Diff for /imach/src/imach.c between versions 1.48 and 1.53

version 1.48, 2002/06/10 13:12:49 version 1.53, 2002/07/23 23:59:37
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 prevalence limits. 
      
   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 unix
 #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  #ifdef windows
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #else  #define ODIRSEPARATOR '/'
 #define DIRSEPARATOR '/'  #else
 #endif  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";  #endif
 int erreur; /* Error number */  
 int nvar;  char version[80]="Imach version 0.8j, July 2002, INED-EUROREVES ";
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  int erreur; /* Error number */
 int npar=NPARMAX;  int nvar;
 int nlstate=2; /* Number of live states */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int ndeath=1; /* Number of dead states */  int npar=NPARMAX;
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int nlstate=2; /* Number of live states */
 int popbased=0;  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int *wav; /* Number of waves for this individuual 0 is possible */  int popbased=0;
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */  int *wav; /* Number of waves for this individuual 0 is possible */
 int mle, weightopt;  int maxwav; /* Maxim number of waves */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int jmin, jmax; /* min, max spacing between 2 waves */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int mle, weightopt;
 double jmean; /* Mean space between 2 waves */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double jmean; /* Mean space between 2 waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fichtm; /* Html File */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficreseij;  FILE *ficlog;
 char filerese[FILENAMELENGTH];  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE  *ficresvij;  FILE *ficresprobmorprev;
 char fileresv[FILENAMELENGTH];  FILE *fichtm; /* Html File */
 FILE  *ficresvpl;  FILE *ficreseij;
 char fileresvpl[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
 char title[MAXLINE];  FILE  *ficresvij;
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char filerest[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 #define NR_END 1  char popfile[FILENAMELENGTH];
 #define FREE_ARG char*  
 #define FTOL 1.0e-10  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 #define NRANSI  #define NR_END 1
 #define ITMAX 200  #define FREE_ARG char*
   #define FTOL 1.0e-10
 #define TOL 2.0e-4  
   #define NRANSI 
 #define CGOLD 0.3819660  #define ITMAX 200 
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define TOL 2.0e-4 
   
 #define GOLD 1.618034  #define CGOLD 0.3819660 
 #define GLIMIT 100.0  #define ZEPS 1.0e-10 
 #define TINY 1.0e-20  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 static double maxarg1,maxarg2;  #define GOLD 1.618034 
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #define GLIMIT 100.0 
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define TINY 1.0e-20 
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  static double maxarg1,maxarg2;
 #define rint(a) floor(a+0.5)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 static double sqrarg;    
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define rint(a) floor(a+0.5)
   
 int imx;  static double sqrarg;
 int stepm;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /* Stepm, step in month: minimum step interpolation*/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 int estepm;  int imx; 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  int stepm;
   /* Stepm, step in month: minimum step interpolation*/
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int estepm;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;  int m,nb;
   int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double *weight;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 int **s; /* Status */  double **pmmij, ***probs, ***mobaverage;
 double *agedc, **covar, idx;  double dateintmean=0;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   double *weight;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **s; /* Status */
 double ftolhess; /* Tolerance for computing hessian */  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 {  double ftolhess; /* Tolerance for computing hessian */
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    l1 = strlen( path );                 /* length of path */  {
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );     char *s;                             /* pointer */
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */     int  l1, l2;                         /* length counters */
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */     l1 = strlen( path );                 /* length of path */
       extern char       *getwd( );     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      s= strrchr( path, DIRSEPARATOR );            /* find last / */
       if ( getwd( dirc ) == NULL ) {     if ( s == NULL ) {                   /* no directory, so use current */
 #else       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       extern char       *getcwd( );         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   #if     defined(__bsd__)                /* get current working directory */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {        extern char       *getwd( );
 #endif  
          return( GLOCK_ERROR_GETCWD );        if ( getwd( dirc ) == NULL ) {
       }  #else
       strcpy( name, path );             /* we've got it */        extern char       *getcwd( );
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       l2 = strlen( s );                 /* length of filename */  #endif
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );           return( GLOCK_ERROR_GETCWD );
       strcpy( name, s );                /* save file name */        }
       strncpy( dirc, path, l1 - l2 );   /* now the directory */        strcpy( name, path );             /* we've got it */
       dirc[l1-l2] = 0;                  /* add zero */     } else {                             /* strip direcotry from path */
    }        s++;                              /* after this, the filename */
    l1 = strlen( dirc );                 /* length of directory */        l2 = strlen( s );                 /* length of filename */
 #ifdef windows        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }        strcpy( name, s );                /* save file name */
 #else        strncpy( dirc, path, l1 - l2 );   /* now the directory */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }        dirc[l1-l2] = 0;                  /* add zero */
 #endif     }
    s = strrchr( name, '.' );            /* find last / */     l1 = strlen( dirc );                 /* length of directory */
    s++;  #ifdef windows
    strcpy(ext,s);                       /* save extension */     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    l1= strlen( name);  #else
    l2= strlen( s)+1;     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
    strncpy( finame, name, l1-l2);  #endif
    finame[l1-l2]= 0;     s = strrchr( name, '.' );            /* find last / */
    return( 0 );                         /* we're done */     s++;
 }     strcpy(ext,s);                       /* save extension */
      l1= strlen( name);
      l2= strlen( s)+1;
 /******************************************/     strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
 void replace(char *s, char*t)     return( 0 );                         /* we're done */
 {  }
   int i;  
   int lg=20;  
   i=0;  /******************************************/
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  void replace(char *s, char*t)
     (s[i] = t[i]);  {
     if (t[i]== '\\') s[i]='/';    int i;
   }    int lg=20;
 }    i=0;
     lg=strlen(t);
 int nbocc(char *s, char occ)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   int i,j=0;      if (t[i]== '\\') s[i]='/';
   int lg=20;    }
   i=0;  }
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  int nbocc(char *s, char occ)
   if  (s[i] == occ ) j++;  {
   }    int i,j=0;
   return j;    int lg=20;
 }    i=0;
     lg=strlen(s);
 void cutv(char *u,char *v, char*t, char occ)    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   int i,lg,j,p=0;    }
   i=0;    return j;
   for(j=0; j<=strlen(t)-1; j++) {  }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  void cutv(char *u,char *v, char*t, char occ)
   {
   lg=strlen(t);    /* cuts string t into u and v where u is ended by char occ excluding it
   for(j=0; j<p; j++) {       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
     (u[j] = t[j]);       gives u="abcedf" and v="ghi2j" */
   }    int i,lg,j,p=0;
      u[p]='\0';    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
    for(j=0; j<= lg; j++) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     if (j>=(p+1))(v[j-p-1] = t[j]);    }
   }  
 }    lg=strlen(t);
     for(j=0; j<p; j++) {
 /********************** nrerror ********************/      (u[j] = t[j]);
     }
 void nrerror(char error_text[])       u[p]='\0';
 {  
   fprintf(stderr,"ERREUR ...\n");     for(j=0; j<= lg; j++) {
   fprintf(stderr,"%s\n",error_text);      if (j>=(p+1))(v[j-p-1] = t[j]);
   exit(1);    }
 }  }
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  /********************** nrerror ********************/
 {  
   double *v;  void nrerror(char error_text[])
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  {
   if (!v) nrerror("allocation failure in vector");    fprintf(stderr,"ERREUR ...\n");
   return v-nl+NR_END;    fprintf(stderr,"%s\n",error_text);
 }    exit(1);
   }
 /************************ free vector ******************/  /*********************** vector *******************/
 void free_vector(double*v, int nl, int nh)  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /************************ivector *******************************/    return v-nl+NR_END;
 int *ivector(long nl,long nh)  }
 {  
   int *v;  /************************ free vector ******************/
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  void free_vector(double*v, int nl, int nh)
   if (!v) nrerror("allocation failure in ivector");  {
   return v-nl+NR_END;    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /******************free ivector **************************/  /************************ivector *******************************/
 void free_ivector(int *v, long nl, long nh)  int *ivector(long nl,long nh)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    int *v;
 }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
 /******************* imatrix *******************************/    return v-nl+NR_END;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  /******************free ivector **************************/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  void free_ivector(int *v, long nl, long nh)
   int **m;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /******************* imatrix *******************************/
   m += NR_END;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   m -= nrl;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
      long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   /* allocate rows and set pointers to them */    int **m; 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /* allocate pointers to rows */ 
   m[nrl] += NR_END;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   m[nrl] -= ncl;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    m -= nrl; 
      
   /* return pointer to array of pointers to rows */    
   return m;    /* 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_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 pointer to array of pointers to rows */ 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    return m; 
   free((FREE_ARG) (m+nrl-NR_END));  } 
 }  
   /****************** free_imatrix *************************/
 /******************* matrix *******************************/  void free_imatrix(m,nrl,nrh,ncl,nch)
 double **matrix(long nrl, long nrh, long ncl, long nch)        int **m;
 {        long nch,ncl,nrh,nrl; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;       /* free an int matrix allocated by imatrix() */ 
   double **m;  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    free((FREE_ARG) (m+nrl-NR_END)); 
   if (!m) nrerror("allocation failure 1 in matrix()");  } 
   m += NR_END;  
   m -= nrl;  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   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()");
   return m;    m += NR_END;
 }    m -= nrl;
   
 /*************************free matrix ************************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] -= ncl;
   free((FREE_ARG)(m+nrl-NR_END));  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /*************************free matrix ************************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double ***m;  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    free((FREE_ARG)(m+nrl-NR_END));
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   m[nrl] += NR_END;    double ***m;
   m[nrl] -= ncl;  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    m -= nrl;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m[nrl][ncl] -= nll;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (j=ncl+1; j<=nch; j++)    m[nrl] += NR_END;
     m[nrl][j]=m[nrl][j-1]+nlay;    m[nrl] -= ncl;
    
   for (i=nrl+1; i<=nrh; i++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       m[i][j]=m[i][j-1]+nlay;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   }    m[nrl][ncl] += NR_END;
   return m;    m[nrl][ncl] -= nll;
 }    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
 /*************************free ma3x ************************/    
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    for (i=nrl+1; i<=nrh; i++) {
 {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      for (j=ncl+1; j<=nch; j++) 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));        m[i][j]=m[i][j-1]+nlay;
   free((FREE_ARG)(m+nrl-NR_END));    }
 }    return m;
   }
 /***************** f1dim *************************/  
 extern int ncom;  /*************************free ma3x ************************/
 extern double *pcom,*xicom;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 extern double (*nrfunc)(double []);  {
      free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double f1dim(double x)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int j;  }
   double f;  
   double *xt;  /***************** f1dim *************************/
    extern int ncom; 
   xt=vector(1,ncom);  extern double *pcom,*xicom;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  extern double (*nrfunc)(double []); 
   f=(*nrfunc)(xt);   
   free_vector(xt,1,ncom);  double f1dim(double x) 
   return f;  { 
 }    int j; 
     double f;
 /*****************brent *************************/    double *xt; 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)   
 {    xt=vector(1,ncom); 
   int iter;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double a,b,d,etemp;    f=(*nrfunc)(xt); 
   double fu,fv,fw,fx;    free_vector(xt,1,ncom); 
   double ftemp;    return f; 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  } 
   double e=0.0;  
    /*****************brent *************************/
   a=(ax < cx ? ax : cx);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   b=(ax > cx ? ax : cx);  { 
   x=w=v=bx;    int iter; 
   fw=fv=fx=(*f)(x);    double a,b,d,etemp;
   for (iter=1;iter<=ITMAX;iter++) {    double fu,fv,fw,fx;
     xm=0.5*(a+b);    double ftemp;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double e=0.0; 
     printf(".");fflush(stdout);   
 #ifdef DEBUG    a=(ax < cx ? ax : cx); 
     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);    b=(ax > cx ? ax : cx); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    x=w=v=bx; 
 #endif    fw=fv=fx=(*f)(x); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    for (iter=1;iter<=ITMAX;iter++) { 
       *xmin=x;      xm=0.5*(a+b); 
       return fx;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     ftemp=fu;      printf(".");fflush(stdout);
     if (fabs(e) > tol1) {      fprintf(ficlog,".");fflush(ficlog);
       r=(x-w)*(fx-fv);  #ifdef DEBUG
       q=(x-v)*(fx-fw);      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);
       p=(x-v)*q-(x-w)*r;      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);
       q=2.0*(q-r);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       if (q > 0.0) p = -p;  #endif
       q=fabs(q);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       etemp=e;        *xmin=x; 
       e=d;        return fx; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      } 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      ftemp=fu;
       else {      if (fabs(e) > tol1) { 
         d=p/q;        r=(x-w)*(fx-fv); 
         u=x+d;        q=(x-v)*(fx-fw); 
         if (u-a < tol2 || b-u < tol2)        p=(x-v)*q-(x-w)*r; 
           d=SIGN(tol1,xm-x);        q=2.0*(q-r); 
       }        if (q > 0.0) p = -p; 
     } else {        q=fabs(q); 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));        etemp=e; 
     }        e=d; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     fu=(*f)(u);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     if (fu <= fx) {        else { 
       if (u >= x) a=x; else b=x;          d=p/q; 
       SHFT(v,w,x,u)          u=x+d; 
         SHFT(fv,fw,fx,fu)          if (u-a < tol2 || b-u < tol2) 
         } else {            d=SIGN(tol1,xm-x); 
           if (u < x) a=u; else b=u;        } 
           if (fu <= fw || w == x) {      } else { 
             v=w;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             w=u;      } 
             fv=fw;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             fw=fu;      fu=(*f)(u); 
           } else if (fu <= fv || v == x || v == w) {      if (fu <= fx) { 
             v=u;        if (u >= x) a=x; else b=x; 
             fv=fu;        SHFT(v,w,x,u) 
           }          SHFT(fv,fw,fx,fu) 
         }          } else { 
   }            if (u < x) a=u; else b=u; 
   nrerror("Too many iterations in brent");            if (fu <= fw || w == x) { 
   *xmin=x;              v=w; 
   return fx;              w=u; 
 }              fv=fw; 
               fw=fu; 
 /****************** mnbrak ***********************/            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,              fv=fu; 
             double (*func)(double))            } 
 {          } 
   double ulim,u,r,q, dum;    } 
   double fu;    nrerror("Too many iterations in brent"); 
      *xmin=x; 
   *fa=(*func)(*ax);    return fx; 
   *fb=(*func)(*bx);  } 
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  /****************** mnbrak ***********************/
       SHFT(dum,*fb,*fa,dum)  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   *cx=(*bx)+GOLD*(*bx-*ax);              double (*func)(double)) 
   *fc=(*func)(*cx);  { 
   while (*fb > *fc) {    double ulim,u,r,q, dum;
     r=(*bx-*ax)*(*fb-*fc);    double fu; 
     q=(*bx-*cx)*(*fb-*fa);   
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    *fa=(*func)(*ax); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    *fb=(*func)(*bx); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if (*fb > *fa) { 
     if ((*bx-u)*(u-*cx) > 0.0) {      SHFT(dum,*ax,*bx,dum) 
       fu=(*func)(u);        SHFT(dum,*fb,*fa,dum) 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        } 
       fu=(*func)(u);    *cx=(*bx)+GOLD*(*bx-*ax); 
       if (fu < *fc) {    *fc=(*func)(*cx); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    while (*fb > *fc) { 
           SHFT(*fb,*fc,fu,(*func)(u))      r=(*bx-*ax)*(*fb-*fc); 
           }      q=(*bx-*cx)*(*fb-*fa); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       u=ulim;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       fu=(*func)(u);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     } else {      if ((*bx-u)*(u-*cx) > 0.0) { 
       u=(*cx)+GOLD*(*cx-*bx);        fu=(*func)(u); 
       fu=(*func)(u);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
     SHFT(*ax,*bx,*cx,u)        if (fu < *fc) { 
       SHFT(*fa,*fb,*fc,fu)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 /*************** linmin ************************/        u=ulim; 
         fu=(*func)(u); 
 int ncom;      } else { 
 double *pcom,*xicom;        u=(*cx)+GOLD*(*cx-*bx); 
 double (*nrfunc)(double []);        fu=(*func)(u); 
        } 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      SHFT(*ax,*bx,*cx,u) 
 {        SHFT(*fa,*fb,*fc,fu) 
   double brent(double ax, double bx, double cx,        } 
                double (*f)(double), double tol, double *xmin);  } 
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*************** linmin ************************/
               double *fc, double (*func)(double));  
   int j;  int ncom; 
   double xx,xmin,bx,ax;  double *pcom,*xicom;
   double fx,fb,fa;  double (*nrfunc)(double []); 
     
   ncom=n;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   pcom=vector(1,n);  { 
   xicom=vector(1,n);    double brent(double ax, double bx, double cx, 
   nrfunc=func;                 double (*f)(double), double tol, double *xmin); 
   for (j=1;j<=n;j++) {    double f1dim(double x); 
     pcom[j]=p[j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     xicom[j]=xi[j];                double *fc, double (*func)(double)); 
   }    int j; 
   ax=0.0;    double xx,xmin,bx,ax; 
   xx=1.0;    double fx,fb,fa;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);   
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    ncom=n; 
 #ifdef DEBUG    pcom=vector(1,n); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    xicom=vector(1,n); 
 #endif    nrfunc=func; 
   for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
     xi[j] *= xmin;      pcom[j]=p[j]; 
     p[j] += xi[j];      xicom[j]=xi[j]; 
   }    } 
   free_vector(xicom,1,n);    ax=0.0; 
   free_vector(pcom,1,n);    xx=1.0; 
 }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 /*************** powell ************************/  #ifdef DEBUG
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             double (*func)(double []))    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {  #endif
   void linmin(double p[], double xi[], int n, double *fret,    for (j=1;j<=n;j++) { 
               double (*func)(double []));      xi[j] *= xmin; 
   int i,ibig,j;      p[j] += xi[j]; 
   double del,t,*pt,*ptt,*xit;    } 
   double fp,fptt;    free_vector(xicom,1,n); 
   double *xits;    free_vector(pcom,1,n); 
   pt=vector(1,n);  } 
   ptt=vector(1,n);  
   xit=vector(1,n);  /*************** powell ************************/
   xits=vector(1,n);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   *fret=(*func)(p);              double (*func)(double [])) 
   for (j=1;j<=n;j++) pt[j]=p[j];  { 
   for (*iter=1;;++(*iter)) {    void linmin(double p[], double xi[], int n, double *fret, 
     fp=(*fret);                double (*func)(double [])); 
     ibig=0;    int i,ibig,j; 
     del=0.0;    double del,t,*pt,*ptt,*xit;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    double fp,fptt;
     for (i=1;i<=n;i++)    double *xits;
       printf(" %d %.12f",i, p[i]);    pt=vector(1,n); 
     printf("\n");    ptt=vector(1,n); 
     for (i=1;i<=n;i++) {    xit=vector(1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    xits=vector(1,n); 
       fptt=(*fret);    *fret=(*func)(p); 
 #ifdef DEBUG    for (j=1;j<=n;j++) pt[j]=p[j]; 
       printf("fret=%lf \n",*fret);    for (*iter=1;;++(*iter)) { 
 #endif      fp=(*fret); 
       printf("%d",i);fflush(stdout);      ibig=0; 
       linmin(p,xit,n,fret,func);      del=0.0; 
       if (fabs(fptt-(*fret)) > del) {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         del=fabs(fptt-(*fret));      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         ibig=i;      for (i=1;i<=n;i++) 
       }        printf(" %d %.12f",i, p[i]);
 #ifdef DEBUG      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("%d %.12e",i,(*fret));      printf("\n");
       for (j=1;j<=n;j++) {      fprintf(ficlog,"\n");
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      for (i=1;i<=n;i++) { 
         printf(" x(%d)=%.12e",j,xit[j]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       }        fptt=(*fret); 
       for(j=1;j<=n;j++)  #ifdef DEBUG
         printf(" p=%.12e",p[j]);        printf("fret=%lf \n",*fret);
       printf("\n");        fprintf(ficlog,"fret=%lf \n",*fret);
 #endif  #endif
     }        printf("%d",i);fflush(stdout);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        fprintf(ficlog,"%d",i);fflush(ficlog);
 #ifdef DEBUG        linmin(p,xit,n,fret,func); 
       int k[2],l;        if (fabs(fptt-(*fret)) > del) { 
       k[0]=1;          del=fabs(fptt-(*fret)); 
       k[1]=-1;          ibig=i; 
       printf("Max: %.12e",(*func)(p));        } 
       for (j=1;j<=n;j++)  #ifdef DEBUG
         printf(" %.12e",p[j]);        printf("%d %.12e",i,(*fret));
       printf("\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
       for(l=0;l<=1;l++) {        for (j=1;j<=n;j++) {
         for (j=1;j<=n;j++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];          printf(" x(%d)=%.12e",j,xit[j]);
           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," x(%d)=%.12e",j,xit[j]);
         }        }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
 #endif          fprintf(ficlog," p=%.12e",p[j]);
         }
         printf("\n");
       free_vector(xit,1,n);        fprintf(ficlog,"\n");
       free_vector(xits,1,n);  #endif
       free_vector(ptt,1,n);      } 
       free_vector(pt,1,n);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       return;  #ifdef DEBUG
     }        int k[2],l;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        k[0]=1;
     for (j=1;j<=n;j++) {        k[1]=-1;
       ptt[j]=2.0*p[j]-pt[j];        printf("Max: %.12e",(*func)(p));
       xit[j]=p[j]-pt[j];        fprintf(ficlog,"Max: %.12e",(*func)(p));
       pt[j]=p[j];        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
     fptt=(*func)(ptt);          fprintf(ficlog," %.12e",p[j]);
     if (fptt < fp) {        }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        printf("\n");
       if (t < 0.0) {        fprintf(ficlog,"\n");
         linmin(p,xit,n,fret,func);        for(l=0;l<=1;l++) {
         for (j=1;j<=n;j++) {          for (j=1;j<=n;j++) {
           xi[j][ibig]=xi[j][n];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
           xi[j][n]=xit[j];            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]);
 #ifdef DEBUG          }
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         for(j=1;j<=n;j++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           printf(" %.12e",xit[j]);        }
         printf("\n");  #endif
 #endif  
       }  
     }        free_vector(xit,1,n); 
   }        free_vector(xits,1,n); 
 }        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 /**** Prevalence limit ****************/        return; 
       } 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 {      for (j=1;j<=n;j++) { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        ptt[j]=2.0*p[j]-pt[j]; 
      matrix by transitions matrix until convergence is reached */        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   int i, ii,j,k;      } 
   double min, max, maxmin, maxmax,sumnew=0.;      fptt=(*func)(ptt); 
   double **matprod2();      if (fptt < fp) { 
   double **out, cov[NCOVMAX], **pmij();        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double **newm;        if (t < 0.0) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)            xi[j][ibig]=xi[j][n]; 
     for (j=1;j<=nlstate+ndeath;j++){            xi[j][n]=xit[j]; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);          }
     }  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
    cov[1]=1.;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            for(j=1;j<=n;j++){
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */            printf(" %.12e",xit[j]);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            fprintf(ficlog," %.12e",xit[j]);
     newm=savm;          }
     /* Covariates have to be included here again */          printf("\n");
      cov[2]=agefin;          fprintf(ficlog,"\n");
    #endif
       for (k=1; k<=cptcovn;k++) {        } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      } 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    } 
       }  } 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /**** Prevalence limit ****************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/       matrix by transitions matrix until convergence is reached */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
     int i, ii,j,k;
     savm=oldm;    double min, max, maxmin, maxmax,sumnew=0.;
     oldm=newm;    double **matprod2();
     maxmax=0.;    double **out, cov[NCOVMAX], **pmij();
     for(j=1;j<=nlstate;j++){    double **newm;
       min=1.;    double agefin, delaymax=50 ; /* Max number of years to converge */
       max=0.;  
       for(i=1; i<=nlstate; i++) {    for (ii=1;ii<=nlstate+ndeath;ii++)
         sumnew=0;      for (j=1;j<=nlstate+ndeath;j++){
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         prlim[i][j]= newm[i][j]/(1-sumnew);      }
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);     cov[1]=1.;
       }   
       maxmin=max-min;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       maxmax=FMAX(maxmax,maxmin);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     }      newm=savm;
     if(maxmax < ftolpl){      /* Covariates have to be included here again */
       return prlim;       cov[2]=agefin;
     }    
   }        for (k=1; k<=cptcovn;k++) {
 }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
 /*************** transition probabilities ***************/        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        for (k=1; k<=cptcovprod;k++)
 {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double s1, s2;  
   /*double t34;*/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int i,j,j1, nc, ii, jj;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for(i=1; i<= nlstate; i++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      savm=oldm;
         /*s2 += param[i][j][nc]*cov[nc];*/      oldm=newm;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      maxmax=0.;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      for(j=1;j<=nlstate;j++){
       }        min=1.;
       ps[i][j]=s2;        max=0.;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        for(i=1; i<=nlstate; i++) {
     }          sumnew=0;
     for(j=i+1; j<=nlstate+ndeath;j++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          prlim[i][j]= newm[i][j]/(1-sumnew);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          max=FMAX(max,prlim[i][j]);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          min=FMIN(min,prlim[i][j]);
       }        }
       ps[i][j]=s2;        maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
   }      }
     /*ps[3][2]=1;*/      if(maxmax < ftolpl){
         return prlim;
   for(i=1; i<= nlstate; i++){      }
      s1=0;    }
     for(j=1; j<i; j++)  }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************** transition probabilities ***************/ 
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(j=1; j<i; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double s1, s2;
     for(j=i+1; j<=nlstate+ndeath; j++)    /*double t34;*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int i,j,j1, nc, ii, jj;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(jj=1; jj<= nlstate+ndeath; jj++){          /*s2 += param[i][j][nc]*cov[nc];*/
       ps[ii][jj]=0;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       ps[ii][ii]=1;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     }        }
   }        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      for(j=i+1; j<=nlstate+ndeath;j++){
     for(jj=1; jj<= nlstate+ndeath; jj++){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      printf("%lf ",ps[ii][jj]);          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);*/
     printf("\n ");        }
     }        ps[i][j]=s2;
     printf("\n ");printf("%lf ",cov[2]);*/      }
 /*    }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      /*ps[3][2]=1;*/
   goto end;*/  
     return ps;    for(i=1; i<= nlstate; i++){
 }       s1=0;
       for(j=1; j<i; j++)
 /**************** Product of 2 matrices ******************/        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        s1+=exp(ps[i][j]);
 {      ps[i][i]=1./(s1+1.);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      for(j=1; j<i; j++)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* in, b, out are matrice of pointers which should have been initialized      for(j=i+1; j<=nlstate+ndeath; j++)
      before: only the contents of out is modified. The function returns        ps[i][j]= exp(ps[i][j])*ps[i][i];
      a pointer to pointers identical to out */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   long i, j, k;    } /* end i */
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      for(jj=1; jj<= nlstate+ndeath; jj++){
         out[i][k] +=in[i][j]*b[j][k];        ps[ii][jj]=0;
         ps[ii][ii]=1;
   return out;      }
 }    }
   
   
 /************* Higher Matrix Product ***************/    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )       printf("%lf ",ps[ii][jj]);
 {     }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      printf("\n ");
      duration (i.e. until      }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      printf("\n ");printf("%lf ",cov[2]);*/
      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).    for(i=1; i<= npar; i++) printf("%f ",x[i]);
      Model is determined by parameters x and covariates have to be    goto end;*/
      included manually here.      return ps;
   }
      */  
   /**************** Product of 2 matrices ******************/
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double **newm;  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   /* Hstepm could be zero and should return the unit matrix */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   for (i=1;i<=nlstate+ndeath;i++)    /* in, b, out are matrice of pointers which should have been initialized 
     for (j=1;j<=nlstate+ndeath;j++){       before: only the contents of out is modified. The function returns
       oldm[i][j]=(i==j ? 1.0 : 0.0);       a pointer to pointers identical to out */
       po[i][j][0]=(i==j ? 1.0 : 0.0);    long i, j, k;
     }    for(i=nrl; i<= nrh; i++)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for(k=ncolol; k<=ncoloh; k++)
   for(h=1; h <=nhstepm; h++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for(d=1; d <=hstepm; d++){          out[i][k] +=in[i][j]*b[j][k];
       newm=savm;  
       /* Covariates have to be included here again */    return out;
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  /************* Higher Matrix Product ***************/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
        duration (i.e. until
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,       (typically every 2 years instead of every month which is too big).
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       Model is determined by parameters x and covariates have to be 
       savm=oldm;       included manually here. 
       oldm=newm;  
     }       */
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {    int i, j, d, h, k;
         po[i][j][h]=newm[i][j];    double **out, cov[NCOVMAX];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double **newm;
          */  
       }    /* Hstepm could be zero and should return the unit matrix */
   } /* end h */    for (i=1;i<=nlstate+ndeath;i++)
   return po;      for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
 /*************** log-likelihood *************/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double func( double *x)    for(h=1; h <=nhstepm; h++){
 {      for(d=1; d <=hstepm; d++){
   int i, ii, j, k, mi, d, kk;        newm=savm;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        /* Covariates have to be included here again */
   double **out;        cov[1]=1.;
   double sw; /* Sum of weights */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double lli; /* Individual log likelihood */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   long ipmx;        for (k=1; k<=cptcovage;k++)
   /*extern weight */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* We are differentiating ll according to initial status */        for (k=1; k<=cptcovprod;k++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  
   */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   cov[1]=1.;        /*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, 
   for(k=1; k<=nlstate; k++) ll[k]=0.;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        savm=oldm;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        oldm=newm;
     for(mi=1; mi<= wav[i]-1; mi++){      }
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(i=1; i<=nlstate+ndeath; i++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for(j=1;j<=nlstate+ndeath;j++) {
       for(d=0; d<dh[mi][i]; d++){          po[i][j][h]=newm[i][j];
         newm=savm;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         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];    } /* end h */
         }    return po;
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;  /*************** log-likelihood *************/
         oldm=newm;  double func( double *x)
          {
            int i, ii, j, k, mi, d, kk;
       } /* end mult */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
          double **out;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double sw; /* Sum of weights */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double lli; /* Individual log likelihood */
       ipmx +=1;    long ipmx;
       sw += weight[i];    /*extern weight */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    /* We are differentiating ll according to initial status */
     } /* end of wave */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   } /* end of individual */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    cov[1]=1.;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;    for(k=1; k<=nlstate; k++) ll[k]=0.;
 }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 /*********** Maximum Likelihood Estimation ***************/        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for(d=0; d<dh[mi][i]; d++){
 {          newm=savm;
   int i,j, iter;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **xi,*delti;          for (kk=1; kk<=cptcovage;kk++) {
   double fret;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   xi=matrix(1,npar,1,npar);          }
   for (i=1;i<=npar;i++)          
     for (j=1;j<=npar;j++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       xi[i][j]=(i==j ? 1.0 : 0.0);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("Powell\n");          savm=oldm;
   powell(p,xi,npar,ftol,&iter,&fret,func);          oldm=newm;
           
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        } /* end mult */
         
 }        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]]);*/
 /**** Computes Hessian and covariance matrix ***/        ipmx +=1;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        sw += weight[i];
 {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double  **a,**y,*x,pd;      } /* end of wave */
   double **hess;    } /* end of individual */
   int i, j,jk;  
   int *indx;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double hessii(double p[], double delta, int theta, double delti[]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double hessij(double p[], double delti[], int i, int j);    return -l;
   void lubksb(double **a, int npar, int *indx, double b[]) ;  }
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   
   hess=matrix(1,npar,1,npar);  /*********** Maximum Likelihood Estimation ***************/
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    int i,j, iter;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double **xi,*delti;
     /*printf(" %f ",p[i]);*/    double fret;
     /*printf(" %lf ",hess[i][i]);*/    xi=matrix(1,npar,1,npar);
   }    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
   for (i=1;i<=npar;i++) {        xi[i][j]=(i==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++)  {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       if (j>i) {    powell(p,xi,npar,ftol,&iter,&fret,func);
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         hess[j][i]=hess[i][j];        fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         /*printf(" %lf ",hess[i][j]);*/    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
     }  }
   }  
   printf("\n");  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  {
      double  **a,**y,*x,pd;
   a=matrix(1,npar,1,npar);    double **hess;
   y=matrix(1,npar,1,npar);    int i, j,jk;
   x=vector(1,npar);    int *indx;
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)    double hessii(double p[], double delta, int theta, double delti[]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double hessij(double p[], double delti[], int i, int j);
   ludcmp(a,npar,indx,&pd);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    hess=matrix(1,npar,1,npar);
     x[j]=1;  
     lubksb(a,npar,indx,x);    printf("\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       matcov[i][j]=x[i];    for (i=1;i<=npar;i++){
     }      printf("%d",i);fflush(stdout);
   }      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
   printf("\n#Hessian matrix#\n");      /*printf(" %f ",p[i]);*/
   for (i=1;i<=npar;i++) {      /*printf(" %lf ",hess[i][i]);*/
     for (j=1;j<=npar;j++) {    }
       printf("%.3e ",hess[i][j]);    
     }    for (i=1;i<=npar;i++) {
     printf("\n");      for (j=1;j<=npar;j++)  {
   }        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
   /* Recompute Inverse */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (i=1;i<=npar;i++)          hess[i][j]=hessij(p,delti,i,j);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          hess[j][i]=hess[i][j];    
   ludcmp(a,npar,indx,&pd);          /*printf(" %lf ",hess[i][j]);*/
         }
   /*  printf("\n#Hessian matrix recomputed#\n");      }
     }
   for (j=1;j<=npar;j++) {    printf("\n");
     for (i=1;i<=npar;i++) x[i]=0;    fprintf(ficlog,"\n");
     x[j]=1;  
     lubksb(a,npar,indx,x);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=1;i<=npar;i++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       y[i][j]=x[i];    
       printf("%.3e ",y[i][j]);    a=matrix(1,npar,1,npar);
     }    y=matrix(1,npar,1,npar);
     printf("\n");    x=vector(1,npar);
   }    indx=ivector(1,npar);
   */    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   free_matrix(a,1,npar,1,npar);    ludcmp(a,npar,indx,&pd);
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);    for (j=1;j<=npar;j++) {
   free_ivector(indx,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   free_matrix(hess,1,npar,1,npar);      x[j]=1;
       lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 }        matcov[i][j]=x[i];
       }
 /*************** hessian matrix ****************/    }
 double hessii( double x[], double delta, int theta, double delti[])  
 {    printf("\n#Hessian matrix#\n");
   int i;    fprintf(ficlog,"\n#Hessian matrix#\n");
   int l=1, lmax=20;    for (i=1;i<=npar;i++) { 
   double k1,k2;      for (j=1;j<=npar;j++) { 
   double p2[NPARMAX+1];        printf("%.3e ",hess[i][j]);
   double res;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      }
   double fx;      printf("\n");
   int k=0,kmax=10;      fprintf(ficlog,"\n");
   double l1;    }
   
   fx=func(x);    /* Recompute Inverse */
   for (i=1;i<=npar;i++) p2[i]=x[i];    for (i=1;i<=npar;i++)
   for(l=0 ; l <=lmax; l++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     l1=pow(10,l);    ludcmp(a,npar,indx,&pd);
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){    /*  printf("\n#Hessian matrix recomputed#\n");
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;    for (j=1;j<=npar;j++) {
       k1=func(p2)-fx;      for (i=1;i<=npar;i++) x[i]=0;
       p2[theta]=x[theta]-delt;      x[j]=1;
       k2=func(p2)-fx;      lubksb(a,npar,indx,x);
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for (i=1;i<=npar;i++){ 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        y[i][j]=x[i];
              printf("%.3e ",y[i][j]);
 #ifdef DEBUG        fprintf(ficlog,"%.3e ",y[i][j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      }
 #endif      printf("\n");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      fprintf(ficlog,"\n");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    }
         k=kmax;    */
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    free_matrix(a,1,npar,1,npar);
         k=kmax; l=lmax*10.;    free_matrix(y,1,npar,1,npar);
       }    free_vector(x,1,npar);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    free_ivector(indx,1,npar);
         delts=delt;    free_matrix(hess,1,npar,1,npar);
       }  
     }  
   }  }
   delti[theta]=delts;  
   return res;  /*************** hessian matrix ****************/
    double hessii( double x[], double delta, int theta, double delti[])
 }  {
     int i;
 double hessij( double x[], double delti[], int thetai,int thetaj)    int l=1, lmax=20;
 {    double k1,k2;
   int i;    double p2[NPARMAX+1];
   int l=1, l1, lmax=20;    double res;
   double k1,k2,k3,k4,res,fx;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double p2[NPARMAX+1];    double fx;
   int k;    int k=0,kmax=10;
     double l1;
   fx=func(x);  
   for (k=1; k<=2; k++) {    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];    for (i=1;i<=npar;i++) p2[i]=x[i];
     p2[thetai]=x[thetai]+delti[thetai]/k;    for(l=0 ; l <=lmax; l++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      l1=pow(10,l);
     k1=func(p2)-fx;      delts=delt;
        for(k=1 ; k <kmax; k=k+1){
     p2[thetai]=x[thetai]+delti[thetai]/k;        delt = delta*(l1*k);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        p2[theta]=x[theta] +delt;
     k2=func(p2)-fx;        k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
     p2[thetai]=x[thetai]-delti[thetai]/k;        k2=func(p2)-fx;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        /*res= (k1-2.0*fx+k2)/delt/delt; */
     k3=func(p2)-fx;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
     p2[thetai]=x[thetai]-delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]-delti[thetaj]/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);
     k4=func(p2)-fx;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #endif
 #ifdef DEBUG        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     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);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 #endif          k=kmax;
   }        }
   return res;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 }          k=kmax; l=lmax*10.;
         }
 /************** Inverse of matrix **************/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 void ludcmp(double **a, int n, int *indx, double *d)          delts=delt;
 {        }
   int i,imax,j,k;      }
   double big,dum,sum,temp;    }
   double *vv;    delti[theta]=delts;
      return res; 
   vv=vector(1,n);    
   *d=1.0;  }
   for (i=1;i<=n;i++) {  
     big=0.0;  double hessij( double x[], double delti[], int thetai,int thetaj)
     for (j=1;j<=n;j++)  {
       if ((temp=fabs(a[i][j])) > big) big=temp;    int i;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    int l=1, l1, lmax=20;
     vv[i]=1.0/big;    double k1,k2,k3,k4,res,fx;
   }    double p2[NPARMAX+1];
   for (j=1;j<=n;j++) {    int k;
     for (i=1;i<j;i++) {  
       sum=a[i][j];    fx=func(x);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    for (k=1; k<=2; k++) {
       a[i][j]=sum;      for (i=1;i<=npar;i++) p2[i]=x[i];
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
     big=0.0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for (i=j;i<=n;i++) {      k1=func(p2)-fx;
       sum=a[i][j];    
       for (k=1;k<j;k++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         sum -= a[i][k]*a[k][j];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       a[i][j]=sum;      k2=func(p2)-fx;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    
         big=dum;      p2[thetai]=x[thetai]-delti[thetai]/k;
         imax=i;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
     }    
     if (j != imax) {      p2[thetai]=x[thetai]-delti[thetai]/k;
       for (k=1;k<=n;k++) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         dum=a[imax][k];      k4=func(p2)-fx;
         a[imax][k]=a[j][k];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         a[j][k]=dum;  #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);
       *d = -(*d);      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);
       vv[imax]=vv[j];  #endif
     }    }
     indx[j]=imax;    return res;
     if (a[j][j] == 0.0) a[j][j]=TINY;  }
     if (j != n) {  
       dum=1.0/(a[j][j]);  /************** Inverse of matrix **************/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  void ludcmp(double **a, int n, int *indx, double *d) 
     }  { 
   }    int i,imax,j,k; 
   free_vector(vv,1,n);  /* Doesn't work */    double big,dum,sum,temp; 
 ;    double *vv; 
 }   
     vv=vector(1,n); 
 void lubksb(double **a, int n, int *indx, double b[])    *d=1.0; 
 {    for (i=1;i<=n;i++) { 
   int i,ii=0,ip,j;      big=0.0; 
   double sum;      for (j=1;j<=n;j++) 
          if ((temp=fabs(a[i][j])) > big) big=temp; 
   for (i=1;i<=n;i++) {      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     ip=indx[i];      vv[i]=1.0/big; 
     sum=b[ip];    } 
     b[ip]=b[i];    for (j=1;j<=n;j++) { 
     if (ii)      for (i=1;i<j;i++) { 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        sum=a[i][j]; 
     else if (sum) ii=i;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     b[i]=sum;        a[i][j]=sum; 
   }      } 
   for (i=n;i>=1;i--) {      big=0.0; 
     sum=b[i];      for (i=j;i<=n;i++) { 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        sum=a[i][j]; 
     b[i]=sum/a[i][i];        for (k=1;k<j;k++) 
   }          sum -= a[i][k]*a[k][j]; 
 }        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
 /************ Frequencies ********************/          big=dum; 
 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)          imax=i; 
 {  /* Some frequencies */        } 
        } 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      if (j != imax) { 
   double ***freq; /* Frequencies */        for (k=1;k<=n;k++) { 
   double *pp;          dum=a[imax][k]; 
   double pos, k2, dateintsum=0,k2cpt=0;          a[imax][k]=a[j][k]; 
   FILE *ficresp;          a[j][k]=dum; 
   char fileresp[FILENAMELENGTH];        } 
          *d = -(*d); 
   pp=vector(1,nlstate);        vv[imax]=vv[j]; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } 
   strcpy(fileresp,"p");      indx[j]=imax; 
   strcat(fileresp,fileres);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {      if (j != n) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        dum=1.0/(a[j][j]); 
     exit(0);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   }      } 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    } 
   j1=0;    free_vector(vv,1,n);  /* Doesn't work */
    ;
   j=cptcoveff;  } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    void lubksb(double **a, int n, int *indx, double b[]) 
   for(k1=1; k1<=j;k1++){  { 
     for(i1=1; i1<=ncodemax[k1];i1++){    int i,ii=0,ip,j; 
       j1++;    double sum; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);   
         scanf("%d", i);*/    for (i=1;i<=n;i++) { 
       for (i=-1; i<=nlstate+ndeath; i++)        ip=indx[i]; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        sum=b[ip]; 
           for(m=agemin; m <= agemax+3; m++)      b[ip]=b[i]; 
             freq[i][jk][m]=0;      if (ii) 
              for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       dateintsum=0;      else if (sum) ii=i; 
       k2cpt=0;      b[i]=sum; 
       for (i=1; i<=imx; i++) {    } 
         bool=1;    for (i=n;i>=1;i--) { 
         if  (cptcovn>0) {      sum=b[i]; 
           for (z1=1; z1<=cptcoveff; z1++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      b[i]=sum/a[i][i]; 
               bool=0;    } 
         }  } 
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  /************ Frequencies ********************/
             k2=anint[m][i]+(mint[m][i]/12.);  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)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  {  /* Some frequencies */
               if(agev[m][i]==0) agev[m][i]=agemax+1;    
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
               if (m<lastpass) {    int first;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double ***freq; /* Frequencies */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double *pp;
               }    double pos, k2, dateintsum=0,k2cpt=0;
                  FILE *ficresp;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    char fileresp[FILENAMELENGTH];
                 dateintsum=dateintsum+k2;    
                 k2cpt++;    pp=vector(1,nlstate);
               }    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
             }    strcpy(fileresp,"p");
           }    strcat(fileresp,fileres);
         }    if((ficresp=fopen(fileresp,"w"))==NULL) {
       }      printf("Problem with prevalence resultfile: %s\n", fileresp);
              fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      exit(0);
     }
       if  (cptcovn>0) {    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         fprintf(ficresp, "\n#********** Variable ");    j1=0;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(ficresp, "**********\n#");    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    first=1;
       fprintf(ficresp, "\n");  
          for(k1=1; k1<=j;k1++){
       for(i=(int)agemin; i <= (int)agemax+3; i++){      for(i1=1; i1<=ncodemax[k1];i1++){
         if(i==(int)agemax+3)        j1++;
           printf("Total");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         else          scanf("%d", i);*/
           printf("Age %d", i);        for (i=-1; i<=nlstate+ndeath; i++)  
         for(jk=1; jk <=nlstate ; jk++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           for(m=-1, 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;
         }        
         for(jk=1; jk <=nlstate ; jk++){        dateintsum=0;
           for(m=-1, pos=0; m <=0 ; m++)        k2cpt=0;
             pos += freq[jk][m][i];        for (i=1; i<=imx; i++) {
           if(pp[jk]>=1.e-10)          bool=1;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          if  (cptcovn>0) {
           else            for (z1=1; z1<=cptcoveff; z1++) 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         }                bool=0;
           }
         for(jk=1; jk <=nlstate ; jk++){          if (bool==1) {
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for(m=firstpass; m<=lastpass; m++){
             pp[jk] += freq[jk][m][i];              k2=anint[m][i]+(mint[m][i]/12.);
         }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=agemax+1;
         for(jk=1,pos=0; jk <=nlstate ; jk++)                if(agev[m][i]==1) agev[m][i]=agemax+2;
           pos += pp[jk];                if (m<lastpass) {
         for(jk=1; jk <=nlstate ; jk++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           if(pos>=1.e-5)                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                }
           else                
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           if( i <= (int) agemax){                  dateintsum=dateintsum+k2;
             if(pos>=1.e-5){                  k2cpt++;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                }
               probs[i][jk][j1]= pp[jk]/pos;              }
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            }
             }          }
             else        }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);         
           }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
         }  
                if  (cptcovn>0) {
         for(jk=-1; jk <=nlstate+ndeath; jk++)          fprintf(ficresp, "\n#********** Variable "); 
           for(m=-1; m <=nlstate+ndeath; m++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          fprintf(ficresp, "**********\n#");
         if(i <= (int) agemax)        }
           fprintf(ficresp,"\n");        for(i=1; i<=nlstate;i++) 
         printf("\n");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       }        fprintf(ficresp, "\n");
     }        
   }        for(i=(int)agemin; i <= (int)agemax+3; i++){
   dateintmean=dateintsum/k2cpt;          if(i==(int)agemax+3){
              fprintf(ficlog,"Total");
   fclose(ficresp);          }else{
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            if(first==1){
   free_vector(pp,1,nlstate);              first=0;
                printf("See log file for details...\n");
   /* End of Freq */            }
 }            fprintf(ficlog,"Age %d", i);
           }
 /************ Prevalence ********************/          for(jk=1; jk <=nlstate ; jk++){
 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)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 {  /* Some frequencies */              pp[jk] += freq[jk][m][i]; 
            }
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          for(jk=1; jk <=nlstate ; jk++){
   double ***freq; /* Frequencies */            for(m=-1, pos=0; m <=0 ; m++)
   double *pp;              pos += freq[jk][m][i];
   double pos, k2;            if(pp[jk]>=1.e-10){
               if(first==1){
   pp=vector(1,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }else{
   j1=0;              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   j=cptcoveff;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            }
            }
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){          for(jk=1; jk <=nlstate ; jk++){
       j1++;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                    pp[jk] += freq[jk][m][i];
       for (i=-1; i<=nlstate+ndeath; i++)            }
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)          for(jk=1,pos=0; jk <=nlstate ; jk++)
             freq[i][jk][m]=0;            pos += pp[jk];
                for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i<=imx; i++) {            if(pos>=1.e-5){
         bool=1;              if(first==1)
         if  (cptcovn>0) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           for (z1=1; z1<=cptcoveff; z1++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }else{
               bool=0;              if(first==1)
         }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         if (bool==1) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           for(m=firstpass; m<=lastpass; m++){            }
             k2=anint[m][i]+(mint[m][i]/12.);            if( i <= (int) agemax){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              if(pos>=1.e-5){
               if(agev[m][i]==0) agev[m][i]=agemax+1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
               if(agev[m][i]==1) agev[m][i]=agemax+2;                probs[i][jk][j1]= pp[jk]/pos;
               if (m<lastpass) {                /*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 (calagedate>0)              }
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              else
                 else                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
                   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(freq[jk][m][i] !=0 ) {
       }              if(first==1)
       for(i=(int)agemin; i <= (int)agemax+3; i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(jk=1; jk <=nlstate ; jk++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              }
             pp[jk] += freq[jk][m][i];          if(i <= (int) agemax)
         }            fprintf(ficresp,"\n");
         for(jk=1; jk <=nlstate ; jk++){          if(first==1)
           for(m=-1, pos=0; m <=0 ; m++)            printf("Others in log...\n");
             pos += freq[jk][m][i];          fprintf(ficlog,"\n");
         }        }
              }
         for(jk=1; jk <=nlstate ; jk++){    }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    dateintmean=dateintsum/k2cpt; 
             pp[jk] += freq[jk][m][i];   
         }    fclose(ficresp);
            free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    free_vector(pp,1,nlstate);
            
         for(jk=1; jk <=nlstate ; jk++){        /* End of Freq */
           if( i <= (int) agemax){  }
             if(pos>=1.e-5){  
               probs[i][jk][j1]= pp[jk]/pos;  /************ 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)
           }  {  /* Some frequencies */
         }   
            int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       }    double ***freq; /* Frequencies */
     }    double *pp;
   }    double pos, k2;
   
      pp=vector(1,nlstate);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    
   free_vector(pp,1,nlstate);    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
      j1=0;
 }  /* End of Freq */    
     j=cptcoveff;
 /************* Waves Concatenation ***************/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    for(k1=1; k1<=j;k1++){
 {      for(i1=1; i1<=ncodemax[k1];i1++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        j1++;
      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 (i=-1; i<=nlstate+ndeath; i++)  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for (jk=-1; jk<=nlstate+ndeath; jk++)  
      and mw[mi+1][i]. dh depends on stepm.            for(m=agemin; m <= agemax+3; m++)
      */              freq[i][jk][m]=0;
        
   int i, mi, m;        for (i=1; i<=imx; i++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          bool=1;
      double sum=0., jmean=0.;*/          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   int j, k=0,jk, ju, jl;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double sum=0.;                bool=0;
   jmin=1e+5;          } 
   jmax=-1;          if (bool==1) { 
   jmean=0.;            for(m=firstpass; m<=lastpass; m++){
   for(i=1; i<=imx; i++){              k2=anint[m][i]+(mint[m][i]/12.);
     mi=0;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     m=firstpass;                if(agev[m][i]==0) agev[m][i]=agemax+1;
     while(s[m][i] <= nlstate){                if(agev[m][i]==1) agev[m][i]=agemax+2;
       if(s[m][i]>=1)                if (m<lastpass) {
         mw[++mi][i]=m;                  if (calagedate>0) 
       if(m >=lastpass)                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
         break;                  else
       else                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         m++;                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
     }/* 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 */        }
       mw[mi][i]=m;        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
     }          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     wav[i]=mi;              pp[jk] += freq[jk][m][i]; 
     if(mi==0)          }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   for(i=1; i<=imx; i++){          }
     for(mi=1; mi<wav[i];mi++){          
       if (stepm <=0)          for(jk=1; jk <=nlstate ; jk++){
         dh[mi][i]=1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       else{              pp[jk] += freq[jk][m][i];
         if (s[mw[mi+1][i]][i] > nlstate) {          }
           if (agedc[i] < 2*AGESUP) {          
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
           if(j==0) j=1;  /* Survives at least one month after exam */          
           k=k+1;          for(jk=1; jk <=nlstate ; jk++){    
           if (j >= jmax) jmax=j;            if( i <= (int) agemax){
           if (j <= jmin) jmin=j;              if(pos>=1.e-5){
           sum=sum+j;                probs[i][jk][j1]= pp[jk]/pos;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */              }
           }            }
         }          }/* end jk */
         else{        }/* end i */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      } /* end i1 */
           k=k+1;    } /* end k1 */
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;    
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
           sum=sum+j;    free_vector(pp,1,nlstate);
         }    
         jk= j/stepm;  }  /* End of Freq */
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  /************* Waves Concatenation ***************/
         if(jl <= -ju)  
           dh[mi][i]=jk;  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
         else  {
           dh[mi][i]=jk+1;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         if(dh[mi][i]==0)       Death is a valid wave (if date is known).
           dh[mi][i]=1; /* At least one step */       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]
     }       and mw[mi+1][i]. dh depends on stepm.
   }       */
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    int i, mi, m;
  }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 /*********** Tricode ****************************/       double sum=0., jmean=0.;*/
 void tricode(int *Tvar, int **nbcode, int imx)    int first;
 {    int j, k=0,jk, ju, jl;
   int Ndum[20],ij=1, k, j, i;    double sum=0.;
   int cptcode=0;    first=0;
   cptcoveff=0;    jmin=1e+5;
      jmax=-1;
   for (k=0; k<19; k++) Ndum[k]=0;    jmean=0.;
   for (k=1; k<=7; k++) ncodemax[k]=0;    for(i=1; i<=imx; i++){
       mi=0;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      m=firstpass;
     for (i=1; i<=imx; i++) {      while(s[m][i] <= nlstate){
       ij=(int)(covar[Tvar[j]][i]);        if(s[m][i]>=1)
       Ndum[ij]++;          mw[++mi][i]=m;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        if(m >=lastpass)
       if (ij > cptcode) cptcode=ij;          break;
     }        else
           m++;
     for (i=0; i<=cptcode; i++) {      }/* end while */
       if(Ndum[i]!=0) ncodemax[j]++;      if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
     ij=1;        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
         mw[mi][i]=m;
     for (i=1; i<=ncodemax[j]; i++) {      }
       for (k=0; k<=19; k++) {  
         if (Ndum[k] != 0) {      wav[i]=mi;
           nbcode[Tvar[j]][ij]=k;      if(mi==0){
                  if(first==0){
           ij++;          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
         }          first=1;
         if (ij > ncodemax[j]) break;        }
       }          if(first==1){
     }          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
   }          }
       } /* end mi==0 */
  for (k=0; k<19; k++) Ndum[k]=0;    }
   
  for (i=1; i<=ncovmodel-2; i++) {    for(i=1; i<=imx; i++){
       ij=Tvar[i];      for(mi=1; mi<wav[i];mi++){
       Ndum[ij]++;        if (stepm <=0)
     }          dh[mi][i]=1;
         else{
  ij=1;          if (s[mw[mi+1][i]][i] > nlstate) {
  for (i=1; i<=10; i++) {            if (agedc[i] < 2*AGESUP) {
    if((Ndum[i]!=0) && (i<=ncovcol)){            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
      Tvaraff[ij]=i;            if(j==0) j=1;  /* Survives at least one month after exam */
      ij++;            k=k+1;
    }            if (j >= jmax) jmax=j;
  }            if (j <= jmin) jmin=j;
              sum=sum+j;
     cptcoveff=ij-1;            /*if (j<0) printf("j=%d num=%d \n",j,i); */
 }            }
           }
 /*********** Health Expectancies ****************/          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 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 )            k=k+1;
             if (j >= jmax) jmax=j;
 {            else if (j <= jmin)jmin=j;
   /* Health expectancies */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;            sum=sum+j;
   double age, agelim, hf;          }
   double ***p3mat,***varhe;          jk= j/stepm;
   double **dnewm,**doldm;          jl= j -jk*stepm;
   double *xp;          ju= j -(jk+1)*stepm;
   double **gp, **gm;          if(jl <= -ju)
   double ***gradg, ***trgradg;            dh[mi][i]=jk;
   int theta;          else
             dh[mi][i]=jk+1;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          if(dh[mi][i]==0)
   xp=vector(1,npar);            dh[mi][i]=1; /* At least one step */
   dnewm=matrix(1,nlstate*2,1,npar);        }
   doldm=matrix(1,nlstate*2,1,nlstate*2);      }
      }
   fprintf(ficreseij,"# Health expectancies\n");    jmean=sum/k;
   fprintf(ficreseij,"# Age");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   for(i=1; i<=nlstate;i++)    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     for(j=1; j<=nlstate;j++)   }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  
   fprintf(ficreseij,"\n");  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
   if(estepm < stepm){  {
     printf ("Problem %d lower than %d\n",estepm, stepm);    int Ndum[20],ij=1, k, j, i;
   }    int cptcode=0;
   else  hstepm=estepm;      cptcoveff=0; 
   /* We compute the life expectancy from trapezoids spaced every estepm months   
    * This is mainly to measure the difference between two models: for example    for (k=0; k<19; k++) Ndum[k]=0;
    * if stepm=24 months pijx are given only every 2 years and by summing them    for (k=1; k<=7; k++) ncodemax[k]=0;
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
    * to the curvature of the survival function. If, for the same date, we      for (i=1; i<=imx; i++) {
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        ij=(int)(covar[Tvar[j]][i]);
    * to compare the new estimate of Life expectancy with the same linear        Ndum[ij]++; 
    * hypothesis. A more precise result, taking into account a more precise        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
    * curvature will be obtained if estepm is as small as stepm. */        if (ij > cptcode) cptcode=ij; 
       }
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=0; i<=cptcode; i++) {
      nhstepm is the number of hstepm from age to agelim        if(Ndum[i]!=0) ncodemax[j]++;
      nstepm is the number of stepm from age to agelin.      }
      Look at hpijx to understand the reason of that which relies in memory size      ij=1; 
      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      for (i=1; i<=ncodemax[j]; i++) {
      means that if the survival funtion is printed only each two years of age and if        for (k=0; k<=19; k++) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          if (Ndum[k] != 0) {
      results. So we changed our mind and took the option of the best precision.            nbcode[Tvar[j]][ij]=k; 
   */            
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            ij++;
           }
   agelim=AGESUP;          if (ij > ncodemax[j]) break; 
   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 */  
     /* if (stepm >= YEARM) hstepm=1;*/   for (k=0; k<19; k++) Ndum[k]=0;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   for (i=1; i<=ncovmodel-2; i++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);     ij=Tvar[i];
     gp=matrix(0,nhstepm,1,nlstate*2);     Ndum[ij]++; 
     gm=matrix(0,nhstepm,1,nlstate*2);   }
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored   ij=1;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */   for (i=1; i<=10; i++) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);       if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; 
        ij++;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */     }
    }
     /* Computing Variances of health expectancies */   
    cptcoveff=ij-1;
      for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*********** Health Expectancies ****************/
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    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 )
    
       cptj=0;  {
       for(j=1; j<= nlstate; j++){    /* Health expectancies */
         for(i=1; i<=nlstate; i++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           cptj=cptj+1;    double age, agelim, hf;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    double ***p3mat,***varhe;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double **dnewm,**doldm;
           }    double *xp;
         }    double **gp, **gm;
       }    double ***gradg, ***trgradg;
          int theta;
        
       for(i=1; i<=npar; i++)    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    xp=vector(1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      dnewm=matrix(1,nlstate*2,1,npar);
          doldm=matrix(1,nlstate*2,1,nlstate*2);
       cptj=0;    
       for(j=1; j<= nlstate; j++){    fprintf(ficreseij,"# Health expectancies\n");
         for(i=1;i<=nlstate;i++){    fprintf(ficreseij,"# Age");
           cptj=cptj+1;    for(i=1; i<=nlstate;i++)
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      for(j=1; j<=nlstate;j++)
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           }    fprintf(ficreseij,"\n");
         }  
       }    if(estepm < stepm){
       for(j=1; j<= nlstate*2; j++)      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(h=0; h<=nhstepm-1; h++){    }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    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
 /* End theta */     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression inbetween and thus overestimating or underestimating according
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);     * 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
      for(h=0; h<=nhstepm-1; h++)     * to compare the new estimate of Life expectancy with the same linear 
       for(j=1; j<=nlstate*2;j++)     * hypothesis. A more precise result, taking into account a more precise
         for(theta=1; theta <=npar; theta++)     * curvature will be obtained if estepm is as small as stepm. */
           trgradg[h][j][theta]=gradg[h][theta][j];  
          /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      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] =0.;       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
      printf("%d|",(int)age);fflush(stdout);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      for(h=0;h<=nhstepm-1;h++){       survival function given by stepm (the optimization length). Unfortunately it
       for(k=0;k<=nhstepm-1;k++){       means that if the survival funtion is printed only each two years of age and if
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);       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] += doldm[i][j]*hf*hf;  
       }    agelim=AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* Computing expectancies */      /* nhstepm age range expressed in number of stepm */
     for(i=1; i<=nlstate;i++)      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       for(j=1; j<=nlstate;j++)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      /* if (stepm >= YEARM) hstepm=1;*/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /* 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]);*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
       gp=matrix(0,nhstepm,1,nlstate*2);
         }      gm=matrix(0,nhstepm,1,nlstate*2);
   
     fprintf(ficreseij,"%3.0f",age );      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     cptj=0;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     for(i=1; i<=nlstate;i++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       for(j=1; j<=nlstate;j++){   
         cptj++;  
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }  
     fprintf(ficreseij,"\n");      /* Computing Variances of health expectancies */
      
     free_matrix(gm,0,nhstepm,1,nlstate*2);       for(theta=1; theta <=npar; theta++){
     free_matrix(gp,0,nhstepm,1,nlstate*2);        for(i=1; i<=npar; i++){ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }    
   printf("\n");        cptj=0;
         for(j=1; j<= nlstate; j++){
   free_vector(xp,1,npar);          for(i=1; i<=nlstate; i++){
   free_matrix(dnewm,1,nlstate*2,1,npar);            cptj=cptj+1;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 }            }
           }
 /************ 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)       
 {       
   /* Variance of health expectancies */        for(i=1; i<=npar; i++) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double **newm;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double **dnewm,**doldm;        
   int i, j, nhstepm, hstepm, h, nstepm ;        cptj=0;
   int k, cptcode;        for(j=1; j<= nlstate; j++){
   double *xp;          for(i=1;i<=nlstate;i++){
   double **gp, **gm;            cptj=cptj+1;
   double ***gradg, ***trgradg;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   double ***p3mat;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double age,agelim, hf;            }
   int theta;          }
         }
   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");        for(j=1; j<= nlstate*2; j++)
   fprintf(ficresvij,"# Age");          for(h=0; h<=nhstepm-1; h++){
   for(i=1; i<=nlstate;i++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);       } 
   fprintf(ficresvij,"\n");     
   /* End theta */
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);  
         for(h=0; h<=nhstepm-1; h++)
   if(estepm < stepm){        for(j=1; j<=nlstate*2;j++)
     printf ("Problem %d lower than %d\n",estepm, stepm);          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   else  hstepm=estepm;         
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.       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] =0.;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */       printf("%d|",(int)age);fflush(stdout);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      survival function given by stepm (the optimization length). Unfortunately it       for(h=0;h<=nhstepm-1;h++){
      means that if the survival funtion is printed only each two years of age and if        for(k=0;k<=nhstepm-1;k++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
      results. So we changed our mind and took the option of the best precision.          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
   */          for(i=1;i<=nlstate*2;i++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            for(j=1;j<=nlstate*2;j++)
   agelim = AGESUP;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      /* Computing expectancies */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1; i<=nlstate;i++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        for(j=1; j<=nlstate;j++)
     gp=matrix(0,nhstepm,1,nlstate);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     gm=matrix(0,nhstepm,1,nlstate);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
     for(theta=1; theta <=npar; theta++){  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficreseij,"%3.0f",age );
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      cptj=0;
       for(i=1; i<=nlstate;i++)
       if (popbased==1) {        for(j=1; j<=nlstate;j++){
         for(i=1; i<=nlstate;i++)          cptj++;
           prlim[i][i]=probs[(int)age][i][ij];          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       }        }
        fprintf(ficreseij,"\n");
       for(j=1; j<= nlstate; j++){     
         for(h=0; h<=nhstepm; h++){      free_matrix(gm,0,nhstepm,1,nlstate*2);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      free_matrix(gp,0,nhstepm,1,nlstate*2);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
         }      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
       }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        }
       for(i=1; i<=npar; i++) /* Computes gradient */    printf("\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    fprintf(ficlog,"\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*2,1,npar);
       if (popbased==1) {    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
         for(i=1; i<=nlstate;i++)    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
           prlim[i][i]=probs[(int)age][i][ij];  }
       }  
   /************ Variance ******************/
       for(j=1; j<= nlstate; j++){  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)
         for(h=0; h<=nhstepm; h++){  {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    /* Variance of health expectancies */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         }    /* double **newm;*/
       }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
       for(j=1; j<= nlstate; j++)    int i, j, nhstepm, hstepm, h, nstepm ;
         for(h=0; h<=nhstepm; h++){    int k, cptcode;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double *xp;
         }    double **gp, **gm;  /* for var eij */
     } /* End theta */    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     for(h=0; h<=nhstepm; h++)    double ***p3mat;
       for(j=1; j<=nlstate;j++)    double age,agelim, hf;
         for(theta=1; theta <=npar; theta++)    double ***mobaverage;
           trgradg[h][j][theta]=gradg[h][theta][j];    int theta;
     char digit[4];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    char digitp[16];
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    char fileresprobmorprev[FILENAMELENGTH];
         vareij[i][j][(int)age] =0.;  
     if(popbased==1)
     for(h=0;h<=nhstepm;h++){      strcpy(digitp,"-populbased-");
       for(k=0;k<=nhstepm;k++){    else
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      strcpy(digitp,"-stablbased-");
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    if(mobilav==1)
         for(i=1;i<=nlstate;i++)      strcat(digitp,"mobilav-");
           for(j=1;j<=nlstate;j++)    else
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      strcat(digitp,"nomobil-");
       }    if (mobilav==1) {
     }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       movingaverage(probs, bage, fage, mobaverage);
     fprintf(ficresvij,"%.0f ",age );    }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    strcpy(fileresprobmorprev,"prmorprev"); 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    sprintf(digit,"%-d",ij);
       }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     fprintf(ficresvij,"\n");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     free_matrix(gp,0,nhstepm,1,nlstate);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     free_matrix(gm,0,nhstepm,1,nlstate);    strcat(fileresprobmorprev,fileres);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   } /* End age */    }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_vector(xp,1,npar);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_matrix(doldm,1,nlstate,1,npar);    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 }      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
 /************ Variance of prevlim ******************/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 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)    }  
 {    fprintf(ficresprobmorprev,"\n");
   /* Variance of prevalence limit */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double **newm;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   double **dnewm,**doldm;      exit(0);
   int i, j, nhstepm, hstepm;    }
   int k, cptcode;    else{
   double *xp;      fprintf(ficgp,"\n# Routine varevsij");
   double *gp, *gm;    }
   double **gradg, **trgradg;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   double age,agelim;      printf("Problem with html file: %s\n", optionfilehtm);
   int theta;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
          exit(0);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    }
   fprintf(ficresvpl,"# Age");    else{
   for(i=1; i<=nlstate;i++)      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
       fprintf(ficresvpl," %1d-%1d",i,i);      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
   fprintf(ficresvpl,"\n");    }
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    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");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
   hstepm=1*YEARM; /* Every year of age */      for(j=1; j<=nlstate;j++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   agelim = AGESUP;    fprintf(ficresvij,"\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    xp=vector(1,npar);
     if (stepm >= YEARM) hstepm=1;    dnewm=matrix(1,nlstate,1,npar);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    doldm=matrix(1,nlstate,1,nlstate);
     gradg=matrix(1,npar,1,nlstate);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     gp=vector(1,nlstate);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     gm=vector(1,nlstate);  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     for(theta=1; theta <=npar; theta++){    gpp=vector(nlstate+1,nlstate+ndeath);
       for(i=1; i<=npar; i++){ /* Computes gradient */    gmp=vector(nlstate+1,nlstate+ndeath);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       }    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if(estepm < stepm){
       for(i=1;i<=nlstate;i++)      printf ("Problem %d lower than %d\n",estepm, stepm);
         gp[i] = prlim[i][i];    }
        else  hstepm=estepm;   
       for(i=1; i<=npar; i++) /* Computes gradient */    /* For example we decided to compute the life expectancy with the smallest unit */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       nhstepm is the number of hstepm from age to agelim 
       for(i=1;i<=nlstate;i++)       nstepm is the number of stepm from age to agelin. 
         gm[i] = prlim[i][i];       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
       for(i=1;i<=nlstate;i++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       survival function given by stepm (the optimization length). Unfortunately it
     } /* End theta */       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 
     trgradg =matrix(1,nlstate,1,npar);       results. So we changed our mind and took the option of the best precision.
     */
     for(j=1; j<=nlstate;j++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for(theta=1; theta <=npar; theta++)    agelim = AGESUP;
         trgradg[j][theta]=gradg[theta][j];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for(i=1;i<=nlstate;i++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       varpl[i][(int)age] =0.;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      gp=matrix(0,nhstepm,1,nlstate);
     for(i=1;i<=nlstate;i++)      gm=matrix(0,nhstepm,1,nlstate);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
   
     fprintf(ficresvpl,"%.0f ",age );      for(theta=1; theta <=npar; theta++){
     for(i=1; i<=nlstate;i++)        for(i=1; i<=npar; i++){ /* Computes gradient */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fprintf(ficresvpl,"\n");        }
     free_vector(gp,1,nlstate);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     free_vector(gm,1,nlstate);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);        if (popbased==1) {
   } /* End age */          if(mobilav !=1){
             for(i=1; i<=nlstate;i++)
   free_vector(xp,1,npar);              prlim[i][i]=probs[(int)age][i][ij];
   free_matrix(doldm,1,nlstate,1,npar);          }else{ /* mobilav=1 */ 
   free_matrix(dnewm,1,nlstate,1,nlstate);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
 }          }
         }
 /************ Variance of one-step probabilities  ******************/    
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        for(j=1; j<= nlstate; j++){
 {          for(h=0; h<=nhstepm; h++){
   int i, j,  i1, k1, l1;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   int k2, l2, j1,  z1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   int k=0,l, cptcode;          }
   int first=1;        }
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;        /* This for computing forces of mortality (h=1)as a weighted average */
   double **dnewm,**doldm;        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
   double *xp;          for(i=1; i<= nlstate; i++)
   double *gp, *gm;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   double **gradg, **trgradg;        }    
   double **mu;        /* end force of mortality */
   double age,agelim, cov[NCOVMAX];  
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        for(i=1; i<=npar; i++) /* Computes gradient */
   int theta;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   char fileresprob[FILENAMELENGTH];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char fileresprobcov[FILENAMELENGTH];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char fileresprobcor[FILENAMELENGTH];   
         if (popbased==1) {
   double ***varpij;          if(mobilav !=1){
             for(i=1; i<=nlstate;i++)
   strcpy(fileresprob,"prob");              prlim[i][i]=probs[(int)age][i][ij];
   strcat(fileresprob,fileres);          }else{ /* mobilav=1 */ 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            for(i=1; i<=nlstate;i++)
     printf("Problem with resultfile: %s\n", fileresprob);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   strcpy(fileresprobcov,"probcov");        }
   strcat(fileresprobcov,fileres);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        for(j=1; j<= nlstate; j++){
     printf("Problem with resultfile: %s\n", fileresprobcov);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   strcpy(fileresprobcor,"probcor");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcat(fileresprobcor,fileres);          }
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        }
     printf("Problem with resultfile: %s\n", fileresprobcor);        /* This for computing force of mortality (h=1)as a weighted average */
   }        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          for(i=1; i<= nlstate; i++)
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            gmp[j] += prlim[i][i]*p3mat[i][j][1];
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        }    
          /* end force of mortality */
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  
   fprintf(ficresprob,"# Age");        for(j=1; j<= nlstate; j++) /* vareij */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          for(h=0; h<=nhstepm; h++){
   fprintf(ficresprobcov,"# Age");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");          }
   fprintf(ficresprobcov,"# Age");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){      } /* End theta */
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }        for(h=0; h<=nhstepm; h++) /* veij */
   fprintf(ficresprob,"\n");        for(j=1; j<=nlstate;j++)
   fprintf(ficresprobcov,"\n");          for(theta=1; theta <=npar; theta++)
   fprintf(ficresprobcor,"\n");            trgradg[h][j][theta]=gradg[h][theta][j];
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        for(theta=1; theta <=npar; theta++)
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          trgradgp[j][theta]=gradgp[theta][j];
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  
   first=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      for(i=1;i<=nlstate;i++)
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        for(j=1;j<=nlstate;j++)
     exit(0);          vareij[i][j][(int)age] =0.;
   }  
   else{      for(h=0;h<=nhstepm;h++){
     fprintf(ficgp,"\n# Routine varprob");        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     printf("Problem with html file: %s\n", optionfilehtm);          for(i=1;i<=nlstate;i++)
     exit(0);            for(j=1;j<=nlstate;j++)
   }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   else{        }
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");      }
     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");      /* 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);
   cov[1]=1;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   j=cptcoveff;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          varppt[j][i]=doldmp[j][i];
   j1=0;      /* end ppptj */
   for(k1=1; k1<=1;k1++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     for(i1=1; i1<=ncodemax[k1];i1++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     j1++;   
       if (popbased==1) {
     if  (cptcovn>0) {        if(mobilav !=1){
       fprintf(ficresprob, "\n#********** Variable ");          for(i=1; i<=nlstate;i++)
       fprintf(ficresprobcov, "\n#********** Variable ");            prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficgp, "\n#********** Variable ");        }else{ /* mobilav=1 */ 
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");          for(i=1; i<=nlstate;i++)
       fprintf(ficresprobcor, "\n#********** Variable ");            prlim[i][i]=mobaverage[(int)age][i][ij];
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
       fprintf(ficresprob, "**********\n#");      }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      
       fprintf(ficresprobcov, "**********\n#");      /* This for computing force of mortality (h=1)as a weighted average */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
       fprintf(ficgp, "**********\n#");        for(i=1; i<= nlstate; i++)
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       fprintf(ficgp, "**********\n#");      }    
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      /* end force of mortality */
       fprintf(fichtm, "**********\n#");  
     }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for (age=bage; age<=fage; age ++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         cov[2]=age;        for(i=1; i<=nlstate;i++){
         for (k=1; k<=cptcovn;k++) {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        }
         }      } 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      fprintf(ficresprobmorprev,"\n");
         for (k=1; k<=cptcovprod;k++)  
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fprintf(ficresvij,"%.0f ",age );
              for(i=1; i<=nlstate;i++)
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        for(j=1; j<=nlstate;j++){
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         gp=vector(1,(nlstate)*(nlstate+ndeath));        }
         gm=vector(1,(nlstate)*(nlstate+ndeath));      fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
         for(theta=1; theta <=npar; theta++){      free_matrix(gm,0,nhstepm,1,nlstate);
           for(i=1; i<=npar; i++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    } /* End age */
              free_vector(gpp,nlstate+1,nlstate+ndeath);
           k=0;    free_vector(gmp,nlstate+1,nlstate+ndeath);
           for(i=1; i<= (nlstate); i++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             for(j=1; j<=(nlstate+ndeath);j++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               k=k+1;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
               gp[k]=pmmij[i][j];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
              fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
           for(i=1; i<=npar; i++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
        fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    /*  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);
           k=0;  */
           for(i=1; i<=(nlstate); i++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;    free_vector(xp,1,npar);
               gm[k]=pmmij[i][j];    free_matrix(doldm,1,nlstate,1,nlstate);
             }    free_matrix(dnewm,1,nlstate,1,npar);
           }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }    fclose(ficresprobmorprev);
     fclose(ficgp);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    fclose(fichtm);
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];  }
          
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  /************ Variance of prevlim ******************/
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  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)
          {
         pmij(pmmij,cov,ncovmodel,x,nlstate);    /* Variance of prevalence limit */
            /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         k=0;    double **newm;
         for(i=1; i<=(nlstate); i++){    double **dnewm,**doldm;
           for(j=1; j<=(nlstate+ndeath);j++){    int i, j, nhstepm, hstepm;
             k=k+1;    int k, cptcode;
             mu[k][(int) age]=pmmij[i][j];    double *xp;
           }    double *gp, *gm;
         }    double **gradg, **trgradg;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    double age,agelim;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    int theta;
             varpij[i][j][(int)age] = doldm[i][j];     
     fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
         /*printf("\n%d ",(int)age);    fprintf(ficresvpl,"# Age");
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    for(i=1; i<=nlstate;i++)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        fprintf(ficresvpl," %1d-%1d",i,i);
      }*/    fprintf(ficresvpl,"\n");
   
         fprintf(ficresprob,"\n%d ",(int)age);    xp=vector(1,npar);
         fprintf(ficresprobcov,"\n%d ",(int)age);    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficresprobcor,"\n%d ",(int)age);    doldm=matrix(1,nlstate,1,nlstate);
     
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    hstepm=1*YEARM; /* Every year of age */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    agelim = AGESUP;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         }      if (stepm >= YEARM) hstepm=1;
         i=0;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         for (k=1; k<=(nlstate);k++){      gradg=matrix(1,npar,1,nlstate);
           for (l=1; l<=(nlstate+ndeath);l++){      gp=vector(1,nlstate);
             i=i++;      gm=vector(1,nlstate);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      for(theta=1; theta <=npar; theta++){
             for (j=1; j<=i;j++){        for(i=1; i<=npar; i++){ /* Computes gradient */
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        }
             }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }        for(i=1;i<=nlstate;i++)
         }/* end of loop for state */          gp[i] = prlim[i][i];
       } /* end of loop for age */      
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        for(i=1; i<=npar; i++) /* Computes gradient */
       for (k1=1; k1<=(nlstate);k1++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (l1=1; l1<=(nlstate+ndeath);l1++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           if(l1==k1) continue;        for(i=1;i<=nlstate;i++)
           i=(k1-1)*(nlstate+ndeath)+l1;          gm[i] = prlim[i][i];
           for (k2=1; k2<=(nlstate);k2++){  
             for (l2=1; l2<=(nlstate+ndeath);l2++){        for(i=1;i<=nlstate;i++)
               if(l2==k2) continue;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               j=(k2-1)*(nlstate+ndeath)+l2;      } /* End theta */
               if(j<=i) continue;  
               for (age=bage; age<=fage; age ++){      trgradg =matrix(1,nlstate,1,npar);
                 if ((int)age %5==0){  
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      for(j=1; j<=nlstate;j++)
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;        for(theta=1; theta <=npar; theta++)
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;          trgradg[j][theta]=gradg[theta][j];
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;      for(i=1;i<=nlstate;i++)
                   /* Computing eigen value of matrix of covariance */        varpl[i][(int)age] =0.;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      for(i=1;i<=nlstate;i++)
                   /* Eigen vectors */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  
                   v21=sqrt(1.-v11*v11);      fprintf(ficresvpl,"%.0f ",age );
                   v12=-v21;      for(i=1; i<=nlstate;i++)
                   v22=v11;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   /*printf(fignu*/      fprintf(ficresvpl,"\n");
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      free_vector(gp,1,nlstate);
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      free_vector(gm,1,nlstate);
                   if(first==1){      free_matrix(gradg,1,npar,1,nlstate);
                     first=0;      free_matrix(trgradg,1,nlstate,1,npar);
                     fprintf(ficgp,"\nset parametric;set nolabel");    } /* End age */
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    free_vector(xp,1,npar);
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);    free_matrix(doldm,1,nlstate,1,npar);
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);    free_matrix(dnewm,1,nlstate,1,nlstate);
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     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)) t \"%d\"",\  /************ Variance of one-step probabilities  ******************/
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  {
                   }else{    int i, j=0,  i1, k1, l1, t, tj;
                     first=0;    int k2, l2, j1,  z1;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    int k=0,l, cptcode;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    int first=1, first1;
                     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)) t \"%d\"",\    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    double **dnewm,**doldm;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    double *xp;
                   }/* if first */    double *gp, *gm;
                 } /* age mod 5 */    double **gradg, **trgradg;
               } /* end loop age */    double **mu;
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);    double age,agelim, cov[NCOVMAX];
               first=1;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
             } /*l12 */    int theta;
           } /* k12 */    char fileresprob[FILENAMELENGTH];
         } /*l1 */    char fileresprobcov[FILENAMELENGTH];
       }/* k1 */    char fileresprobcor[FILENAMELENGTH];
     } /* loop covariates */  
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    double ***varpij;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    strcpy(fileresprob,"prob"); 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    strcat(fileresprob,fileres);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf("Problem with resultfile: %s\n", fileresprob);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   free_vector(xp,1,npar);    }
   fclose(ficresprob);    strcpy(fileresprobcov,"probcov"); 
   fclose(ficresprobcov);    strcat(fileresprobcov,fileres);
   fclose(ficresprobcor);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   fclose(ficgp);      printf("Problem with resultfile: %s\n", fileresprobcov);
   fclose(fichtm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 }    }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
 /******************* Printing html file ***********/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      printf("Problem with resultfile: %s\n", fileresprobcor);
                   int lastpass, int stepm, int weightopt, char model[],\      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    }
                   int popforecast, int estepm ,\    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   double jprev1, double mprev1,double anprev1, \    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   double jprev2, double mprev2,double anprev2){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   int jj1, k1, i1, cpt;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /*char optionfilehtm[FILENAMELENGTH];*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     printf("Problem with %s \n",optionfilehtm), exit(0);    
   }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    fprintf(ficresprobcov,"# Age");
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    fprintf(ficresprobcov,"# Age");
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n        fprintf(ficresprobcov," p%1d-%1d ",i,j);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        fprintf(ficresprobcor," p%1d-%1d ",i,j);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n      }  
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    fprintf(ficresprob,"\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    fprintf(ficresprobcov,"\n");
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    fprintf(ficresprobcor,"\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);    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  if(popforecast==1) fprintf(fichtm,"\n    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         <br>",fileres,fileres,fileres,fileres);    first=1;
  else    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
    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);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 fprintf(fichtm," <li>Graphs</li><p>");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
  m=cptcoveff;    }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    else{
       fprintf(ficgp,"\n# Routine varprob");
  jj1=0;    }
  for(k1=1; k1<=m;k1++){    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    for(i1=1; i1<=ncodemax[k1];i1++){      printf("Problem with html file: %s\n", optionfilehtm);
      jj1++;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      if (cptcovn > 0) {      exit(0);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    }
        for (cpt=1; cpt<=cptcoveff;cpt++)    else{
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      fprintf(fichtm,"\n");
      }  
      /* Pij */      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>      fprintf(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");
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          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");
      /* Quasi-incidences */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    }
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
        /* Stable prevalence in each health state */   
        for(cpt=1; cpt<nlstate;cpt++){    cov[1]=1;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    tj=cptcoveff;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
        }    j1=0;
     for(cpt=1; cpt<=nlstate;cpt++) {    for(t=1; t<=tj;t++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for(i1=1; i1<=ncodemax[t];i1++){ 
 interval) in state (%d): v%s%d%d.png <br>        j1++;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          
      }        if  (cptcovn>0) {
      for(cpt=1; cpt<=nlstate;cpt++) {          fprintf(ficresprob, "\n#********** Variable "); 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          fprintf(ficresprob, "**********\n#");
      }          fprintf(ficresprobcov, "\n#********** Variable "); 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 health expectancies in states (1) and (2): e%s%d.png<br>          fprintf(ficresprobcov, "**********\n#");
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          
    }          fprintf(ficgp, "\n#********** Variable "); 
  }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fclose(fichtm);          fprintf(ficgp, "**********\n#");
 }          
           
 /******************* Gnuplot file **************/          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          
   int ng;          fprintf(ficresprobcor, "\n#********** Variable ");    
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with file %s",optionfilegnuplot);          fprintf(ficgp, "**********\n#");    
   }        }
         
 #ifdef windows        for (age=bage; age<=fage; age ++){ 
     fprintf(ficgp,"cd \"%s\" \n",pathc);          cov[2]=age;
 #endif          for (k=1; k<=cptcovn;k++) {
 m=pow(2,cptcoveff);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
            }
  /* 1eme*/          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for (k=1; k<=cptcovprod;k++)
    for (k1=1; k1<= m ; k1 ++) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
 #ifdef windows          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      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);          gp=vector(1,(nlstate)*(nlstate+ndeath));
 #endif          gm=vector(1,(nlstate)*(nlstate+ndeath));
 #ifdef unix      
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for(theta=1; theta <=npar; theta++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);            for(i=1; i<=npar; i++)
 #endif              xp[i] = x[i] + (i==theta ?delti[theta]:0);
             
 for (i=1; i<= nlstate ; i ++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            
   else fprintf(ficgp," \%%*lf (\%%*lf)");            k=0;
 }            for(i=1; i<= (nlstate); i++){
     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(j=1; j<=(nlstate+ndeath);j++){
     for (i=1; i<= nlstate ; i ++) {                k=k+1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                gp[k]=pmmij[i][j];
   else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }            }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            
      for (i=1; i<= nlstate ; i ++) {            for(i=1; i<=npar; i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              xp[i] = x[i] - (i==theta ?delti[theta]:0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      
 }              pmij(pmmij,cov,ncovmodel,xp,nlstate);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            k=0;
 #ifdef unix            for(i=1; i<=(nlstate); i++){
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");              for(j=1; j<=(nlstate+ndeath);j++){
 #endif                k=k+1;
    }                gm[k]=pmmij[i][j];
   }              }
   /*2 eme*/            }
        
   for (k1=1; k1<= m ; k1 ++) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          }
      
     for (i=1; i<= nlstate+1 ; i ++) {          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       k=2*i;            for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              trgradg[j][theta]=gradg[theta][j];
       for (j=1; j<= nlstate+1 ; j ++) {          
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
 }            
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          pmij(pmmij,cov,ncovmodel,x,nlstate);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          k=0;
       for (j=1; j<= nlstate+1 ; j ++) {          for(i=1; i<=(nlstate); i++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(j=1; j<=(nlstate+ndeath);j++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              k=k+1;
 }                mu[k][(int) age]=pmmij[i][j];
       fprintf(ficgp,"\" t\"\" w l 0,");            }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              varpij[i][j][(int)age] = doldm[i][j];
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          /*printf("\n%d ",(int)age);
       else fprintf(ficgp,"\" t\"\" w l 0,");       for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   }         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         }*/
   /*3eme*/  
           fprintf(ficresprob,"\n%d ",(int)age);
   for (k1=1; k1<= m ; k1 ++) {          fprintf(ficresprobcov,"\n%d ",(int)age);
     for (cpt=1; cpt<= nlstate ; cpt ++) {          fprintf(ficresprobcor,"\n%d ",(int)age);
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          i=0;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
 */              i=i++;
       for (i=1; i< nlstate ; i ++) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         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(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
       }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   }              }
              }
   /* CV preval stat */          }/* end of loop for state */
     for (k1=1; k1<= m ; k1 ++) {        } /* end of loop for age */
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;        /* Confidence intervalle of pij  */
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        fprintf(ficgp,"\nset noparametric;unset label");
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       for (i=1; i< nlstate ; i ++)        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(ficgp,"+$%d",k+i+1);        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
              fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       l=3+(nlstate+ndeath)*cpt;        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        */
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         fprintf(ficgp,"+$%d",l+i+1);        first1=1;
       }        for (k2=1; k2<=(nlstate);k2++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     }            if(l2==k2) continue;
   }              j=(k2-1)*(nlstate+ndeath)+l2;
              for (k1=1; k1<=(nlstate);k1++){
   /* proba elementaires */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
    for(i=1,jk=1; i <=nlstate; i++){                if(l1==k1) continue;
     for(k=1; k <=(nlstate+ndeath); k++){                i=(k1-1)*(nlstate+ndeath)+l1;
       if (k != i) {                if(i<=j) continue;
         for(j=1; j <=ncovmodel; j++){                for (age=bage; age<=fage; age ++){ 
                          if ((int)age %5==0){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           jk++;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           fprintf(ficgp,"\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    mu1=mu[i][(int) age]/stepm*YEARM ;
       }                    mu2=mu[j][(int) age]/stepm*YEARM;
     }                    c12=cv12/sqrt(v1*v2);
    }                    /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
      for(jk=1; jk <=m; jk++) {                    /* Eigen vectors */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
        if (ng==2)                    /*v21=sqrt(1.-v11*v11); *//* error */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");                    v21=(lc1-v1)/cv12*v11;
        else                    v12=-v21;
          fprintf(ficgp,"\nset title \"Probability\"\n");                    v22=v11;
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);                    tnalp=v21/v11;
        i=1;                    if(first1==1){
        for(k2=1; k2<=nlstate; k2++) {                      first1=0;
          k3=i;                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
          for(k=1; k<=(nlstate+ndeath); k++) {                    }
            if (k != k2){                    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);
              if(ng==2)                    /*printf(fignu*/
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
              else                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                    if(first==1){
              ij=1;                      first=0;
              for(j=3; j <=ncovmodel; j++) {                      fprintf(ficgp,"\nset parametric;unset label");
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                  ij++;                      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);
                }                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                else                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
              }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
              fprintf(ficgp,")/(1");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                                    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
              for(k1=1; k1 <=nlstate; k1++){                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                ij=1;                    }else{
                for(j=3; j <=ncovmodel; j++){                      first=0;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                    ij++;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                  }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                  else                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                }                    }/* if first */
                fprintf(ficgp,")");                  } /* age mod 5 */
              }                } /* end loop age */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                first=1;
              i=i+ncovmodel;              } /*l12 */
            }            } /* k12 */
          }          } /*l1 */
        }        }/* k1 */
      }      } /* loop covariates */
    }      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    fclose(ficgp);      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 }  /* end gnuplot */      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 /*************** Moving average **************/      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    }
     free_vector(xp,1,npar);
   int i, cpt, cptcod;    fclose(ficresprob);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    fclose(ficresprobcov);
       for (i=1; i<=nlstate;i++)    fclose(ficresprobcor);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    fclose(ficgp);
           mobaverage[(int)agedeb][i][cptcod]=0.;    fclose(fichtm);
      }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /******************* Printing html file ***********/
           for (cpt=0;cpt<=4;cpt++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                    int lastpass, int stepm, int weightopt, char model[],\
           }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                    int popforecast, int estepm ,\
         }                    double jprev1, double mprev1,double anprev1, \
       }                    double jprev2, double mprev2,double anprev2){
     }    int jj1, k1, i1, cpt;
        /*char optionfilehtm[FILENAMELENGTH];*/
 }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
 /************** Forecasting ******************/    }
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  
       fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   - 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
   int *popage;   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   double *popeffectif,*popcount;   - Life expectancies by age and initial health status (estepm=%2d months): 
   double ***p3mat;     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   char fileresf[FILENAMELENGTH];    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
  agelim=AGESUP;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
    m=cptcoveff;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
     jj1=0;
   strcpy(fileresf,"f");   for(k1=1; k1<=m;k1++){
   strcat(fileresf,fileres);     for(i1=1; i1<=ncodemax[k1];i1++){
   if((ficresf=fopen(fileresf,"w"))==NULL) {       jj1++;
     printf("Problem with forecast resultfile: %s\n", fileresf);       if (cptcovn > 0) {
   }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   printf("Computing forecasting: result on file '%s' \n", fileresf);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   if (mobilav==1) {       /* Pij */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       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>
     movingaverage(agedeb, fage, ageminpar, mobaverage);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
   }       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
   stepsize=(int) (stepm+YEARM-1)/YEARM;  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
   if (stepm<=12) stepsize=1;         /* Stable prevalence in each health state */
           for(cpt=1; cpt<nlstate;cpt++){
   agelim=AGESUP;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
    <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   hstepm=1;         }
   hstepm=hstepm/stepm;       for(cpt=1; cpt<=nlstate;cpt++) {
   yp1=modf(dateintmean,&yp);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
   anprojmean=yp;  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   yp2=modf((yp1*12),&yp);       }
   mprojmean=yp;       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   yp1=modf((yp2*30.5),&yp);  health expectancies in states (1) and (2): e%s%d.png<br>
   jprojmean=yp;  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
   if(jprojmean==0) jprojmean=1;     } /* end i1 */
   if(mprojmean==0) jprojmean=1;   }/* End k1 */
     fprintf(fichtm,"</ul>");
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
    
   for(cptcov=1;cptcov<=i2;cptcov++){   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
       k=k+1;   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
       fprintf(ficresf,"\n#******");   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
       for(j=1;j<=cptcoveff;j++) {   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Variances and covariances 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 (no covariance): <a href=\"t%s\">t%s</a> <br>\n
       fprintf(ficresf,"******\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);
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);   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=0; cpt<=(anproj2-anproj1);cpt++) {          <br>",fileres,fileres,fileres,fileres);
         fprintf(ficresf,"\n");   else 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);       fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   m=cptcoveff;
           nhstepm = nhstepm/hstepm;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   jj1=0;
           oldm=oldms;savm=savms;   for(k1=1; k1<=m;k1++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       for(i1=1; i1<=ncodemax[k1];i1++){
               jj1++;
           for (h=0; h<=nhstepm; h++){       if (cptcovn > 0) {
             if (h==(int) (calagedate+YEARM*cpt)) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);         for (cpt=1; cpt<=cptcoveff;cpt++) 
             }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             for(j=1; j<=nlstate+ndeath;j++) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               kk1=0.;kk2=0;       }
               for(i=1; i<=nlstate;i++) {                     for(cpt=1; cpt<=nlstate;cpt++) {
                 if (mobilav==1)         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  interval) in state (%d): v%s%d%d.png <br>
                 else {  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       }
                 }     } /* end i1 */
                   }/* End k1 */
               }   fprintf(fichtm,"</ul>");
               if (h==(int)(calagedate+12*cpt)){  fclose(fichtm);
                 fprintf(ficresf," %.3f", kk1);  }
                          
               }  /******************* Gnuplot file **************/
             }  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         }    int ng;
       }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     }      printf("Problem with file %s",optionfilegnuplot);
   }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
            }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   #ifdef windows
   fclose(ficresf);      fprintf(ficgp,"cd \"%s\" \n",pathc);
 }  #endif
 /************** Forecasting ******************/  m=pow(2,cptcoveff);
 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){    
     /* 1eme*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    for (cpt=1; cpt<= nlstate ; cpt ++) {
   int *popage;     for (k1=1; k1<= m ; k1 ++) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   double *popeffectif,*popcount;       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 ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       }
   agelim=AGESUP;       fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
         fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
   strcpy(filerespop,"pop");       for (i=1; i<= nlstate ; i ++) {
   strcat(filerespop,fileres);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if((ficrespop=fopen(filerespop,"w"))==NULL) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("Problem with forecast resultfile: %s\n", filerespop);       }  
   }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
   printf("Computing forecasting: result on file '%s' \n", filerespop);     }
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /*2 eme*/
     
   if (mobilav==1) {    for (k1=1; k1<= m ; k1 ++) { 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   }      
       for (i=1; i<= nlstate+1 ; i ++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;        k=2*i;
   if (stepm<=12) stepsize=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   agelim=AGESUP;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            else fprintf(ficgp," \%%*lf (\%%*lf)");
   hstepm=1;        }   
   hstepm=hstepm/stepm;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   if (popforecast==1) {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
     if((ficpop=fopen(popfile,"r"))==NULL) {        for (j=1; j<= nlstate+1 ; j ++) {
       printf("Problem with population file : %s\n",popfile);exit(0);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     popage=ivector(0,AGESUP);        }   
     popeffectif=vector(0,AGESUP);        fprintf(ficgp,"\" t\"\" w l 0,");
     popcount=vector(0,AGESUP);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
            for (j=1; j<= nlstate+1 ; j ++) {
     i=1;            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
     imx=i;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        else fprintf(ficgp,"\" t\"\" w l 0,");
   }      }
     }
   for(cptcov=1;cptcov<=i2;cptcov++){    
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /*3eme*/
       k=k+1;    
       fprintf(ficrespop,"\n#******");    for (k1=1; k1<= m ; k1 ++) { 
       for(j=1;j<=cptcoveff;j++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k=2+nlstate*(2*cpt-2);
       }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       fprintf(ficrespop,"******\n");        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
       fprintf(ficrespop,"# Age");        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       if (popforecast==1)  fprintf(ficrespop," [Population]");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       for (cpt=0; cpt<=0;cpt++) {          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                  
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for (i=1; i< nlstate ; i ++) {
           nhstepm = nhstepm/hstepm;          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);
                    
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } 
           oldm=oldms;savm=savms;      }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }
            
           for (h=0; h<=nhstepm; h++){    /* CV preval stat */
             if (h==(int) (calagedate+YEARM*cpt)) {    for (k1=1; k1<= m ; k1 ++) { 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for (cpt=1; cpt<nlstate ; cpt ++) {
             }        k=3;
             for(j=1; j<=nlstate+ndeath;j++) {        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
               kk1=0.;kk2=0;        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
               for(i=1; i<=nlstate;i++) {                      
                 if (mobilav==1)        for (i=1; i< nlstate ; i ++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          fprintf(ficgp,"+$%d",k+i+1);
                 else {        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        
                 }        l=3+(nlstate+ndeath)*cpt;
               }        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
               if (h==(int)(calagedate+12*cpt)){        for (i=1; i< nlstate ; i ++) {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          l=3+(nlstate+ndeath)*cpt;
                   /*fprintf(ficrespop," %.3f", kk1);          fprintf(ficgp,"+$%d",l+i+1);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }
               }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
             }      } 
             for(i=1; i<=nlstate;i++){    }  
               kk1=0.;    
                 for(j=1; j<=nlstate;j++){    /* proba elementaires */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for(i=1,jk=1; i <=nlstate; i++){
                 }      for(k=1; k <=(nlstate+ndeath); k++){
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        if (k != i) {
             }          for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            jk++; 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            fprintf(ficgp,"\n");
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }      }
       }     }
    
   /******/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);           if (ng==2)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         else
           nhstepm = nhstepm/hstepm;           fprintf(ficgp,"\nset title \"Probability\"\n");
                   fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         i=1;
           oldm=oldms;savm=savms;         for(k2=1; k2<=nlstate; k2++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             k3=i;
           for (h=0; h<=nhstepm; h++){           for(k=1; k<=(nlstate+ndeath); k++) {
             if (h==(int) (calagedate+YEARM*cpt)) {             if (k != k2){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);               if(ng==2)
             }                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
             for(j=1; j<=nlstate+ndeath;j++) {               else
               kk1=0.;kk2=0;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
               for(i=1; i<=nlstate;i++) {                             ij=1;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                   for(j=3; j <=ncovmodel; j++) {
               }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             }                   ij++;
           }                 }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                 else
         }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       }               }
    }               fprintf(ficgp,")/(1");
   }               
                 for(k1=1; k1 <=nlstate; k1++){   
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
   if (popforecast==1) {                 for(j=3; j <=ncovmodel; j++){
     free_ivector(popage,0,AGESUP);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     free_vector(popeffectif,0,AGESUP);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     free_vector(popcount,0,AGESUP);                     ij++;
   }                   }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                   else
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   fclose(ficrespop);                 }
 }                 fprintf(ficgp,")");
                }
 /***********************************************/               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 /**************** Main Program *****************/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 /***********************************************/               i=i+ncovmodel;
              }
 int main(int argc, char *argv[])           } /* end k */
 {         } /* end k2 */
        } /* end jk */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;     } /* end ng */
   double agedeb, agefin,hf;     fclose(ficgp); 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  }  /* end gnuplot */
   
   double fret;  
   double **xi,tmp,delta;  /*************** Moving average **************/
   void movingaverage(double ***probs, double bage,double fage, double ***mobaverage){
   double dum; /* Dummy variable */  
   double ***p3mat;    int i, cpt, cptcod;
   int *indx;    double age;
   char line[MAXLINE], linepar[MAXLINE];    for (age=bage; age<=fage; age++)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      for (i=1; i<=nlstate;i++)
   int firstobs=1, lastobs=10;        for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
   int sdeb, sfin; /* Status at beginning and end */          mobaverage[(int)age][i][cptcod]=0.;
   int c,  h , cpt,l;    
   int ju,jl, mi;    for (age=bage+4; age<=fage; age++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      for (i=1; i<=nlstate;i++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   int mobilav=0,popforecast=0;          for (cpt=0;cpt<=4;cpt++){
   int hstepm, nhstepm;            mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]+probs[(int)age-cpt][i][cptcod];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          }
           mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]/5;
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;      }
   double **prlim;    }
   double *severity;    
   double ***param; /* Matrix of parameters */  }
   double  *p;  
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  /************** Forecasting ******************/
   double *delti; /* Scale */  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){
   double ***eij, ***vareij;    
   double **varpl; /* Variances of prevalence limits by age */    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   double *epj, vepp;    int *popage;
   double kk1, kk2;    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double *popeffectif,*popcount;
      double ***p3mat;
     char fileresf[FILENAMELENGTH];
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
    agelim=AGESUP;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   char z[1]="c", occ;  
 #include <sys/time.h>    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 #include <time.h>   
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];   
      strcpy(fileresf,"f"); 
   /* long total_usecs;    strcat(fileresf,fileres);
   struct timeval start_time, end_time;    if((ficresf=fopen(fileresf,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", fileresf);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   getcwd(pathcd, size);    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   printf("\n%s",version);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     scanf("%s",pathtot);  
   }    if (mobilav==1) {
   else{      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     strcpy(pathtot,argv[1]);      movingaverage(probs, ageminpar,fage, mobaverage);
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    if (stepm<=12) stepsize=1;
   /* cutv(path,optionfile,pathtot,'\\');*/    
     agelim=AGESUP;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    hstepm=1;
   chdir(path);    hstepm=hstepm/stepm; 
   replace(pathc,path);    yp1=modf(dateintmean,&yp);
     anprojmean=yp;
 /*-------- arguments in the command line --------*/    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
   strcpy(fileres,"r");    yp1=modf((yp2*30.5),&yp);
   strcat(fileres, optionfilefiname);    jprojmean=yp;
   strcat(fileres,".txt");    /* Other files have txt extension */    if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   /*---------arguments file --------*/    
     fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    
     printf("Problem with optionfile %s\n",optionfile);    for(cptcov=1;cptcov<=i2;cptcov++){
     goto end;      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   }        k=k+1;
         fprintf(ficresf,"\n#******");
   strcpy(filereso,"o");        for(j=1;j<=cptcoveff;j++) {
   strcat(filereso,fileres);          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   if((ficparo=fopen(filereso,"w"))==NULL) {        }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        fprintf(ficresf,"******\n");
   }        fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
     fgets(line, MAXLINE, ficpar);          fprintf(ficresf,"\n");
     puts(line);          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
     fputs(line,ficparo);  
   }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   ungetc(c,ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
   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);            
   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);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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);            oldm=oldms;savm=savms;
 while((c=getc(ficpar))=='#' && c!= EOF){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);            for (h=0; h<=nhstepm; h++){
     puts(line);              if (h==(int) (calagedate+YEARM*cpt)) {
     fputs(line,ficparo);                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
   }              } 
   ungetc(c,ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
                  kk1=0.;kk2=0;
                    for(i=1; i<=nlstate;i++) {              
   covar=matrix(0,NCOVMAX,1,n);                  if (mobilav==1) 
   cptcovn=0;                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                  else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   ncovmodel=2+cptcovn;                  }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                  
                  }
   /* Read guess parameters */                if (h==(int)(calagedate+12*cpt)){
   /* Reads comments: lines beginning with '#' */                  fprintf(ficresf," %.3f", kk1);
   while((c=getc(ficpar))=='#' && c!= EOF){                          
     ungetc(c,ficpar);                }
     fgets(line, MAXLINE, ficpar);              }
     puts(line);            }
     fputs(line,ficparo);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          }
   ungetc(c,ficpar);        }
        }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    }
     for(i=1; i <=nlstate; i++)         
     for(j=1; j <=nlstate+ndeath-1; j++){    if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);    fclose(ficresf);
       printf("%1d%1d",i,j);  }
       for(k=1; k<=ncovmodel;k++){  /************** Forecasting ******************/
         fscanf(ficpar," %lf",&param[i][j][k]);  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){
         printf(" %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       }    int *popage;
       fscanf(ficpar,"\n");    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       printf("\n");    double *popeffectif,*popcount;
       fprintf(ficparo,"\n");    double ***p3mat,***tabpop,***tabpopprev;
     }    char filerespop[FILENAMELENGTH];
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   p=param[1][1];    agelim=AGESUP;
      calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    
     puts(line);    strcpy(filerespop,"pop"); 
     fputs(line,ficparo);    strcat(filerespop,fileres);
   }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    printf("Computing forecasting: result on file '%s' \n", filerespop);
   for(i=1; i <=nlstate; i++){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    if (mobilav==1) {
       for(k=1; k<=ncovmodel;k++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      movingaverage(probs, ageminpar, fage, mobaverage);
         printf(" %le",delti3[i][j][k]);    }
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    stepsize=(int) (stepm+YEARM-1)/YEARM;
       fscanf(ficpar,"\n");    if (stepm<=12) stepsize=1;
       printf("\n");    
       fprintf(ficparo,"\n");    agelim=AGESUP;
     }    
   }    hstepm=1;
   delti=delti3[1][1];    hstepm=hstepm/stepm; 
      
   /* Reads comments: lines beginning with '#' */    if (popforecast==1) {
   while((c=getc(ficpar))=='#' && c!= EOF){      if((ficpop=fopen(popfile,"r"))==NULL) {
     ungetc(c,ficpar);        printf("Problem with population file : %s\n",popfile);exit(0);
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
     puts(line);      } 
     fputs(line,ficparo);      popage=ivector(0,AGESUP);
   }      popeffectif=vector(0,AGESUP);
   ungetc(c,ficpar);      popcount=vector(0,AGESUP);
        
   matcov=matrix(1,npar,1,npar);      i=1;   
   for(i=1; i <=npar; i++){      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     fscanf(ficpar,"%s",&str);     
     printf("%s",str);      imx=i;
     fprintf(ficparo,"%s",str);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     for(j=1; j <=i; j++){    }
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);    for(cptcov=1;cptcov<=i2;cptcov++){
       fprintf(ficparo," %.5le",matcov[i][j]);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     }        k=k+1;
     fscanf(ficpar,"\n");        fprintf(ficrespop,"\n#******");
     printf("\n");        for(j=1;j<=cptcoveff;j++) {
     fprintf(ficparo,"\n");          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   }        }
   for(i=1; i <=npar; i++)        fprintf(ficrespop,"******\n");
     for(j=i+1;j<=npar;j++)        fprintf(ficrespop,"# Age");
       matcov[i][j]=matcov[j][i];        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
            if (popforecast==1)  fprintf(ficrespop," [Population]");
   printf("\n");        
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     /*-------- Rewriting paramater file ----------*/          
      strcpy(rfileres,"r");    /* "Rparameterfile */          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
      strcat(rfileres,".");    /* */            nhstepm = nhstepm/hstepm; 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            
     if((ficres =fopen(rfileres,"w"))==NULL) {            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            oldm=oldms;savm=savms;
     }            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     fprintf(ficres,"#%s\n",version);          
                for (h=0; h<=nhstepm; h++){
     /*-------- data file ----------*/              if (h==(int) (calagedate+YEARM*cpt)) {
     if((fic=fopen(datafile,"r"))==NULL)    {                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       printf("Problem with datafile: %s\n", datafile);goto end;              } 
     }              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
     n= lastobs;                for(i=1; i<=nlstate;i++) {              
     severity = vector(1,maxwav);                  if (mobilav==1) 
     outcome=imatrix(1,maxwav+1,1,n);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     num=ivector(1,n);                  else {
     moisnais=vector(1,n);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     annais=vector(1,n);                  }
     moisdc=vector(1,n);                }
     andc=vector(1,n);                if (h==(int)(calagedate+12*cpt)){
     agedc=vector(1,n);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     cod=ivector(1,n);                    /*fprintf(ficrespop," %.3f", kk1);
     weight=vector(1,n);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                }
     mint=matrix(1,maxwav,1,n);              }
     anint=matrix(1,maxwav,1,n);              for(i=1; i<=nlstate;i++){
     s=imatrix(1,maxwav+1,1,n);                kk1=0.;
     adl=imatrix(1,maxwav+1,1,n);                      for(j=1; j<=nlstate;j++){
     tab=ivector(1,NCOVMAX);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     ncodemax=ivector(1,8);                  }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
     i=1;              }
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {              if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
                        fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         for (j=maxwav;j>=1;j--){            }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           strcpy(line,stra);          }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   
         }    /******/
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          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--){ 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            nhstepm = nhstepm/hstepm; 
             
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (j=ncovcol;j>=1;j--){            oldm=oldms;savm=savms;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         }            for (h=0; h<=nhstepm; h++){
         num[i]=atol(stra);              if (h==(int) (calagedate+YEARM*cpt)) {
                        fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              } 
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
         i=i+1;                for(i=1; i<=nlstate;i++) {              
       }                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     }                }
     /* printf("ii=%d", ij);                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
        scanf("%d",i);*/              }
   imx=i-1; /* Number of individuals */            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* for (i=1; i<=imx; i++){          }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        }
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;     } 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    }
     }*/   
    /*  for (i=1; i<=imx; i++){    if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      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 (popforecast==1) {
        free_ivector(popage,0,AGESUP);
        free_vector(popeffectif,0,AGESUP);
   /* Calculation of the number of parameter from char model*/      free_vector(popcount,0,AGESUP);
   Tvar=ivector(1,15);    }
   Tprod=ivector(1,15);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   Tvaraff=ivector(1,15);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   Tvard=imatrix(1,15,1,2);    fclose(ficrespop);
   Tage=ivector(1,15);        }
      
   if (strlen(model) >1){  /***********************************************/
     j=0, j1=0, k1=1, k2=1;  /**************** Main Program *****************/
     j=nbocc(model,'+');  /***********************************************/
     j1=nbocc(model,'*');  
     cptcovn=j+1;  int main(int argc, char *argv[])
     cptcovprod=j1;  {
      
     strcpy(modelsav,model);    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double agedeb, agefin,hf;
       printf("Error. Non available option model=%s ",model);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
       goto end;  
     }    double fret;
        double **xi,tmp,delta;
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');    double dum; /* Dummy variable */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    double ***p3mat;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    double ***mobaverage;
       /*scanf("%d",i);*/    int *indx;
       if (strchr(strb,'*')) {    char line[MAXLINE], linepar[MAXLINE];
         cutv(strd,strc,strb,'*');    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
         if (strcmp(strc,"age")==0) {    int firstobs=1, lastobs=10;
           cptcovprod--;    int sdeb, sfin; /* Status at beginning and end */
           cutv(strb,stre,strd,'V');    int c,  h , cpt,l;
           Tvar[i]=atoi(stre);    int ju,jl, mi;
           cptcovage++;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
             Tage[cptcovage]=i;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
             /*printf("stre=%s ", stre);*/    int mobilav=0,popforecast=0;
         }    int hstepm, nhstepm;
         else if (strcmp(strd,"age")==0) {    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    double bage, fage, age, agelim, agebase;
           Tvar[i]=atoi(stre);    double ftolpl=FTOL;
           cptcovage++;    double **prlim;
           Tage[cptcovage]=i;    double *severity;
         }    double ***param; /* Matrix of parameters */
         else {    double  *p;
           cutv(strb,stre,strc,'V');    double **matcov; /* Matrix of covariance */
           Tvar[i]=ncovcol+k1;    double ***delti3; /* Scale */
           cutv(strb,strc,strd,'V');    double *delti; /* Scale */
           Tprod[k1]=i;    double ***eij, ***vareij;
           Tvard[k1][1]=atoi(strc);    double **varpl; /* Variances of prevalence limits by age */
           Tvard[k1][2]=atoi(stre);    double *epj, vepp;
           Tvar[cptcovn+k2]=Tvard[k1][1];    double kk1, kk2;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
           for (k=1; k<=lastobs;k++)    
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    char *alph[]={"a","a","b","c","d","e"}, str[4];
           k2=k2+2;  
         }  
       }    char z[1]="c", occ;
       else {  #include <sys/time.h>
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  #include <time.h>
        /*  scanf("%d",i);*/    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
       cutv(strd,strc,strb,'V');   
       Tvar[i]=atoi(strc);    /* long total_usecs;
       }    struct timeval start_time, end_time;
       strcpy(modelsav,stra);      
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         scanf("%d",i);*/    getcwd(pathcd, size);
     }  
 }    printf("\n%s",version);
      if(argc <=1){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      printf("\nEnter the parameter file name: ");
   printf("cptcovprod=%d ", cptcovprod);      scanf("%s",pathtot);
   scanf("%d ",i);*/    }
     fclose(fic);    else{
       strcpy(pathtot,argv[1]);
     /*  if(mle==1){*/    }
     if (weightopt != 1) { /* Maximisation without weights*/    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
       for(i=1;i<=n;i++) weight[i]=1.0;    /*cygwin_split_path(pathtot,path,optionfile);
     }      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /*-calculation of age at interview from date of interview and age at death -*/    /* cutv(path,optionfile,pathtot,'\\');*/
     agev=matrix(1,maxwav,1,imx);  
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     for (i=1; i<=imx; i++) {     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       for(m=2; (m<= maxwav); m++) {    chdir(path);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    replace(pathc,path);
          anint[m][i]=9999;  
          s[m][i]=-1;  /*-------- arguments in the command line --------*/
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    /* Log file */
       }    strcat(filelog, optionfilefiname);
     }    strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
     for (i=1; i<=imx; i++)  {      printf("Problem with logfile %s\n",filelog);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      goto end;
       for(m=1; (m<= maxwav); m++){    }
         if(s[m][i] >0){    fprintf(ficlog,"Log filename:%s\n",filelog);
           if (s[m][i] >= nlstate+1) {    fprintf(ficlog,"\n%s",version);
             if(agedc[i]>0)    fprintf(ficlog,"\nEnter the parameter file name: ");
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
                 agev[m][i]=agedc[i];    fflush(ficlog);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {    /* */
               if (andc[i]!=9999){    strcpy(fileres,"r");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    strcat(fileres, optionfilefiname);
               agev[m][i]=-1;    strcat(fileres,".txt");    /* Other files have txt extension */
               }  
             }    /*---------arguments file --------*/
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    if((ficpar=fopen(optionfile,"r"))==NULL)    {
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      printf("Problem with optionfile %s\n",optionfile);
             if(mint[m][i]==99 || anint[m][i]==9999)      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
               agev[m][i]=1;      goto end;
             else if(agev[m][i] <agemin){    }
               agemin=agev[m][i];  
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    strcpy(filereso,"o");
             }    strcat(filereso,fileres);
             else if(agev[m][i] >agemax){    if((ficparo=fopen(filereso,"w"))==NULL) {
               agemax=agev[m][i];      printf("Problem with Output resultfile: %s\n", filereso);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
             }      goto end;
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/  
           }    /* Reads comments: lines beginning with '#' */
           else { /* =9 */    while((c=getc(ficpar))=='#' && c!= EOF){
             agev[m][i]=1;      ungetc(c,ficpar);
             s[m][i]=-1;      fgets(line, MAXLINE, ficpar);
           }      puts(line);
         }      fputs(line,ficparo);
         else /*= 0 Unknown */    }
           agev[m][i]=1;    ungetc(c,ficpar);
       }  
        fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     }    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     for (i=1; i<=imx; i++)  {    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);
       for(m=1; (m<= maxwav); m++){  while((c=getc(ficpar))=='#' && c!= EOF){
         if (s[m][i] > (nlstate+ndeath)) {      ungetc(c,ficpar);
           printf("Error: Wrong value in nlstate or ndeath\n");        fgets(line, MAXLINE, ficpar);
           goto end;      puts(line);
         }      fputs(line,ficparo);
       }    }
     }    ungetc(c,ficpar);
     
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     
     covar=matrix(0,NCOVMAX,1,n); 
     free_vector(severity,1,maxwav);    cptcovn=0; 
     free_imatrix(outcome,1,maxwav+1,1,n);    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    ncovmodel=2+cptcovn;
     /* free_matrix(mint,1,maxwav,1,n);    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
        free_matrix(anint,1,maxwav,1,n);*/    
     free_vector(moisdc,1,n);    /* Read guess parameters */
     free_vector(andc,1,n);    /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
          ungetc(c,ficpar);
     wav=ivector(1,imx);      fgets(line, MAXLINE, ficpar);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      puts(line);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      fputs(line,ficparo);
        }
     /* Concatenates waves */    ungetc(c,ficpar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++)
       Tcode=ivector(1,100);      for(j=1; j <=nlstate+ndeath-1; j++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        fscanf(ficpar,"%1d%1d",&i1,&j1);
       ncodemax[1]=1;        fprintf(ficparo,"%1d%1d",i1,j1);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        if(mle==1)
                printf("%1d%1d",i,j);
    codtab=imatrix(1,100,1,10);        fprintf(ficlog,"%1d%1d",i,j);
    h=0;        for(k=1; k<=ncovmodel;k++){
    m=pow(2,cptcoveff);          fscanf(ficpar," %lf",&param[i][j][k]);
            if(mle==1){
    for(k=1;k<=cptcoveff; k++){            printf(" %lf",param[i][j][k]);
      for(i=1; i <=(m/pow(2,k));i++){            fprintf(ficlog," %lf",param[i][j][k]);
        for(j=1; j <= ncodemax[k]; j++){          }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          else
            h++;            fprintf(ficlog," %lf",param[i][j][k]);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          fprintf(ficparo," %lf",param[i][j][k]);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        }
          }        fscanf(ficpar,"\n");
        }        if(mle==1)
      }          printf("\n");
    }        fprintf(ficlog,"\n");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        fprintf(ficparo,"\n");
       codtab[1][2]=1;codtab[2][2]=2; */      }
    /* for(i=1; i <=m ;i++){    
       for(k=1; k <=cptcovn; k++){      npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  
       }    p=param[1][1];
       printf("\n");    
       }    /* Reads comments: lines beginning with '#' */
       scanf("%d",i);*/    while((c=getc(ficpar))=='#' && c!= EOF){
          ungetc(c,ficpar);
    /* Calculates basic frequencies. Computes observed prevalence at single age      fgets(line, MAXLINE, ficpar);
        and prints on file fileres'p'. */      puts(line);
       fputs(line,ficparo);
        }
        ungetc(c,ficpar);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(i=1; i <=nlstate; i++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for(j=1; j <=nlstate+ndeath-1; j++){
              fscanf(ficpar,"%1d%1d",&i1,&j1);
     /* For Powell, parameters are in a vector p[] starting at p[1]        printf("%1d%1d",i,j);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        fprintf(ficparo,"%1d%1d",i1,j1);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
     if(mle==1){          printf(" %le",delti3[i][j][k]);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(ficparo," %le",delti3[i][j][k]);
     }        }
            fscanf(ficpar,"\n");
     /*--------- results files --------------*/        printf("\n");
     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);        fprintf(ficparo,"\n");
        }
     }
    jk=1;    delti=delti3[1][1];
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /* Reads comments: lines beginning with '#' */
    for(i=1,jk=1; i <=nlstate; i++){    while((c=getc(ficpar))=='#' && c!= EOF){
      for(k=1; k <=(nlstate+ndeath); k++){      ungetc(c,ficpar);
        if (k != i)      fgets(line, MAXLINE, ficpar);
          {      puts(line);
            printf("%d%d ",i,k);      fputs(line,ficparo);
            fprintf(ficres,"%1d%1d ",i,k);    }
            for(j=1; j <=ncovmodel; j++){    ungetc(c,ficpar);
              printf("%f ",p[jk]);    
              fprintf(ficres,"%f ",p[jk]);    matcov=matrix(1,npar,1,npar);
              jk++;    for(i=1; i <=npar; i++){
            }      fscanf(ficpar,"%s",&str);
            printf("\n");      if(mle==1)
            fprintf(ficres,"\n");        printf("%s",str);
          }      fprintf(ficlog,"%s",str);
      }      fprintf(ficparo,"%s",str);
    }      for(j=1; j <=i; j++){
  if(mle==1){        fscanf(ficpar," %le",&matcov[i][j]);
     /* Computing hessian and covariance matrix */        if(mle==1){
     ftolhess=ftol; /* Usually correct */          printf(" %.5le",matcov[i][j]);
     hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(ficlog," %.5le",matcov[i][j]);
  }        }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        else
     printf("# Scales (for hessian or gradient estimation)\n");          fprintf(ficlog," %.5le",matcov[i][j]);
      for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficparo," %.5le",matcov[i][j]);
       for(j=1; j <=nlstate+ndeath; j++){      }
         if (j!=i) {      fscanf(ficpar,"\n");
           fprintf(ficres,"%1d%1d",i,j);      if(mle==1)
           printf("%1d%1d",i,j);        printf("\n");
           for(k=1; k<=ncovmodel;k++){      fprintf(ficlog,"\n");
             printf(" %.5e",delti[jk]);      fprintf(ficparo,"\n");
             fprintf(ficres," %.5e",delti[jk]);    }
             jk++;    for(i=1; i <=npar; i++)
           }      for(j=i+1;j<=npar;j++)
           printf("\n");        matcov[i][j]=matcov[j][i];
           fprintf(ficres,"\n");     
         }    if(mle==1)
       }      printf("\n");
      }    fprintf(ficlog,"\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");      /*-------- Rewriting paramater file ----------*/
     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");       strcpy(rfileres,"r");    /* "Rparameterfile */
     for(i=1;i<=npar;i++){       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       /*  if (k>nlstate) k=1;       strcat(rfileres,".");    /* */
       i1=(i-1)/(ncovmodel*nlstate)+1;       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/        printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficres,"%3d",i);        fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       printf("%3d",i);      }
       for(j=1; j<=i;j++){      fprintf(ficres,"#%s\n",version);
         fprintf(ficres," %.5e",matcov[i][j]);      
         printf(" %.5e",matcov[i][j]);      /*-------- data file ----------*/
       }      if((fic=fopen(datafile,"r"))==NULL)    {
       fprintf(ficres,"\n");        printf("Problem with datafile: %s\n", datafile);goto end;
       printf("\n");        fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
       k++;      }
     }  
          n= lastobs;
     while((c=getc(ficpar))=='#' && c!= EOF){      severity = vector(1,maxwav);
       ungetc(c,ficpar);      outcome=imatrix(1,maxwav+1,1,n);
       fgets(line, MAXLINE, ficpar);      num=ivector(1,n);
       puts(line);      moisnais=vector(1,n);
       fputs(line,ficparo);      annais=vector(1,n);
     }      moisdc=vector(1,n);
     ungetc(c,ficpar);      andc=vector(1,n);
     estepm=0;      agedc=vector(1,n);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      cod=ivector(1,n);
     if (estepm==0 || estepm < stepm) estepm=stepm;      weight=vector(1,n);
     if (fage <= 2) {      for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
       bage = ageminpar;      mint=matrix(1,maxwav,1,n);
       fage = agemaxpar;      anint=matrix(1,maxwav,1,n);
     }      s=imatrix(1,maxwav+1,1,n);
          adl=imatrix(1,maxwav+1,1,n);    
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      tab=ivector(1,NCOVMAX);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      ncodemax=ivector(1,8);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
        i=1;
     while((c=getc(ficpar))=='#' && c!= EOF){      while (fgets(line, MAXLINE, fic) != NULL)    {
     ungetc(c,ficpar);        if ((i >= firstobs) && (i <=lastobs)) {
     fgets(line, MAXLINE, ficpar);          
     puts(line);          for (j=maxwav;j>=1;j--){
     fputs(line,ficparo);            cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
   }            strcpy(line,stra);
   ungetc(c,ficpar);            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);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
                cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
     fgets(line, MAXLINE, ficpar);          cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
     puts(line);  
     fputs(line,ficparo);          cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
   }          for (j=ncovcol;j>=1;j--){
   ungetc(c,ficpar);            cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
            } 
           num[i]=atol(stra);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
             printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);            i=i+1;
   fprintf(ficres,"pop_based=%d\n",popbased);          }
        } 
   while((c=getc(ficpar))=='#' && c!= EOF){      /* printf("ii=%d", ij);
     ungetc(c,ficpar);         scanf("%d",i);*/
     fgets(line, MAXLINE, ficpar);    imx=i-1; /* Number of individuals */
     puts(line);  
     fputs(line,ficparo);    /* for (i=1; i<=imx; i++){
   }      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
   ungetc(c,ficpar);      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;
   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);      }*/
 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);     /*  for (i=1; i<=imx; i++){
 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);       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]));}*/
     
 while((c=getc(ficpar))=='#' && c!= EOF){   
     ungetc(c,ficpar);    /* Calculation of the number of parameter from char model*/
     fgets(line, MAXLINE, ficpar);    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     puts(line);    Tprod=ivector(1,15); 
     fputs(line,ficparo);    Tvaraff=ivector(1,15); 
   }    Tvard=imatrix(1,15,1,2);
   ungetc(c,ficpar);    Tage=ivector(1,15);      
      
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    if (strlen(model) >1){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      j=0, j1=0, k1=1, k2=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);      j=nbocc(model,'+');
       j1=nbocc(model,'*');
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      cptcovn=j+1;
       cptcovprod=j1;
 /*------------ gnuplot -------------*/      
   strcpy(optionfilegnuplot,optionfilefiname);      strcpy(modelsav,model); 
   strcat(optionfilegnuplot,".gp");      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        printf("Error. Non available option model=%s ",model);
     printf("Problem with file %s",optionfilegnuplot);        fprintf(ficlog,"Error. Non available option model=%s ",model);
   }        goto end;
   fclose(ficgp);      }
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);      
 /*--------- index.htm --------*/      for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
   strcpy(optionfilehtm,optionfile);        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
   strcat(optionfilehtm,".htm");        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        /*scanf("%d",i);*/
     printf("Problem with %s \n",optionfilehtm), exit(0);        if (strchr(strb,'*')) {  /* Model includes a product */
   }          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            cptcovprod--;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            cutv(strb,stre,strd,'V');
 \n            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
 Total number of observations=%d <br>\n            cptcovage++;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              Tage[cptcovage]=i;
 <hr  size=\"2\" color=\"#EC5E5E\">              /*printf("stre=%s ", stre);*/
  <ul><li>Parameter files<br>\n          }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          else if (strcmp(strd,"age")==0) { /* or age*Vn */
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);            cptcovprod--;
   fclose(fichtm);            cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);            cptcovage++;
              Tage[cptcovage]=i;
 /*------------ free_vector  -------------*/          }
  chdir(path);          else {  /* Age is not in the model */
              cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
  free_ivector(wav,1,imx);            Tvar[i]=ncovcol+k1;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              Tprod[k1]=i;
  free_ivector(num,1,n);            Tvard[k1][1]=atoi(strc); /* m*/
  free_vector(agedc,1,n);            Tvard[k1][2]=atoi(stre); /* n */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            Tvar[cptcovn+k2]=Tvard[k1][1];
  fclose(ficparo);            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
  fclose(ficres);            for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
   /*--------------- Prevalence limit --------------*/            k2=k2+2;
            }
   strcpy(filerespl,"pl");        }
   strcat(filerespl,fileres);        else { /* no more sum */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;         /*  scanf("%d",i);*/
   }        cutv(strd,strc,strb,'V');
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        Tvar[i]=atoi(strc);
   fprintf(ficrespl,"#Prevalence limit\n");        }
   fprintf(ficrespl,"#Age ");        strcpy(modelsav,stra);  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
   fprintf(ficrespl,"\n");          scanf("%d",i);*/
        } /* end of loop + */
   prlim=matrix(1,nlstate,1,nlstate);    } /* end model */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("cptcovprod=%d ", cptcovprod);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    scanf("%d ",i);*/
   k=0;      fclose(fic);
   agebase=ageminpar;  
   agelim=agemaxpar;      /*  if(mle==1){*/
   ftolpl=1.e-10;      if (weightopt != 1) { /* Maximisation without weights*/
   i1=cptcoveff;        for(i=1;i<=n;i++) weight[i]=1.0;
   if (cptcovn < 1){i1=1;}      }
       /*-calculation of age at interview from date of interview and age at death -*/
   for(cptcov=1;cptcov<=i1;cptcov++){      agev=matrix(1,maxwav,1,imx);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;      for (i=1; i<=imx; i++) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        for(m=2; (m<= maxwav); m++) {
         fprintf(ficrespl,"\n#******");         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
         for(j=1;j<=cptcoveff;j++)           anint[m][i]=9999;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           s[m][i]=-1;
         fprintf(ficrespl,"******\n");         }
               if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
         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++)      for (i=1; i<=imx; i++)  {
           fprintf(ficrespl," %.5f", prlim[i][i]);        agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
           fprintf(ficrespl,"\n");        for(m=1; (m<= maxwav); m++){
         }          if(s[m][i] >0){
       }            if (s[m][i] >= nlstate+1) {
     }              if(agedc[i]>0)
   fclose(ficrespl);                if(moisdc[i]!=99 && andc[i]!=9999)
                   agev[m][i]=agedc[i];
   /*------------- h Pij x at various ages ------------*/              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                if (andc[i]!=9999){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                printf("Warning negative age at death: %d line:%d\n",num[i],i);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
   }                agev[m][i]=-1;
   printf("Computing pij: result on file '%s' \n", filerespij);                }
                }
   stepsize=(int) (stepm+YEARM-1)/YEARM;            }
   /*if (stepm<=24) stepsize=2;*/            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]);
   agelim=AGESUP;              if(mint[m][i]==99 || anint[m][i]==9999)
   hstepm=stepsize*YEARM; /* Every year of age */                agev[m][i]=1;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              else if(agev[m][i] <agemin){ 
                  agemin=agev[m][i];
   k=0;                /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
   for(cptcov=1;cptcov<=i1;cptcov++){              }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              else if(agev[m][i] >agemax){
       k=k+1;                agemax=agev[m][i];
         fprintf(ficrespij,"\n#****** ");               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
         for(j=1;j<=cptcoveff;j++)              }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              /*agev[m][i]=anint[m][i]-annais[i];*/
         fprintf(ficrespij,"******\n");              /*   agev[m][i] = age[i]+2*m;*/
                    }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            else { /* =9 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              agev[m][i]=1;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              s[m][i]=-1;
           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);            else /*= 0 Unknown */
           fprintf(ficrespij,"# Age");            agev[m][i]=1;
           for(i=1; i<=nlstate;i++)        }
             for(j=1; j<=nlstate+ndeath;j++)      
               fprintf(ficrespij," %1d-%1d",i,j);      }
           fprintf(ficrespij,"\n");      for (i=1; i<=imx; i++)  {
            for (h=0; h<=nhstepm; h++){        for(m=1; (m<= maxwav); m++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          if (s[m][i] > (nlstate+ndeath)) {
             for(i=1; i<=nlstate;i++)            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);   
               for(j=1; j<=nlstate+ndeath;j++)            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);   
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            goto end;
             fprintf(ficrespij,"\n");          }
              }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           fprintf(ficrespij,"\n");  
         }  printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     }   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   }  
       free_vector(severity,1,maxwav);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      free_imatrix(outcome,1,maxwav+1,1,n);
       free_vector(moisnais,1,n);
   fclose(ficrespij);      free_vector(annais,1,n);
       /* free_matrix(mint,1,maxwav,1,n);
          free_matrix(anint,1,maxwav,1,n);*/
   /*---------- Forecasting ------------------*/      free_vector(moisdc,1,n);
   if((stepm == 1) && (strcmp(model,".")==0)){      free_vector(andc,1,n);
     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);     
   }      wav=ivector(1,imx);
   else{      dh=imatrix(1,lastpass-firstpass+1,1,imx);
     erreur=108;      mw=imatrix(1,lastpass-firstpass+1,1,imx);
     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);     
   }      /* Concatenates waves */
          concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
   /*---------- Health expectancies and variances ------------*/  
         Tcode=ivector(1,100);
   strcpy(filerest,"t");        nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   strcat(filerest,fileres);        ncodemax[1]=1;
   if((ficrest=fopen(filerest,"w"))==NULL) {        if (cptcovn > 0) tricode(Tvar,nbcode,imx);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        
   }     codtab=imatrix(1,100,1,10);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     h=0;
      m=pow(2,cptcoveff);
    
   strcpy(filerese,"e");     for(k=1;k<=cptcoveff; k++){
   strcat(filerese,fileres);       for(i=1; i <=(m/pow(2,k));i++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {         for(j=1; j <= ncodemax[k]; j++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
   }             h++;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);             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]);*/
  strcpy(fileresv,"v");           } 
   strcat(fileresv,fileres);         }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);     } 
   }     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        codtab[1][2]=1;codtab[2][2]=2; */
   calagedate=-1;     /* for(i=1; i <=m ;i++){ 
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(k=1; k <=cptcovn; k++){
         printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        printf("\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;        scanf("%d",i);*/
       fprintf(ficrest,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)     /* Calculates basic frequencies. Computes observed prevalence at single age
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         and prints on file fileres'p'. */
       fprintf(ficrest,"******\n");  
       
       fprintf(ficreseij,"\n#****** ");     
       for(j=1;j<=cptcoveff;j++)      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       fprintf(ficreseij,"******\n");      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       fprintf(ficresvij,"\n#****** ");      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       for(j=1;j<=cptcoveff;j++)       
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* For Powell, parameters are in a vector p[] starting at p[1]
       fprintf(ficresvij,"******\n");         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) */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      if(mle==1){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
        }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      
       oldm=oldms;savm=savms;      /*--------- results files --------------*/
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      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(ficrest,"#Total LEs with variances: e.. (std) ");     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficrest,"\n");     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      for(i=1,jk=1; i <=nlstate; i++){
       epj=vector(1,nlstate+1);       for(k=1; k <=(nlstate+ndeath); k++){
       for(age=bage; age <=fage ;age++){         if (k != i) 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           {
         if (popbased==1) {             printf("%d%d ",i,k);
           for(i=1; i<=nlstate;i++)             fprintf(ficlog,"%d%d ",i,k);
             prlim[i][i]=probs[(int)age][i][k];             fprintf(ficres,"%1d%1d ",i,k);
         }             for(j=1; j <=ncovmodel; j++){
                       printf("%f ",p[jk]);
         fprintf(ficrest," %4.0f",age);               fprintf(ficlog,"%f ",p[jk]);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){               fprintf(ficres,"%f ",p[jk]);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {               jk++; 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];             }
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/             printf("\n");
           }             fprintf(ficlog,"\n");
           epj[nlstate+1] +=epj[j];             fprintf(ficres,"\n");
         }           }
        }
         for(i=1, vepp=0.;i <=nlstate;i++)     }
           for(j=1;j <=nlstate;j++)     if(mle==1){
             vepp += vareij[i][j][(int)age];       /* Computing hessian and covariance matrix */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));       ftolhess=ftol; /* Usually correct */
         for(j=1;j <=nlstate;j++){       hesscov(matcov, p, npar, delti, ftolhess, func);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));     }
         }     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
         fprintf(ficrest,"\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++){
 free_matrix(mint,1,maxwav,1,n);         if (j!=i) {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);           fprintf(ficres,"%1d%1d",i,j);
     free_vector(weight,1,n);           printf("%1d%1d",i,j);
   fclose(ficreseij);           fprintf(ficlog,"%1d%1d",i,j);
   fclose(ficresvij);           for(k=1; k<=ncovmodel;k++){
   fclose(ficrest);             printf(" %.5e",delti[jk]);
   fclose(ficpar);             fprintf(ficlog," %.5e",delti[jk]);
   free_vector(epj,1,nlstate+1);             fprintf(ficres," %.5e",delti[jk]);
               jk++;
   /*------- Variance limit prevalence------*/             }
            printf("\n");
   strcpy(fileresvpl,"vpl");           fprintf(ficlog,"\n");
   strcat(fileresvpl,fileres);           fprintf(ficres,"\n");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {         }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       }
     exit(0);     }
   }     
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);     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");
   k=0;     if(mle==1)
   for(cptcov=1;cptcov<=i1;cptcov++){       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");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     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");
       k=k+1;     for(i=1;i<=npar;i++){
       fprintf(ficresvpl,"\n#****** ");       /*  if (k>nlstate) k=1;
       for(j=1;j<=cptcoveff;j++)           i1=(i-1)/(ncovmodel*nlstate)+1; 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
       fprintf(ficresvpl,"******\n");           printf("%s%d%d",alph[k],i1,tab[i]);*/
             fprintf(ficres,"%3d",i);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);       if(mle==1)
       oldm=oldms;savm=savms;         printf("%3d",i);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       fprintf(ficlog,"%3d",i);
     }       for(j=1; j<=i;j++){
  }         fprintf(ficres," %.5e",matcov[i][j]);
          if(mle==1)
   fclose(ficresvpl);           printf(" %.5e",matcov[i][j]);
          fprintf(ficlog," %.5e",matcov[i][j]);
   /*---------- End : free ----------------*/       }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       fprintf(ficres,"\n");
         if(mle==1)
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         printf("\n");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       fprintf(ficlog,"\n");
         k++;
       }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     while((c=getc(ficpar))=='#' && c!= EOF){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       ungetc(c,ficpar);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       fgets(line, MAXLINE, ficpar);
         puts(line);
   free_matrix(matcov,1,npar,1,npar);       fputs(line,ficparo);
   free_vector(delti,1,npar);     }
   free_matrix(agev,1,maxwav,1,imx);     ungetc(c,ficpar);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     estepm=0;
      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
   fprintf(fichtm,"\n</body>");     if (estepm==0 || estepm < stepm) estepm=stepm;
   fclose(fichtm);     if (fage <= 2) {
   fclose(ficgp);       bage = ageminpar;
         fage = agemaxpar;
      }
   if(erreur >0)     
     printf("End of Imach with error or warning %d\n",erreur);     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
   else   printf("End of Imach\n");     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
   /* 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);*/     while((c=getc(ficpar))=='#' && c!= EOF){
   /*printf("Total time was %d uSec.\n", total_usecs);*/       ungetc(c,ficpar);
   /*------ End -----------*/       fgets(line, MAXLINE, ficpar);
        puts(line);
        fputs(line,ficparo);
  end:     }
 #ifdef windows     ungetc(c,ficpar);
   /* chdir(pathcd);*/    
 #endif     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);
  /*system("wgnuplot graph.plt");*/     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);
  /*system("../gp37mgw/wgnuplot graph.plt");*/     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);
  /*system("cd ../gp37mgw");*/     
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/     while((c=getc(ficpar))=='#' && c!= EOF){
  strcpy(plotcmd,GNUPLOTPROGRAM);       ungetc(c,ficpar);
  strcat(plotcmd," ");       fgets(line, MAXLINE, ficpar);
  strcat(plotcmd,optionfilegnuplot);       puts(line);
  system(plotcmd);       fputs(line,ficparo);
      }
 #ifdef windows     ungetc(c,ficpar);
   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: ");     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     scanf("%s",z);     dateprev2=anprev2+mprev2/12.+jprev2/365.;
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    fscanf(ficpar,"pop_based=%d\n",&popbased);
     else if (z[0] == 'g') system(plotcmd);    fprintf(ficparo,"pop_based=%d\n",popbased);   
     else if (z[0] == 'q') exit(0);    fprintf(ficres,"pop_based=%d\n",popbased);   
   }    
 #endif    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);
     }
     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 --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing prevalence limit: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Prevalence limit\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==1) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       movingaverage(probs, ageminpar, fage, mobaverage);
     }
   
     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 !=1){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav=1 */ 
               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 limit prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of Prevalence limit: 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==1) 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);
    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 
   }
   
   

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  Added in v.1.53


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