m*/
           }            Tvard[k1][2]=atoi(stre); /* n */
           epj[nlstate+1] +=epj[j];            Tvar[cptcovn+k2]=Tvard[k1][1];
         }            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
         for(i=1, vepp=0.;i <=nlstate;i++)              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
           for(j=1;j <=nlstate;j++)            k1++;
             vepp += vareij[i][j][(int)age];            k2=k2+2;
         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]));        else { /* no more sum */
         }          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
         fprintf(ficrest,"\n");         /*  scanf("%d",i);*/
       }        cutv(strd,strc,strb,'V');
     }        Tvar[i]=atoi(strc);
   }        }
 free_matrix(mint,1,maxwav,1,n);        strcpy(modelsav,stra);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
     free_vector(weight,1,n);          scanf("%d",i);*/
   fclose(ficreseij);      } /* end of loop + */
   fclose(ficresvij);    } /* end model */
   fclose(ficrest);    
   fclose(ficpar);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   free_vector(epj,1,nlstate+1);    printf("cptcovprod=%d ", cptcovprod);
      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   /*------- Variance limit prevalence------*/      scanf("%d ",i);*/
       fclose(fic);
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);      /*  if(mle==1){*/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if (weightopt != 1) { /* Maximisation without weights*/
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        for(i=1;i<=n;i++) weight[i]=1.0;
     exit(0);      }
   }      /*-calculation of age at interview from date of interview and age at death -*/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      agev=matrix(1,maxwav,1,imx);
   
   k=0;      for (i=1; i<=imx; i++) {
   for(cptcov=1;cptcov<=i1;cptcov++){        for(m=2; (m<= maxwav); m++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
       k=k+1;           anint[m][i]=9999;
       fprintf(ficresvpl,"\n#****** ");           s[m][i]=-1;
       for(j=1;j<=cptcoveff;j++)         }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       fprintf(ficresvpl,"******\n");        }
            }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      for (i=1; i<=imx; i++)  {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        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) {
   fclose(ficresvpl);              if(agedc[i]>0)
                 if(moisdc[i]!=99 && andc[i]!=9999)
   /*---------- End : free ----------------*/                  agev[m][i]=agedc[i];
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                if (andc[i]!=9999){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                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;
   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);            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]);
   free_matrix(matcov,1,npar,1,npar);              if(mint[m][i]==99 || anint[m][i]==9999)
   free_vector(delti,1,npar);                agev[m][i]=1;
   free_matrix(agev,1,maxwav,1,imx);              else if(agev[m][i] <agemin){ 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                agemin=agev[m][i];
                 /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
   if(erreur >0)              }
     printf("End of Imach with error or warning %d\n",erreur);              else if(agev[m][i] >agemax){
   else   printf("End of Imach\n");                agemax=agev[m][i];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
                }
   /* 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);*/              /*agev[m][i]=anint[m][i]-annais[i];*/
   /*printf("Total time was %d uSec.\n", total_usecs);*/              /*   agev[m][i] = age[i]+2*m;*/
   /*------ End -----------*/            }
             else { /* =9 */
               agev[m][i]=1;
  end:              s[m][i]=-1;
 #ifdef windows            }
   /* chdir(pathcd);*/          }
 #endif          else /*= 0 Unknown */
  /*system("wgnuplot graph.plt");*/            agev[m][i]=1;
  /*system("../gp37mgw/wgnuplot graph.plt");*/        }
  /*system("cd ../gp37mgw");*/      
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      }
  strcpy(plotcmd,GNUPLOTPROGRAM);      for (i=1; i<=imx; i++)  {
  strcat(plotcmd," ");        for(m=1; (m<= maxwav); m++){
  strcat(plotcmd,optionfilegnuplot);          if (s[m][i] > (nlstate+ndeath)) {
  system(plotcmd);            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);   
 #ifdef windows            goto end;
   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");  printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     else if (z[0] == 'e') system(optionfilehtm);   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
     else if (z[0] == 'g') system(plotcmd);  
     else if (z[0] == 'q') exit(0);      free_vector(severity,1,maxwav);
   }      free_imatrix(outcome,1,maxwav+1,1,n);
 #endif      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.1.42  
changed lines
  Added in v.1.56


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