Diff for /imach/src/imach.c between versions 1.36 and 1.66

version 1.36, 2002/03/29 15:27:27 version 1.66, 2003/01/28 17:23:35
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
   probabibility 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, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/    **********************************************************************/
     
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "wgnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 8 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #ifdef windows
   #define DIRSEPARATOR '\\'
 int erreur; /* Error number */  #define ODIRSEPARATOR '/'
 int nvar;  #else
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  #define DIRSEPARATOR '/'
 int npar=NPARMAX;  #define ODIRSEPARATOR '\\'
 int nlstate=2; /* Number of live states */  #endif
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  char version[80]="Imach version 0.91, November 2002, INED-EUROREVES ";
 int popbased=0;  int erreur; /* Error number */
   int nvar;
 int *wav; /* Number of waves for this individuual 0 is possible */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int maxwav; /* Maxim number of waves */  int npar=NPARMAX;
 int jmin, jmax; /* min, max spacing between 2 waves */  int nlstate=2; /* Number of live states */
 int mle, weightopt;  int ndeath=1; /* Number of dead states */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int popbased=0;
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  int *wav; /* Number of waves for this individuual 0 is possible */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  int maxwav; /* Maxim number of waves */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  int jmin, jmax; /* min, max spacing between 2 waves */
 FILE *ficgp,*ficresprob,*ficpop;  int mle, weightopt;
 FILE *ficreseij;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   char filerese[FILENAMELENGTH];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  FILE  *ficresvij;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   char fileresv[FILENAMELENGTH];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  FILE  *ficresvpl;  double jmean; /* Mean space between 2 waves */
   char fileresvpl[FILENAMELENGTH];  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define NR_END 1  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define FREE_ARG char*  FILE *ficlog;
 #define FTOL 1.0e-10  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 #define NRANSI  FILE *fichtm; /* Html File */
 #define ITMAX 200  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 #define TOL 2.0e-4  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 #define CGOLD 0.3819660  FILE  *ficresvpl;
 #define ZEPS 1.0e-10  char fileresvpl[FILENAMELENGTH];
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #define GOLD 1.618034  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 static double maxarg1,maxarg2;  char filerest[FILENAMELENGTH];
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileregp[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char popfile[FILENAMELENGTH];
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 #define rint(a) floor(a+0.5)  
   #define NR_END 1
 static double sqrarg;  #define FREE_ARG char*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define FTOL 1.0e-10
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NRANSI 
 int imx;  #define ITMAX 200 
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  #define TOL 2.0e-4 
   
 int estepm;  #define CGOLD 0.3819660 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define GOLD 1.618034 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define GLIMIT 100.0 
 double **pmmij, ***probs, ***mobaverage;  #define TINY 1.0e-20 
 double dateintmean=0;  
   static double maxarg1,maxarg2;
 double *weight;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 int **s; /* Status */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /**************** split *************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  int imx; 
    char *s;                             /* pointer */  int stepm;
    int  l1, l2;                         /* length counters */  /* Stepm, step in month: minimum step interpolation*/
   
    l1 = strlen( path );                 /* length of path */  int estepm;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  int m,nb;
 #else  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    s = strrchr( path, '/' );            /* find last / */  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #endif  double **pmmij, ***probs;
    if ( s == NULL ) {                   /* no directory, so use current */  double dateintmean=0;
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  double *weight;
   int **s; /* Status */
       if ( getwd( dirc ) == NULL ) {  double *agedc, **covar, idx;
 #else  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       extern char       *getcwd( );  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double ftolhess; /* Tolerance for computing hessian */
 #endif  
          return( GLOCK_ERROR_GETCWD );  /**************** split *************************/
       }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       strcpy( name, path );             /* we've got it */  {
    } else {                             /* strip direcotry from path */    char  *ss;                            /* pointer */
       s++;                              /* after this, the filename */    int   l1, l2;                         /* length counters */
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    l1 = strlen(path );                   /* length of path */
       strcpy( name, s );                /* save file name */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       dirc[l1-l2] = 0;                  /* add zero */    if ( ss == NULL ) {                   /* no directory, so use current */
    }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
    l1 = strlen( dirc );                 /* length of directory */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #ifdef windows  #if     defined(__bsd__)                /* get current working directory */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      extern char *getwd( );
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      if ( getwd( dirc ) == NULL ) {
 #endif  #else
    s = strrchr( name, '.' );            /* find last / */      extern char *getcwd( );
    s++;  
    strcpy(ext,s);                       /* save extension */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
    l1= strlen( name);  #endif
    l2= strlen( s)+1;        return( GLOCK_ERROR_GETCWD );
    strncpy( finame, name, l1-l2);      }
    finame[l1-l2]= 0;      strcpy( name, path );               /* we've got it */
    return( 0 );                         /* we're done */    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /******************************************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void replace(char *s, char*t)      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   int i;    l1 = strlen( dirc );                  /* length of directory */
   int lg=20;  #ifdef windows
   i=0;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   lg=strlen(t);  #else
   for(i=0; i<= lg; i++) {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     (s[i] = t[i]);  #endif
     if (t[i]== '\\') s[i]='/';    ss = strrchr( name, '.' );            /* find last / */
   }    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 int nbocc(char *s, char occ)    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   int i,j=0;    finame[l1-l2]= 0;
   int lg=20;    return( 0 );                          /* we're done */
   i=0;  }
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  /******************************************/
   }  
   return j;  void replace(char *s, char*t)
 }  {
     int i;
 void cutv(char *u,char *v, char*t, char occ)    int lg=20;
 {    i=0;
   int i,lg,j,p=0;    lg=strlen(t);
   i=0;    for(i=0; i<= lg; i++) {
   for(j=0; j<=strlen(t)-1; j++) {      (s[i] = t[i]);
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      if (t[i]== '\\') s[i]='/';
   }    }
   }
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int nbocc(char *s, char occ)
     (u[j] = t[j]);  {
   }    int i,j=0;
      u[p]='\0';    int lg=20;
     i=0;
    for(j=0; j<= lg; j++) {    lg=strlen(s);
     if (j>=(p+1))(v[j-p-1] = t[j]);    for(i=0; i<= lg; i++) {
   }    if  (s[i] == occ ) j++;
 }    }
     return j;
 /********************** nrerror ********************/  }
   
 void nrerror(char error_text[])  void cutv(char *u,char *v, char*t, char occ)
 {  {
   fprintf(stderr,"ERREUR ...\n");    /* cuts string t into u and v where u is ended by char occ excluding it
   fprintf(stderr,"%s\n",error_text);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   exit(1);       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
 /*********************** vector *******************/    i=0;
 double *vector(int nl, int nh)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double *v;    }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    lg=strlen(t);
   return v-nl+NR_END;    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /************************ free vector ******************/       u[p]='\0';
 void free_vector(double*v, int nl, int nh)  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(v+nl-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /********************** nrerror ********************/
 {  
   int *v;  void nrerror(char error_text[])
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    fprintf(stderr,"ERREUR ...\n");
   return v-nl+NR_END;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /******************free ivector **************************/  /*********************** vector *******************/
 void free_ivector(int *v, long nl, long 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");
 /******************* 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 vector ******************/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  void free_vector(double*v, int nl, int 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()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
      int *v;
      v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* allocate rows and set pointers to them */    if (!v) nrerror("allocation failure in ivector");
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    return v-nl+NR_END;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  {
      free((FREE_ARG)(v+nl-NR_END));
   /* return pointer to array of pointers to rows */  }
   return m;  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /****************** free_imatrix *************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void free_imatrix(m,nrl,nrh,ncl,nch)  { 
       int **m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       long nch,ncl,nrh,nrl;    int **m; 
      /* free an int matrix allocated by imatrix() */    
 {    /* allocate pointers to rows */ 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   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)    
 {    /* allocate rows and set pointers to them */ 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double **m;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    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 */ 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  } 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;        int **m;
   return m;        long nch,ncl,nrh,nrl; 
 }       /* free an int matrix allocated by imatrix() */ 
   { 
 /*************************free matrix ************************/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    free((FREE_ARG) (m+nrl-NR_END)); 
 {  } 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 /******************* ma3x *******************************/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    double **m;
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ***m;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m -= nrl;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   m -= nrl;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m[nrl] -= ncl;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   m[nrl] -= ncl;    return m;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /*************************free matrix ************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   m[nrl][ncl] -= nll;    free((FREE_ARG)(m+nrl-NR_END));
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  
    /******************* ma3x *******************************/
   for (i=nrl+1; i<=nrh; i++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  {
     for (j=ncl+1; j<=nch; j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       m[i][j]=m[i][j-1]+nlay;    double ***m;
   }  
   return m;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*************************free ma3x ************************/    m -= nrl;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl] += NR_END;
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /***************** f1dim *************************/  
 extern int ncom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 extern double (*nrfunc)(double []);    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
 double f1dim(double x)    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   int j;    
   double f;    for (i=nrl+1; i<=nrh; i++) {
   double *xt;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
        for (j=ncl+1; j<=nch; j++) 
   xt=vector(1,ncom);        m[i][j]=m[i][j-1]+nlay;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    }
   f=(*nrfunc)(xt);    return m;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int iter;    free((FREE_ARG)(m+nrl-NR_END));
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /***************** f1dim *************************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern int ncom; 
   double e=0.0;  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
   a=(ax < cx ? ax : cx);   
   b=(ax > cx ? ax : cx);  double f1dim(double x) 
   x=w=v=bx;  { 
   fw=fv=fx=(*f)(x);    int j; 
   for (iter=1;iter<=ITMAX;iter++) {    double f;
     xm=0.5*(a+b);    double *xt; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);   
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    xt=vector(1,ncom); 
     printf(".");fflush(stdout);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #ifdef DEBUG    f=(*nrfunc)(xt); 
     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);    free_vector(xt,1,ncom); 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return f; 
 #endif  } 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /*****************brent *************************/
       return fx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     ftemp=fu;    int iter; 
     if (fabs(e) > tol1) {    double a,b,d,etemp;
       r=(x-w)*(fx-fv);    double fu,fv,fw,fx;
       q=(x-v)*(fx-fw);    double ftemp;
       p=(x-v)*q-(x-w)*r;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       q=2.0*(q-r);    double e=0.0; 
       if (q > 0.0) p = -p;   
       q=fabs(q);    a=(ax < cx ? ax : cx); 
       etemp=e;    b=(ax > cx ? ax : cx); 
       e=d;    x=w=v=bx; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    fw=fv=fx=(*f)(x); 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (iter=1;iter<=ITMAX;iter++) { 
       else {      xm=0.5*(a+b); 
         d=p/q;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         u=x+d;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         if (u-a < tol2 || b-u < tol2)      printf(".");fflush(stdout);
           d=SIGN(tol1,xm-x);      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
     } else {      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);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      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);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #endif
     fu=(*f)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     if (fu <= fx) {        *xmin=x; 
       if (u >= x) a=x; else b=x;        return fx; 
       SHFT(v,w,x,u)      } 
         SHFT(fv,fw,fx,fu)      ftemp=fu;
         } else {      if (fabs(e) > tol1) { 
           if (u < x) a=u; else b=u;        r=(x-w)*(fx-fv); 
           if (fu <= fw || w == x) {        q=(x-v)*(fx-fw); 
             v=w;        p=(x-v)*q-(x-w)*r; 
             w=u;        q=2.0*(q-r); 
             fv=fw;        if (q > 0.0) p = -p; 
             fw=fu;        q=fabs(q); 
           } else if (fu <= fv || v == x || v == w) {        etemp=e; 
             v=u;        e=d; 
             fv=fu;        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)); 
         }        else { 
   }          d=p/q; 
   nrerror("Too many iterations in brent");          u=x+d; 
   *xmin=x;          if (u-a < tol2 || b-u < tol2) 
   return fx;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /****************** mnbrak ***********************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             double (*func)(double))      fu=(*f)(u); 
 {      if (fu <= fx) { 
   double ulim,u,r,q, dum;        if (u >= x) a=x; else b=x; 
   double fu;        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
   *fa=(*func)(*ax);          } else { 
   *fb=(*func)(*bx);            if (u < x) a=u; else b=u; 
   if (*fb > *fa) {            if (fu <= fw || w == x) { 
     SHFT(dum,*ax,*bx,dum)              v=w; 
       SHFT(dum,*fb,*fa,dum)              w=u; 
       }              fv=fw; 
   *cx=(*bx)+GOLD*(*bx-*ax);              fw=fu; 
   *fc=(*func)(*cx);            } else if (fu <= fv || v == x || v == w) { 
   while (*fb > *fc) {              v=u; 
     r=(*bx-*ax)*(*fb-*fc);              fv=fu; 
     q=(*bx-*cx)*(*fb-*fa);            } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/          } 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    } 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    nrerror("Too many iterations in brent"); 
     if ((*bx-u)*(u-*cx) > 0.0) {    *xmin=x; 
       fu=(*func)(u);    return fx; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  } 
       fu=(*func)(u);  
       if (fu < *fc) {  /****************** mnbrak ***********************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           }              double (*func)(double)) 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  { 
       u=ulim;    double ulim,u,r,q, dum;
       fu=(*func)(u);    double fu; 
     } else {   
       u=(*cx)+GOLD*(*cx-*bx);    *fa=(*func)(*ax); 
       fu=(*func)(u);    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     SHFT(*ax,*bx,*cx,u)      SHFT(dum,*ax,*bx,dum) 
       SHFT(*fa,*fb,*fc,fu)        SHFT(dum,*fb,*fa,dum) 
       }        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /*************** linmin ************************/    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 int ncom;      q=(*bx-*cx)*(*fb-*fa); 
 double *pcom,*xicom;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 double (*nrfunc)(double []);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
        ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double brent(double ax, double bx, double cx,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
                double (*f)(double), double tol, double *xmin);        fu=(*func)(u); 
   double f1dim(double x);        if (fu < *fc) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
               double *fc, double (*func)(double));            SHFT(*fb,*fc,fu,(*func)(u)) 
   int j;            } 
   double xx,xmin,bx,ax;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double fx,fb,fa;        u=ulim; 
          fu=(*func)(u); 
   ncom=n;      } else { 
   pcom=vector(1,n);        u=(*cx)+GOLD*(*cx-*bx); 
   xicom=vector(1,n);        fu=(*func)(u); 
   nrfunc=func;      } 
   for (j=1;j<=n;j++) {      SHFT(*ax,*bx,*cx,u) 
     pcom[j]=p[j];        SHFT(*fa,*fb,*fc,fu) 
     xicom[j]=xi[j];        } 
   }  } 
   ax=0.0;  
   xx=1.0;  /*************** linmin ************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int ncom; 
 #ifdef DEBUG  double *pcom,*xicom;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double (*nrfunc)(double []); 
 #endif   
   for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     xi[j] *= xmin;  { 
     p[j] += xi[j];    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
   free_vector(xicom,1,n);    double f1dim(double x); 
   free_vector(pcom,1,n);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 }                double *fc, double (*func)(double)); 
     int j; 
 /*************** powell ************************/    double xx,xmin,bx,ax; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double fx,fb,fa;
             double (*func)(double []))   
 {    ncom=n; 
   void linmin(double p[], double xi[], int n, double *fret,    pcom=vector(1,n); 
               double (*func)(double []));    xicom=vector(1,n); 
   int i,ibig,j;    nrfunc=func; 
   double del,t,*pt,*ptt,*xit;    for (j=1;j<=n;j++) { 
   double fp,fptt;      pcom[j]=p[j]; 
   double *xits;      xicom[j]=xi[j]; 
   pt=vector(1,n);    } 
   ptt=vector(1,n);    ax=0.0; 
   xit=vector(1,n);    xx=1.0; 
   xits=vector(1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   *fret=(*func)(p);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (j=1;j<=n;j++) pt[j]=p[j];  #ifdef DEBUG
   for (*iter=1;;++(*iter)) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fp=(*fret);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     ibig=0;  #endif
     del=0.0;    for (j=1;j<=n;j++) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      xi[j] *= xmin; 
     for (i=1;i<=n;i++)      p[j] += xi[j]; 
       printf(" %d %.12f",i, p[i]);    } 
     printf("\n");    free_vector(xicom,1,n); 
     for (i=1;i<=n;i++) {    free_vector(pcom,1,n); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  } 
       fptt=(*fret);  
 #ifdef DEBUG  /*************** powell ************************/
       printf("fret=%lf \n",*fret);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 #endif              double (*func)(double [])) 
       printf("%d",i);fflush(stdout);  { 
       linmin(p,xit,n,fret,func);    void linmin(double p[], double xi[], int n, double *fret, 
       if (fabs(fptt-(*fret)) > del) {                double (*func)(double [])); 
         del=fabs(fptt-(*fret));    int i,ibig,j; 
         ibig=i;    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
 #ifdef DEBUG    double *xits;
       printf("%d %.12e",i,(*fret));    pt=vector(1,n); 
       for (j=1;j<=n;j++) {    ptt=vector(1,n); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    xit=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xits=vector(1,n); 
       }    *fret=(*func)(p); 
       for(j=1;j<=n;j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(" p=%.12e",p[j]);    for (*iter=1;;++(*iter)) { 
       printf("\n");      fp=(*fret); 
 #endif      ibig=0; 
     }      del=0.0; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 #ifdef DEBUG      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       int k[2],l;      for (i=1;i<=n;i++) 
       k[0]=1;        printf(" %d %.12f",i, p[i]);
       k[1]=-1;      fprintf(ficlog," %d %.12f",i, p[i]);
       printf("Max: %.12e",(*func)(p));      printf("\n");
       for (j=1;j<=n;j++)      fprintf(ficlog,"\n");
         printf(" %.12e",p[j]);      for (i=1;i<=n;i++) { 
       printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for(l=0;l<=1;l++) {        fptt=(*fret); 
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        printf("fret=%lf \n",*fret);
           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,"fret=%lf \n",*fret);
         }  #endif
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
       free_vector(xit,1,n);          ibig=i; 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);  #ifdef DEBUG
       free_vector(pt,1,n);        printf("%d %.12e",i,(*fret));
       return;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=n;j++) {          printf(" x(%d)=%.12e",j,xit[j]);
       ptt[j]=2.0*p[j]-pt[j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       xit[j]=p[j]-pt[j];        }
       pt[j]=p[j];        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
     fptt=(*func)(ptt);          fprintf(ficlog," p=%.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);  #endif
         for (j=1;j<=n;j++) {      } 
           xi[j][ibig]=xi[j][n];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           xi[j][n]=xit[j];  #ifdef DEBUG
         }        int k[2],l;
 #ifdef DEBUG        k[0]=1;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        k[1]=-1;
         for(j=1;j<=n;j++)        printf("Max: %.12e",(*func)(p));
           printf(" %.12e",xit[j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         printf("\n");        for (j=1;j<=n;j++) {
 #endif          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /**** Prevalence limit ****************/          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            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]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          }
      matrix by transitions matrix until convergence is reached */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, ii,j,k;        }
   double min, max, maxmin, maxmax,sumnew=0.;  #endif
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;        free_vector(xit,1,n); 
   double agefin, delaymax=50 ; /* Max number of years to converge */        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        free_vector(pt,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        return; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
    cov[1]=1.;        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        pt[j]=p[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      } 
     newm=savm;      fptt=(*func)(ptt); 
     /* Covariates have to be included here again */      if (fptt < fp) { 
      cov[2]=agefin;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
       for (k=1; k<=cptcovn;k++) {          linmin(p,xit,n,fret,func); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          for (j=1;j<=n;j++) { 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/            xi[j][ibig]=xi[j][n]; 
       }            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          }
       for (k=1; k<=cptcovprod;k++)  #ifdef DEBUG
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          for(j=1;j<=n;j++){
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            printf(" %.12e",xit[j]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/            fprintf(ficlog," %.12e",xit[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          }
           printf("\n");
     savm=oldm;          fprintf(ficlog,"\n");
     oldm=newm;  #endif
     maxmax=0.;        }
     for(j=1;j<=nlstate;j++){      } 
       min=1.;    } 
       max=0.;  } 
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /**** Prevalence limit (stable prevalence)  ****************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
     if(maxmax < ftolpl){    double **matprod2();
       return prlim;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /*************** transition probabilities ***************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      }
 {  
   double s1, s2;     cov[1]=1.;
   /*double t34;*/   
   int i,j,j1, nc, ii, jj;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for(i=1; i<= nlstate; i++){      newm=savm;
     for(j=1; j<i;j++){      /* Covariates have to be included here again */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       cov[2]=agefin;
         /*s2 += param[i][j][nc]*cov[nc];*/    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (k=1; k<=cptcovn;k++) {
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          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]]);*/
       ps[i][j]=s2;        }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     for(j=i+1; j<=nlstate+ndeath;j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        /*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]);*/
       ps[i][j]=s2;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     }  
   }      savm=oldm;
     /*ps[3][2]=1;*/      oldm=newm;
       maxmax=0.;
   for(i=1; i<= nlstate; i++){      for(j=1;j<=nlstate;j++){
      s1=0;        min=1.;
     for(j=1; j<i; j++)        max=0.;
       s1+=exp(ps[i][j]);        for(i=1; i<=nlstate; i++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          sumnew=0;
       s1+=exp(ps[i][j]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     ps[i][i]=1./(s1+1.);          prlim[i][j]= newm[i][j]/(1-sumnew);
     for(j=1; j<i; j++)          max=FMAX(max,prlim[i][j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          min=FMIN(min,prlim[i][j]);
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        maxmin=max-min;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        maxmax=FMAX(maxmax,maxmin);
   } /* end i */      }
       if(maxmax < ftolpl){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        return prlim;
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;  }
     }  
   }  /*************** transition probabilities ***************/ 
   
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    double s1, s2;
      printf("%lf ",ps[ii][jj]);    /*double t34;*/
    }    int i,j,j1, nc, ii, jj;
     printf("\n ");  
     }      for(i=1; i<= nlstate; i++){
     printf("\n ");printf("%lf ",cov[2]);*/      for(j=1; j<i;j++){
 /*        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          /*s2 += param[i][j][nc]*cov[nc];*/
   goto end;*/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     return ps;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 }        }
         ps[i][j]=s2;
 /**************** Product of 2 matrices ******************/        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      for(j=i+1; j<=nlstate+ndeath;j++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /* in, b, out are matrice of pointers which should have been initialized        }
      before: only the contents of out is modified. The function returns        ps[i][j]=s2;
      a pointer to pointers identical to out */      }
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)      /*ps[3][2]=1;*/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(i=1; i<= nlstate; i++){
         out[i][k] +=in[i][j]*b[j][k];       s1=0;
       for(j=1; j<i; j++)
   return out;        s1+=exp(ps[i][j]);
 }      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
 /************* Higher Matrix Product ***************/      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for(j=i+1; j<=nlstate+ndeath; j++)
 {        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      duration (i.e. until    } /* end i */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      (typically every 2 years instead of every month which is too big).      for(jj=1; jj<= nlstate+ndeath; jj++){
      Model is determined by parameters x and covariates have to be        ps[ii][jj]=0;
      included manually here.        ps[ii][ii]=1;
       }
      */    }
   
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   double **newm;      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
   /* Hstepm could be zero and should return the unit matrix */     }
   for (i=1;i<=nlstate+ndeath;i++)      printf("\n ");
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[i][j]=(i==j ? 1.0 : 0.0);      printf("\n ");printf("%lf ",cov[2]);*/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*
     }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    goto end;*/
   for(h=1; h <=nhstepm; h++){      return ps;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /**************** Product of 2 matrices ******************/
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (k=1; k<=cptcovprod;k++)    /* in, b, out are matrice of pointers which should have been initialized 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     long i, j, k;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for(i=nrl; i<= nrh; i++)
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for(k=ncolol; k<=ncoloh; k++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          out[i][k] +=in[i][j]*b[j][k];
       savm=oldm;  
       oldm=newm;    return out;
     }  }
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  /************* Higher Matrix Product ***************/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
   } /* end h */    /* Computes the transition matrix starting at age 'age' over 
   return po;       'nhstepm*hstepm*stepm' months (i.e. until
 }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /*************** log-likelihood *************/       (typically every 2 years instead of every month which is too big 
 double func( double *x)       for the memory).
 {       Model is determined by parameters x and covariates have to be 
   int i, ii, j, k, mi, d, kk;       included manually here. 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;       */
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    int i, j, d, h, k;
   long ipmx;    double **out, cov[NCOVMAX];
   /*extern weight */    double **newm;
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* Hstepm could be zero and should return the unit matrix */
   /*for(i=1;i<imx;i++)    for (i=1;i<=nlstate+ndeath;i++)
     printf(" %d\n",s[4][i]);      for (j=1;j<=nlstate+ndeath;j++){
   */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   cov[1]=1.;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for(k=1; k<=nlstate; k++) ll[k]=0.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for(h=1; h <=nhstepm; h++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for(d=1; d <=hstepm; d++){
     for(mi=1; mi<= wav[i]-1; mi++){        newm=savm;
       for (ii=1;ii<=nlstate+ndeath;ii++)        /* Covariates have to be included here again */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        cov[1]=1.;
       for(d=0; d<dh[mi][i]; d++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         newm=savm;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovage;k++)
         for (kk=1; kk<=cptcovage;kk++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        for (k=1; k<=cptcovprod;k++)
         }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         savm=oldm;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         oldm=newm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                             pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       } /* end mult */        oldm=newm;
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      for(i=1; i<=nlstate+ndeath; i++)
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for(j=1;j<=nlstate+ndeath;j++) {
       ipmx +=1;          po[i][j][h]=newm[i][j];
       sw += weight[i];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;           */
     } /* end of wave */        }
   } /* end of individual */    } /* end h */
     return po;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  /*************** log-likelihood *************/
 }  double func( double *x)
   {
     int i, ii, j, k, mi, d, kk;
 /*********** Maximum Likelihood Estimation ***************/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double sw; /* Sum of weights */
 {    double lli; /* Individual log likelihood */
   int i,j, iter;    int s1, s2;
   double **xi,*delti;    double bbh;
   double fret;    long ipmx;
   xi=matrix(1,npar,1,npar);    /*extern weight */
   for (i=1;i<=npar;i++)    /* We are differentiating ll according to initial status */
     for (j=1;j<=npar;j++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       xi[i][j]=(i==j ? 1.0 : 0.0);    /*for(i=1;i<imx;i++) 
   printf("Powell\n");      printf(" %d\n",s[4][i]);
   powell(p,xi,npar,ftol,&iter,&fret,func);    */
     cov[1]=1.;
    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));    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /**** Computes Hessian and covariance matrix ***/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   double  **a,**y,*x,pd;            for (j=1;j<=nlstate+ndeath;j++){
   double **hess;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j,jk;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int *indx;            }
           for(d=0; d<dh[mi][i]; d++){
   double hessii(double p[], double delta, int theta, double delti[]);            newm=savm;
   double hessij(double p[], double delti[], int i, int j);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   void lubksb(double **a, int npar, int *indx, double b[]) ;            for (kk=1; kk<=cptcovage;kk++) {
   void ludcmp(double **a, int npar, int *indx, double *d) ;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   hess=matrix(1,npar,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\nCalculation of the hessian matrix. Wait...\n");            savm=oldm;
   for (i=1;i<=npar;i++){            oldm=newm;
     printf("%d",i);fflush(stdout);          } /* end mult */
     hess[i][i]=hessii(p,ftolhess,i,delti);        
     /*printf(" %f ",p[i]);*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     /*printf(" %lf ",hess[i][i]);*/          /* But now since version 0.9 we anticipate for bias and large stepm.
   }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
   for (i=1;i<=npar;i++) {           * the nearest (and in case of equal distance, to the lowest) interval but now
     for (j=1;j<=npar;j++)  {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if (j>i) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         printf(".%d%d",i,j);fflush(stdout);           * probability in order to take into account the bias as a fraction of the way
         hess[i][j]=hessij(p,delti,i,j);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         hess[j][i]=hess[i][j];               * -stepm/2 to stepm/2 .
         /*printf(" %lf ",hess[i][j]);*/           * For stepm=1 the results are the same as for previous versions of Imach.
       }           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
   }          s1=s[mw[mi][i]][i];
   printf("\n");          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          /* bias is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   a=matrix(1,npar,1,npar);           */
   y=matrix(1,npar,1,npar);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   x=vector(1,npar);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));  /* linear interpolation */
   indx=ivector(1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (i=1;i<=npar;i++)          /*if(lli ==000.0)*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   ludcmp(a,npar,indx,&pd);          ipmx +=1;
           sw += weight[i];
   for (j=1;j<=npar;j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++) x[i]=0;        } /* end of wave */
     x[j]=1;      } /* end of individual */
     lubksb(a,npar,indx,x);    }  else if(mle==2){
     for (i=1;i<=npar;i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       matcov[i][j]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   printf("\n#Hessian matrix#\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++) {            }
       printf("%.3e ",hess[i][j]);          for(d=0; d<=dh[mi][i]; d++){
     }            newm=savm;
     printf("\n");            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];
   /* Recompute Inverse */            }
   for (i=1;i<=npar;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   ludcmp(a,npar,indx,&pd);            savm=oldm;
             oldm=newm;
   /*  printf("\n#Hessian matrix recomputed#\n");          } /* end mult */
         
   for (j=1;j<=npar;j++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for (i=1;i<=npar;i++) x[i]=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
     x[j]=1;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     lubksb(a,npar,indx,x);           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (i=1;i<=npar;i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
       y[i][j]=x[i];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       printf("%.3e ",y[i][j]);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
     printf("\n");           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   }           * -stepm/2 to stepm/2 .
   */           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   free_matrix(a,1,npar,1,npar);           */
   free_matrix(y,1,npar,1,npar);          s1=s[mw[mi][i]][i];
   free_vector(x,1,npar);          s2=s[mw[mi+1][i]][i];
   free_ivector(indx,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(hess,1,npar,1,npar);          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
 }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 /*************** hessian matrix ****************/          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
 double hessii( double x[], double delta, int theta, double delti[])          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int l=1, lmax=20;          ipmx +=1;
   double k1,k2;          sw += weight[i];
   double p2[NPARMAX+1];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double res;        } /* end of wave */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } /* end of individual */
   double fx;    }  else if(mle==3){  /* exponential inter-extrapolation */
   int k=0,kmax=10;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double l1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   fx=func(x);          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++) p2[i]=x[i];            for (j=1;j<=nlstate+ndeath;j++){
   for(l=0 ; l <=lmax; l++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     l1=pow(10,l);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     delts=delt;            }
     for(k=1 ; k <kmax; k=k+1){          for(d=0; d<dh[mi][i]; d++){
       delt = delta*(l1*k);            newm=savm;
       p2[theta]=x[theta] +delt;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       k1=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
       p2[theta]=x[theta]-delt;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       k2=func(p2)-fx;            }
       /*res= (k1-2.0*fx+k2)/delt/delt; */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
 #ifdef DEBUG            oldm=newm;
       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);          } /* end mult */
 #endif        
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /* But now since version 0.9 we anticipate for bias and large stepm.
         k=kmax;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */           * the nearest (and in case of equal distance, to the lowest) interval but now
         k=kmax; l=lmax*10.;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * probability in order to take into account the bias as a fraction of the way
         delts=delt;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
   delti[theta]=delts;           */
   return res;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 double hessij( double x[], double delti[], int thetai,int thetaj)           * is higher than the multiple of stepm and negative otherwise.
 {           */
   int i;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   int l=1, l1, lmax=20;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double k1,k2,k3,k4,res,fx;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double p2[NPARMAX+1];          /*if(lli ==000.0)*/
   int k;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
   fx=func(x);          sw += weight[i];
   for (k=1; k<=2; k++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<=npar;i++) p2[i]=x[i];        } /* end of wave */
     p2[thetai]=x[thetai]+delti[thetai]/k;      } /* end of individual */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }else{  /* ml=4 no inter-extrapolation */
     k1=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k2=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]-delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k3=func(p2)-fx;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
     p2[thetai]=x[thetai]-delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k4=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            }
 #ifdef DEBUG          
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   return res;            oldm=newm;
 }          } /* end mult */
         
 /************** Inverse of matrix **************/          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 void ludcmp(double **a, int n, int *indx, double *d)          ipmx +=1;
 {          sw += weight[i];
   int i,imax,j,k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double big,dum,sum,temp;        } /* end of wave */
   double *vv;      } /* end of individual */
      } /* End of if */
   vv=vector(1,n);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   *d=1.0;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (i=1;i<=n;i++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     big=0.0;    return -l;
     for (j=1;j<=n;j++)  }
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /*********** Maximum Likelihood Estimation ***************/
   }  
   for (j=1;j<=n;j++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    int i,j, iter;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    double **xi,*delti;
       a[i][j]=sum;    double fret;
     }    xi=matrix(1,npar,1,npar);
     big=0.0;    for (i=1;i<=npar;i++)
     for (i=j;i<=n;i++) {      for (j=1;j<=npar;j++)
       sum=a[i][j];        xi[i][j]=(i==j ? 1.0 : 0.0);
       for (k=1;k<j;k++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         sum -= a[i][k]*a[k][j];    powell(p,xi,npar,ftol,&iter,&fret,func);
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         big=dum;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         imax=i;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
     }  }
     if (j != imax) {  
       for (k=1;k<=n;k++) {  /**** Computes Hessian and covariance matrix ***/
         dum=a[imax][k];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    double  **a,**y,*x,pd;
       }    double **hess;
       *d = -(*d);    int i, j,jk;
       vv[imax]=vv[j];    int *indx;
     }  
     indx[j]=imax;    double hessii(double p[], double delta, int theta, double delti[]);
     if (a[j][j] == 0.0) a[j][j]=TINY;    double hessij(double p[], double delti[], int i, int j);
     if (j != n) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
       dum=1.0/(a[j][j]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    hess=matrix(1,npar,1,npar);
   }  
   free_vector(vv,1,n);  /* Doesn't work */    printf("\nCalculation of the hessian matrix. Wait...\n");
 ;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 }    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
 void lubksb(double **a, int n, int *indx, double b[])      fprintf(ficlog,"%d",i);fflush(ficlog);
 {      hess[i][i]=hessii(p,ftolhess,i,delti);
   int i,ii=0,ip,j;      /*printf(" %f ",p[i]);*/
   double sum;      /*printf(" %lf ",hess[i][i]);*/
      }
   for (i=1;i<=n;i++) {    
     ip=indx[i];    for (i=1;i<=npar;i++) {
     sum=b[ip];      for (j=1;j<=npar;j++)  {
     b[ip]=b[i];        if (j>i) { 
     if (ii)          printf(".%d%d",i,j);fflush(stdout);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     else if (sum) ii=i;          hess[i][j]=hessij(p,delti,i,j);
     b[i]=sum;          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
   for (i=n;i>=1;i--) {        }
     sum=b[i];      }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    }
     b[i]=sum/a[i][i];    printf("\n");
   }    fprintf(ficlog,"\n");
 }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 /************ Frequencies ********************/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    
 {  /* Some frequencies */    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    x=vector(1,npar);
   double ***freq; /* Frequencies */    indx=ivector(1,npar);
   double *pp;    for (i=1;i<=npar;i++)
   double pos, k2, dateintsum=0,k2cpt=0;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   FILE *ficresp;    ludcmp(a,npar,indx,&pd);
   char fileresp[FILENAMELENGTH];  
      for (j=1;j<=npar;j++) {
   pp=vector(1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      x[j]=1;
   strcpy(fileresp,"p");      lubksb(a,npar,indx,x);
   strcat(fileresp,fileres);      for (i=1;i<=npar;i++){ 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        matcov[i][j]=x[i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);      }
     exit(0);    }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    printf("\n#Hessian matrix#\n");
   j1=0;    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   j=cptcoveff;      for (j=1;j<=npar;j++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        printf("%.3e ",hess[i][j]);
          fprintf(ficlog,"%.3e ",hess[i][j]);
   for(k1=1; k1<=j;k1++){      }
     for(i1=1; i1<=ncodemax[k1];i1++){      printf("\n");
       j1++;      fprintf(ficlog,"\n");
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    }
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      /* Recompute Inverse */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for (i=1;i<=npar;i++)
           for(m=agemin; m <= agemax+3; m++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             freq[i][jk][m]=0;    ludcmp(a,npar,indx,&pd);
        
       dateintsum=0;    /*  printf("\n#Hessian matrix recomputed#\n");
       k2cpt=0;  
       for (i=1; i<=imx; i++) {    for (j=1;j<=npar;j++) {
         bool=1;      for (i=1;i<=npar;i++) x[i]=0;
         if  (cptcovn>0) {      x[j]=1;
           for (z1=1; z1<=cptcoveff; z1++)      lubksb(a,npar,indx,x);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (i=1;i<=npar;i++){ 
               bool=0;        y[i][j]=x[i];
         }        printf("%.3e ",y[i][j]);
         if (bool==1) {        fprintf(ficlog,"%.3e ",y[i][j]);
           for(m=firstpass; m<=lastpass; m++){      }
             k2=anint[m][i]+(mint[m][i]/12.);      printf("\n");
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      fprintf(ficlog,"\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }
               if(agev[m][i]==1) agev[m][i]=agemax+2;    */
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    free_matrix(a,1,npar,1,npar);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    free_matrix(y,1,npar,1,npar);
               }    free_vector(x,1,npar);
                  free_ivector(indx,1,npar);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    free_matrix(hess,1,npar,1,npar);
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  
               }  }
             }  
           }  /*************** hessian matrix ****************/
         }  double hessii( double x[], double delta, int theta, double delti[])
       }  {
            int i;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int l=1, lmax=20;
     double k1,k2;
       if  (cptcovn>0) {    double p2[NPARMAX+1];
         fprintf(ficresp, "\n#********** Variable ");    double res;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         fprintf(ficresp, "**********\n#");    double fx;
       }    int k=0,kmax=10;
       for(i=1; i<=nlstate;i++)    double l1;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");    fx=func(x);
          for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for(l=0 ; l <=lmax; l++){
         if(i==(int)agemax+3)      l1=pow(10,l);
           printf("Total");      delts=delt;
         else      for(k=1 ; k <kmax; k=k+1){
           printf("Age %d", i);        delt = delta*(l1*k);
         for(jk=1; jk <=nlstate ; jk++){        p2[theta]=x[theta] +delt;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        k1=func(p2)-fx;
             pp[jk] += freq[jk][m][i];        p2[theta]=x[theta]-delt;
         }        k2=func(p2)-fx;
         for(jk=1; jk <=nlstate ; jk++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
           for(m=-1, pos=0; m <=0 ; m++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             pos += freq[jk][m][i];        
           if(pp[jk]>=1.e-10)  #ifdef DEBUG
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        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);
           else        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);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  #endif
         }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(jk=1; jk <=nlstate ; jk++){          k=kmax;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        }
             pp[jk] += freq[jk][m][i];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
         }
         for(jk=1,pos=0; jk <=nlstate ; jk++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           pos += pp[jk];          delts=delt;
         for(jk=1; jk <=nlstate ; jk++){        }
           if(pos>=1.e-5)      }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    }
           else    delti[theta]=delts;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    return res; 
           if( i <= (int) agemax){    
             if(pos>=1.e-5){  }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;  double hessij( double x[], double delti[], int thetai,int thetaj)
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  {
             }    int i;
             else    int l=1, l1, lmax=20;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double k1,k2,k3,k4,res,fx;
           }    double p2[NPARMAX+1];
         }    int k;
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)    fx=func(x);
           for(m=-1; m <=nlstate+ndeath; m++)    for (k=1; k<=2; k++) {
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for (i=1;i<=npar;i++) p2[i]=x[i];
         if(i <= (int) agemax)      p2[thetai]=x[thetai]+delti[thetai]/k;
           fprintf(ficresp,"\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         printf("\n");      k1=func(p2)-fx;
       }    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   dateintmean=dateintsum/k2cpt;      k2=func(p2)-fx;
      
   fclose(ficresp);      p2[thetai]=x[thetai]-delti[thetai]/k;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   free_vector(pp,1,nlstate);      k3=func(p2)-fx;
      
   /* End of Freq */      p2[thetai]=x[thetai]-delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
 /************ Prevalence ********************/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 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)  #ifdef DEBUG
 {  /* Some frequencies */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #endif
   double ***freq; /* Frequencies */    }
   double *pp;    return res;
   double pos, k2;  }
   
   pp=vector(1,nlstate);  /************** Inverse of matrix **************/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  void ludcmp(double **a, int n, int *indx, double *d) 
    { 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int i,imax,j,k; 
   j1=0;    double big,dum,sum,temp; 
      double *vv; 
   j=cptcoveff;   
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    vv=vector(1,n); 
      *d=1.0; 
  for(k1=1; k1<=j;k1++){    for (i=1;i<=n;i++) { 
     for(i1=1; i1<=ncodemax[k1];i1++){      big=0.0; 
       j1++;      for (j=1;j<=n;j++) 
          if ((temp=fabs(a[i][j])) > big) big=temp; 
       for (i=-1; i<=nlstate+ndeath; i++)        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        vv[i]=1.0/big; 
           for(m=agemin; m <= agemax+3; m++)    } 
             freq[i][jk][m]=0;    for (j=1;j<=n;j++) { 
            for (i=1;i<j;i++) { 
       for (i=1; i<=imx; i++) {        sum=a[i][j]; 
         bool=1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         if  (cptcovn>0) {        a[i][j]=sum; 
           for (z1=1; z1<=cptcoveff; z1++)      } 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      big=0.0; 
               bool=0;      for (i=j;i<=n;i++) { 
         }        sum=a[i][j]; 
         if (bool==1) {        for (k=1;k<j;k++) 
           for(m=firstpass; m<=lastpass; m++){          sum -= a[i][k]*a[k][j]; 
             k2=anint[m][i]+(mint[m][i]/12.);        a[i][j]=sum; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;          big=dum; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          imax=i; 
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        } 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */      } 
             }      if (j != imax) { 
           }        for (k=1;k<=n;k++) { 
         }          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
         for(i=(int)agemin; i <= (int)agemax+3; i++){          a[j][k]=dum; 
           for(jk=1; jk <=nlstate ; jk++){        } 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        *d = -(*d); 
               pp[jk] += freq[jk][m][i];        vv[imax]=vv[j]; 
           }      } 
           for(jk=1; jk <=nlstate ; jk++){      indx[j]=imax; 
             for(m=-1, pos=0; m <=0 ; m++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
             pos += freq[jk][m][i];      if (j != n) { 
         }        dum=1.0/(a[j][j]); 
                for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          for(jk=1; jk <=nlstate ; jk++){      } 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } 
              pp[jk] += freq[jk][m][i];    free_vector(vv,1,n);  /* Doesn't work */
          }  ;
            } 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
   void lubksb(double **a, int n, int *indx, double b[]) 
          for(jk=1; jk <=nlstate ; jk++){            { 
            if( i <= (int) agemax){    int i,ii=0,ip,j; 
              if(pos>=1.e-5){    double sum; 
                probs[i][jk][j1]= pp[jk]/pos;   
              }    for (i=1;i<=n;i++) { 
            }      ip=indx[i]; 
          }      sum=b[ip]; 
                b[ip]=b[i]; 
         }      if (ii) 
     }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   }      else if (sum) ii=i; 
        b[i]=sum; 
      } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for (i=n;i>=1;i--) { 
   free_vector(pp,1,nlstate);      sum=b[i]; 
        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 }  /* End of Freq */      b[i]=sum/a[i][i]; 
     } 
 /************* Waves Concatenation ***************/  } 
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  /************ Frequencies ********************/
 {  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  {  /* Some frequencies */
      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    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int first;
      and mw[mi+1][i]. dh depends on stepm.    double ***freq; /* Frequencies */
      */    double *pp;
     double pos, k2, dateintsum=0,k2cpt=0;
   int i, mi, m;    FILE *ficresp;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    char fileresp[FILENAMELENGTH];
      double sum=0., jmean=0.;*/    
     pp=vector(1,nlstate);
   int j, k=0,jk, ju, jl;    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   double sum=0.;    strcpy(fileresp,"p");
   jmin=1e+5;    strcat(fileresp,fileres);
   jmax=-1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   jmean=0.;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   for(i=1; i<=imx; i++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     mi=0;      exit(0);
     m=firstpass;    }
     while(s[m][i] <= nlstate){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
       if(s[m][i]>=1)    j1=0;
         mw[++mi][i]=m;    
       if(m >=lastpass)    j=cptcoveff;
         break;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       else  
         m++;    first=1;
     }/* end while */  
     if (s[m][i] > nlstate){    for(k1=1; k1<=j;k1++){
       mi++;     /* Death is another wave */      for(i1=1; i1<=ncodemax[k1];i1++){
       /* if(mi==0)  never been interviewed correctly before death */        j1++;
          /* Only death is a correct wave */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       mw[mi][i]=m;          scanf("%d", i);*/
     }        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
     wav[i]=mi;            for(m=agemin; m <= agemax+3; m++)
     if(mi==0)              freq[i][jk][m]=0;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        
   }        dateintsum=0;
         k2cpt=0;
   for(i=1; i<=imx; i++){        for (i=1; i<=imx; i++) {
     for(mi=1; mi<wav[i];mi++){          bool=1;
       if (stepm <=0)          if  (cptcovn>0) {
         dh[mi][i]=1;            for (z1=1; z1<=cptcoveff; z1++) 
       else{              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         if (s[mw[mi+1][i]][i] > nlstate) {                bool=0;
           if (agedc[i] < 2*AGESUP) {          }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          if (bool==1){
           if(j==0) j=1;  /* Survives at least one month after exam */            for(m=firstpass; m<=lastpass; m++){
           k=k+1;              k2=anint[m][i]+(mint[m][i]/12.);
           if (j >= jmax) jmax=j;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
           if (j <= jmin) jmin=j;                if(agev[m][i]==0) agev[m][i]=agemax+1;
           sum=sum+j;                if(agev[m][i]==1) agev[m][i]=agemax+2;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                if (m<lastpass) {
           }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         }                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
         else{                }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                
           k=k+1;                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           if (j >= jmax) jmax=j;                  dateintsum=dateintsum+k2;
           else if (j <= jmin)jmin=j;                  k2cpt++;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                }
           sum=sum+j;              }
         }            }
         jk= j/stepm;          }
         jl= j -jk*stepm;        }
         ju= j -(jk+1)*stepm;         
         if(jl <= -ju)        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
           dh[mi][i]=jk;  
         else        if  (cptcovn>0) {
           dh[mi][i]=jk+1;          fprintf(ficresp, "\n#********** Variable "); 
         if(dh[mi][i]==0)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           dh[mi][i]=1; /* At least one step */          fprintf(ficresp, "**********\n#");
       }        }
     }        for(i=1; i<=nlstate;i++) 
   }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   jmean=sum/k;        fprintf(ficresp, "\n");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        
  }        for(i=(int)agemin; i <= (int)agemax+3; i++){
 /*********** Tricode ****************************/          if(i==(int)agemax+3){
 void tricode(int *Tvar, int **nbcode, int imx)            fprintf(ficlog,"Total");
 {          }else{
   int Ndum[20],ij=1, k, j, i;            if(first==1){
   int cptcode=0;              first=0;
   cptcoveff=0;              printf("See log file for details...\n");
              }
   for (k=0; k<19; k++) Ndum[k]=0;            fprintf(ficlog,"Age %d", i);
   for (k=1; k<=7; k++) ncodemax[k]=0;          }
           for(jk=1; jk <=nlstate ; jk++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for (i=1; i<=imx; i++) {              pp[jk] += freq[jk][m][i]; 
       ij=(int)(covar[Tvar[j]][i]);          }
       Ndum[ij]++;          for(jk=1; jk <=nlstate ; jk++){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            for(m=-1, pos=0; m <=0 ; m++)
       if (ij > cptcode) cptcode=ij;              pos += freq[jk][m][i];
     }            if(pp[jk]>=1.e-10){
               if(first==1){
     for (i=0; i<=cptcode; i++) {              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       if(Ndum[i]!=0) ncodemax[j]++;              }
     }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     ij=1;            }else{
               if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for (i=1; i<=ncodemax[j]; i++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for (k=0; k<=19; k++) {            }
         if (Ndum[k] != 0) {          }
           nbcode[Tvar[j]][ij]=k;  
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/          for(jk=1; jk <=nlstate ; jk++){
           ij++;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         }              pp[jk] += freq[jk][m][i];
         if (ij > ncodemax[j]) break;          }
       }    
     }          for(jk=1,pos=0; jk <=nlstate ; jk++)
   }              pos += pp[jk];
           for(jk=1; jk <=nlstate ; jk++){
  for (k=0; k<19; k++) Ndum[k]=0;            if(pos>=1.e-5){
               if(first==1)
  for (i=1; i<=ncovmodel-2; i++) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       ij=Tvar[i];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       Ndum[ij]++;            }else{
     }              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  ij=1;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  for (i=1; i<=10; i++) {            }
    if((Ndum[i]!=0) && (i<=ncovcol)){            if( i <= (int) agemax){
      Tvaraff[ij]=i;              if(pos>=1.e-5){
      ij++;                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]);*/
                }
     cptcoveff=ij-1;              else
 }                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
             }
 /*********** Health Expectancies ****************/          }
           
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)          for(jk=-1; jk <=nlstate+ndeath; jk++)
 {            for(m=-1; m <=nlstate+ndeath; m++)
   /* Health expectancies */              if(freq[jk][m][i] !=0 ) {
   int i, j, nhstepm, hstepm, h, nstepm;              if(first==1)
   double age, agelim, hf;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double ***p3mat;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
   fprintf(ficreseij,"# Health expectancies\n");          if(i <= (int) agemax)
   fprintf(ficreseij,"# Age");            fprintf(ficresp,"\n");
   for(i=1; i<=nlstate;i++)          if(first==1)
     for(j=1; j<=nlstate;j++)            printf("Others in log...\n");
       fprintf(ficreseij," %1d-%1d",i,j);          fprintf(ficlog,"\n");
   fprintf(ficreseij,"\n");        }
       }
   if(estepm < stepm){    }
     printf ("Problem %d lower than %d\n",estepm, stepm);    dateintmean=dateintsum/k2cpt; 
   }   
   else  hstepm=estepm;      fclose(ficresp);
   /* We compute the life expectancy from trapezoids spaced every estepm months    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
    * This is mainly to measure the difference between two models: for example    free_vector(pp,1,nlstate);
    * if stepm=24 months pijx are given only every 2 years and by summing them    
    * we are calculating an estimate of the Life Expectancy assuming a linear    /* End of Freq */
    * progression inbetween and thus overestimating or underestimating according  }
    * 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  /************ Prevalence ********************/
    * to compare the new estimate of Life expectancy with the same linear  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)
    * hypothesis. A more precise result, taking into account a more precise  {  /* Some frequencies */
    * curvature will be obtained if estepm is as small as stepm. */   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   /* For example we decided to compute the life expectancy with the smallest unit */    double ***freq; /* Frequencies */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double *pp;
      nhstepm is the number of hstepm from age to agelim    double pos, k2;
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size    pp=vector(1,nlstate);
      and note for a fixed period like estepm months */    
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
      survival function given by stepm (the optimization length). Unfortunately it    j1=0;
      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    j=cptcoveff;
      results. So we changed our mind and took the option of the best precision.    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   */    
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   agelim=AGESUP;        j1++;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     /* nhstepm age range expressed in number of stepm */        for (i=-1; i<=nlstate+ndeath; i++)  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            for(m=agemin; m <= agemax+3; m++)
     /* if (stepm >= YEARM) hstepm=1;*/              freq[i][jk][m]=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<=imx; i++) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          bool=1;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          if  (cptcovn>0) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              for (z1=1; z1<=cptcoveff; z1++) 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(i=1; i<=nlstate;i++)                bool=0;
       for(j=1; j<=nlstate;j++)          } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          if (bool==1) { 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            for(m=firstpass; m<=lastpass; m++){
           /* 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]);*/              k2=anint[m][i]+(mint[m][i]/12.);
         }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     fprintf(ficreseij,"%3.0f",age );                if(agev[m][i]==0) agev[m][i]=agemax+1;
     for(i=1; i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=agemax+2;
       for(j=1; j<=nlstate;j++){                if (m<lastpass) {
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);                  if (calagedate>0) 
       }                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
     fprintf(ficreseij,"\n");                  else
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    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]; 
 }                }
               }
 /************ 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=(int)agemin; i <= (int)agemax+3; i++){ 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(jk=1; jk <=nlstate ; jk++){
   double **newm;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   double **dnewm,**doldm;              pp[jk] += freq[jk][m][i]; 
   int i, j, nhstepm, hstepm, h, nstepm ;          }
   int k, cptcode;          for(jk=1; jk <=nlstate ; jk++){
   double *xp;            for(m=-1, pos=0; m <=0 ; m++)
   double **gp, **gm;              pos += freq[jk][m][i];
   double ***gradg, ***trgradg;          }
   double ***p3mat;          
   double age,agelim, hf;          for(jk=1; jk <=nlstate ; jk++){
   int theta;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");          }
   fprintf(ficresvij,"# Age");          
   for(i=1; i<=nlstate;i++)          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
     for(j=1; j<=nlstate;j++)          
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for(jk=1; jk <=nlstate ; jk++){    
   fprintf(ficresvij,"\n");            if( i <= (int) agemax){
               if(pos>=1.e-5){
   xp=vector(1,npar);                probs[i][jk][j1]= pp[jk]/pos;
   dnewm=matrix(1,nlstate,1,npar);              }
   doldm=matrix(1,nlstate,1,nlstate);            }
            }/* end jk */
   if(estepm < stepm){        }/* end i */
     printf ("Problem %d lower than %d\n",estepm, stepm);      } /* end i1 */
   }    } /* end k1 */
   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.    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
      nhstepm is the number of hstepm from age to agelim    free_vector(pp,1,nlstate);
      nstepm is the number of stepm from age to agelin.    
      Look at hpijx to understand the reason of that which relies in memory size  }  /* End of Freq */
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  /************* Waves Concatenation ***************/
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  {
      results. So we changed our mind and took the option of the best precision.    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   */       Death is a valid wave (if date is known).
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   agelim = AGESUP;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       and mw[mi+1][i]. dh depends on stepm.
     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 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, mi, m;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     gp=matrix(0,nhstepm,1,nlstate);       double sum=0., jmean=0.;*/
     gm=matrix(0,nhstepm,1,nlstate);    int first;
     int j, k=0,jk, ju, jl;
     for(theta=1; theta <=npar; theta++){    double sum=0.;
       for(i=1; i<=npar; i++){ /* Computes gradient */    first=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    jmin=1e+5;
       }    jmax=-1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      jmean=0.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(i=1; i<=imx; i++){
       mi=0;
       if (popbased==1) {      m=firstpass;
         for(i=1; i<=nlstate;i++)      while(s[m][i] <= nlstate){
           prlim[i][i]=probs[(int)age][i][ij];        if(s[m][i]>=1)
       }          mw[++mi][i]=m;
          if(m >=lastpass)
       for(j=1; j<= nlstate; j++){          break;
         for(h=0; h<=nhstepm; h++){        else
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          m++;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      }/* end while */
         }      if (s[m][i] > nlstate){
       }        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
       for(i=1; i<=npar; i++) /* Computes gradient */           /* Only death is a correct wave */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        mw[mi][i]=m;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
        wav[i]=mi;
       if (popbased==1) {      if(mi==0){
         for(i=1; i<=nlstate;i++)        if(first==0){
           prlim[i][i]=probs[(int)age][i][ij];          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
       }          first=1;
         }
       for(j=1; j<= nlstate; j++){        if(first==1){
         for(h=0; h<=nhstepm; h++){          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      } /* end mi==0 */
         }    }
       }  
     for(i=1; i<=imx; i++){
       for(j=1; j<= nlstate; j++)      for(mi=1; mi<wav[i];mi++){
         for(h=0; h<=nhstepm; h++){        if (stepm <=0)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          dh[mi][i]=1;
         }        else{
     } /* End theta */          if (s[mw[mi+1][i]][i] > nlstate) {
             if (agedc[i] < 2*AGESUP) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */
     for(h=0; h<=nhstepm; h++)            k=k+1;
       for(j=1; j<=nlstate;j++)            if (j >= jmax) jmax=j;
         for(theta=1; theta <=npar; theta++)            if (j <= jmin) jmin=j;
           trgradg[h][j][theta]=gradg[h][theta][j];            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            }
     for(i=1;i<=nlstate;i++)          }
       for(j=1;j<=nlstate;j++)          else{
         vareij[i][j][(int)age] =0.;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             k=k+1;
     for(h=0;h<=nhstepm;h++){            if (j >= jmax) jmax=j;
       for(k=0;k<=nhstepm;k++){            else if (j <= jmin)jmin=j;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            sum=sum+j;
         for(i=1;i<=nlstate;i++)          }
           for(j=1;j<=nlstate;j++)          jk= j/stepm;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          jl= j -jk*stepm;
       }          ju= j -(jk+1)*stepm;
     }          if(mle <=1){ 
             if(jl==0){
     fprintf(ficresvij,"%.0f ",age );              dh[mi][i]=jk;
     for(i=1; i<=nlstate;i++)              bh[mi][i]=0;
       for(j=1; j<=nlstate;j++){            }else{ /* We want a negative bias in order to only have interpolation ie
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);                    * at the price of an extra matrix product in likelihood */
       }              dh[mi][i]=jk+1;
     fprintf(ficresvij,"\n");              bh[mi][i]=ju;
     free_matrix(gp,0,nhstepm,1,nlstate);            }
     free_matrix(gm,0,nhstepm,1,nlstate);          }else{
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            if(jl <= -ju){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              dh[mi][i]=jk;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              bh[mi][i]=jl;       /* bias is positive if real duration
   } /* End age */                                   * is higher than the multiple of stepm and negative otherwise.
                                     */
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);            else{
   free_matrix(dnewm,1,nlstate,1,nlstate);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
 }            }
             if(dh[mi][i]==0){
 /************ Variance of prevlim ******************/              dh[mi][i]=1; /* At least one step */
 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)              bh[mi][i]=ju; /* At least one step */
 {              printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
   /* Variance of prevalence limit */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);
   double **newm;          }
   double **dnewm,**doldm;        } /* end if mle */
   int i, j, nhstepm, hstepm;      } /* end wave */
   int k, cptcode;    }
   double *xp;    jmean=sum/k;
   double *gp, *gm;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double **gradg, **trgradg;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double age,agelim;   }
   int theta;  
      /*********** Tricode ****************************/
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  void tricode(int *Tvar, int **nbcode, int imx)
   fprintf(ficresvpl,"# Age");  {
   for(i=1; i<=nlstate;i++)    
       fprintf(ficresvpl," %1d-%1d",i,i);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficresvpl,"\n");    int cptcode=0;
     cptcoveff=0; 
   xp=vector(1,npar);   
   dnewm=matrix(1,nlstate,1,npar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   doldm=matrix(1,nlstate,1,nlstate);    for (k=1; k<=7; k++) ncodemax[k]=0;
    
   hstepm=1*YEARM; /* Every year of age */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   agelim = AGESUP;                                 modality*/ 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        Ndum[ij]++; /*store the modality */
     if (stepm >= YEARM) hstepm=1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     gradg=matrix(1,npar,1,nlstate);                                         Tvar[j]. If V=sex and male is 0 and 
     gp=vector(1,nlstate);                                         female is 1, then  cptcode=1.*/
     gm=vector(1,nlstate);      }
   
     for(theta=1; theta <=npar; theta++){      for (i=0; i<=cptcode; i++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      ij=1; 
       for(i=1;i<=nlstate;i++)      for (i=1; i<=ncodemax[j]; i++) {
         gp[i] = prlim[i][i];        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
       for(i=1; i<=npar; i++) /* Computes gradient */            nbcode[Tvar[j]][ij]=k; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            
       for(i=1;i<=nlstate;i++)            ij++;
         gm[i] = prlim[i][i];          }
           if (ij > ncodemax[j]) break; 
       for(i=1;i<=nlstate;i++)        }  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      } 
     } /* End theta */    }  
   
     trgradg =matrix(1,nlstate,1,npar);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
     for(j=1; j<=nlstate;j++)   for (i=1; i<=ncovmodel-2; i++) { 
       for(theta=1; theta <=npar; theta++)     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         trgradg[j][theta]=gradg[theta][j];     ij=Tvar[i];
      Ndum[ij]++;
     for(i=1;i<=nlstate;i++)   }
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);   ij=1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);   for (i=1; i<= maxncov; i++) {
     for(i=1;i<=nlstate;i++)     if((Ndum[i]!=0) && (i<=ncovcol)){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       Tvaraff[ij]=i; /*For printing */
        ij++;
     fprintf(ficresvpl,"%.0f ",age );     }
     for(i=1; i<=nlstate;i++)   }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));   
     fprintf(ficresvpl,"\n");   cptcoveff=ij-1; /*Number of simple covariates*/
     free_vector(gp,1,nlstate);  }
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);  /*********** Health Expectancies ****************/
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  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 )
   
   free_vector(xp,1,npar);  {
   free_matrix(doldm,1,nlstate,1,npar);    /* Health expectancies */
   free_matrix(dnewm,1,nlstate,1,nlstate);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
 }    double ***p3mat,***varhe;
     double **dnewm,**doldm;
 /************ Variance of one-step probabilities  ******************/    double *xp;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double **gp, **gm;
 {    double ***gradg, ***trgradg;
   int i, j;    int theta;
   int k=0, cptcode;  
   double **dnewm,**doldm;    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
   double *xp;    xp=vector(1,npar);
   double *gp, *gm;    dnewm=matrix(1,nlstate*2,1,npar);
   double **gradg, **trgradg;    doldm=matrix(1,nlstate*2,1,nlstate*2);
   double age,agelim, cov[NCOVMAX];    
   int theta;    fprintf(ficreseij,"# Health expectancies\n");
   char fileresprob[FILENAMELENGTH];    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
   strcpy(fileresprob,"prob");      for(j=1; j<=nlstate;j++)
   strcat(fileresprob,fileres);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    fprintf(ficreseij,"\n");
     printf("Problem with resultfile: %s\n", fileresprob);  
   }    if(estepm < stepm){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
     else  hstepm=estepm;   
   xp=vector(1,npar);    /* We compute the life expectancy from trapezoids spaced every estepm months
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);     * This is mainly to measure the difference between two models: for example
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));     * if stepm=24 months pijx are given only every 2 years and by summing them
       * we are calculating an estimate of the Life Expectancy assuming a linear 
   cov[1]=1;     * progression in between and thus overestimating or underestimating according
   for (age=bage; age<=fage; age ++){     * to the curvature of the survival function. If, for the same date, we 
     cov[2]=age;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     gradg=matrix(1,npar,1,9);     * to compare the new estimate of Life expectancy with the same linear 
     trgradg=matrix(1,9,1,npar);     * hypothesis. A more precise result, taking into account a more precise
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));     * curvature will be obtained if estepm is as small as stepm. */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
        /* For example we decided to compute the life expectancy with the smallest unit */
     for(theta=1; theta <=npar; theta++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(i=1; i<=npar; i++)       nhstepm is the number of hstepm from age to agelim 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       nstepm is the number of stepm from age to agelin. 
             Look at hpijx to understand the reason of that which relies in memory size
       pmij(pmmij,cov,ncovmodel,xp,nlstate);       and note for a fixed period like estepm months */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       k=0;       survival function given by stepm (the optimization length). Unfortunately it
       for(i=1; i<= (nlstate+ndeath); i++){       means that if the survival funtion is printed only each two years of age and if
         for(j=1; j<=(nlstate+ndeath);j++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
            k=k+1;       results. So we changed our mind and took the option of the best precision.
           gp[k]=pmmij[i][j];    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }  
     agelim=AGESUP;
       for(i=1; i<=npar; i++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* 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 */ 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      /* if (stepm >= YEARM) hstepm=1;*/
       k=0;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(i=1; i<=(nlstate+ndeath); i++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1; j<=(nlstate+ndeath);j++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
           k=k+1;      gp=matrix(0,nhstepm,1,nlstate*2);
           gm[k]=pmmij[i][j];      gm=matrix(0,nhstepm,1,nlstate*2);
         }  
       }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
               in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];     
     }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)      /* Computing Variances of health expectancies */
       trgradg[j][theta]=gradg[theta][j];  
         for(theta=1; theta <=npar; theta++){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for(i=1; i<=npar; i++){ 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
      pmij(pmmij,cov,ncovmodel,x,nlstate);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     
      k=0;        cptj=0;
      for(i=1; i<=(nlstate+ndeath); i++){        for(j=1; j<= nlstate; j++){
        for(j=1; j<=(nlstate+ndeath);j++){          for(i=1; i<=nlstate; i++){
          k=k+1;            cptj=cptj+1;
          gm[k]=pmmij[i][j];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
      }            }
                }
      /*printf("\n%d ",(int)age);        }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       
               
         for(i=1; i<=npar; i++) 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      }*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
   fprintf(ficresprob,"\n%d ",(int)age);        cptj=0;
         for(j=1; j<= nlstate; j++){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for(i=1;i<=nlstate;i++){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            cptj=cptj+1;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(j=1; j<= nlstate*2; j++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(h=0; h<=nhstepm-1; h++){
 }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  free_vector(xp,1,npar);          }
 fclose(ficresprob);       } 
      
 }  /* End theta */
   
 /******************* Printing html file ***********/       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
  int lastpass, int stepm, int weightopt, char model[],\       for(h=0; h<=nhstepm-1; h++)
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        for(j=1; j<=nlstate*2;j++)
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\          for(theta=1; theta <=npar; theta++)
  char version[], int popforecast, int estepm ){            trgradg[h][j][theta]=gradg[h][theta][j];
   int jj1, k1, i1, cpt;       
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/       for(i=1;i<=nlstate*2;i++)
         for(j=1;j<=nlstate*2;j++)
   strcpy(optionfilehtm,optionfile);          varhe[i][j][(int)age] =0.;
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       printf("%d|",(int)age);fflush(stdout);
     printf("Problem with %s \n",optionfilehtm), exit(0);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
 \n          for(i=1;i<=nlstate*2;i++)
 Total number of observations=%d <br>\n            for(j=1;j<=nlstate*2;j++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 <hr  size=\"2\" color=\"#EC5E5E\">        }
  <ul><li>Outputs files<br>\n      }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      /* Computing expectancies */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n      for(i=1; i<=nlstate;i++)
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        for(j=1; j<=nlstate;j++)
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);            
   /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
  fprintf(fichtm,"\n  
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n          }
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      fprintf(ficreseij,"%3.0f",age );
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      cptj=0;
       for(i=1; i<=nlstate;i++)
  if(popforecast==1) fprintf(fichtm,"\n        for(j=1; j<=nlstate;j++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          cptj++;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         <br>",fileres,fileres,fileres,fileres);        }
  else      fprintf(ficreseij,"\n");
    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," <li>Graphs</li><p>");      free_matrix(gm,0,nhstepm,1,nlstate*2);
       free_matrix(gp,0,nhstepm,1,nlstate*2);
  m=cptcoveff;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  jj1=0;    }
  for(k1=1; k1<=m;k1++){    printf("\n");
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficlog,"\n");
        jj1++;  
        if (cptcovn > 0) {    free_vector(xp,1,npar);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    free_matrix(dnewm,1,nlstate*2,1,npar);
          for (cpt=1; cpt<=cptcoveff;cpt++)    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  }
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  /************ Variance ******************/
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      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(cpt=1; cpt<nlstate;cpt++){  {
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    /* Variance of health expectancies */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        }    /* double **newm;*/
     for(cpt=1; cpt<=nlstate;cpt++) {    double **dnewm,**doldm;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double **dnewmp,**doldmp;
 interval) in state (%d): v%s%d%d.gif <br>    int i, j, nhstepm, hstepm, h, nstepm ;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      int k, cptcode;
      }    double *xp;
      for(cpt=1; cpt<=nlstate;cpt++) {    double **gp, **gm;  /* for var eij */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    double ***gradg, ***trgradg; /*for var eij */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double **gradgp, **trgradgp; /* for var p point j */
      }    double *gpp, *gmp; /* for var p point j */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
 health expectancies in states (1) and (2): e%s%d.gif<br>    double ***p3mat;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    double age,agelim, hf;
 fprintf(fichtm,"\n</body>");    double ***mobaverage;
    }    int theta;
    }    char digit[4];
 fclose(fichtm);    char digitp[25];
 }  
     char fileresprobmorprev[FILENAMELENGTH];
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    if(popbased==1){
       if(mobilav!=0)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   strcpy(optionfilegnuplot,optionfilefiname);    }
   strcat(optionfilegnuplot,".gp.txt");    else 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      strcpy(digitp,"-stablbased-");
     printf("Problem with file %s",optionfilegnuplot);  
   }    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #ifdef windows      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     fprintf(ficgp,"cd \"%s\" \n",pathc);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 #endif        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 m=pow(2,cptcoveff);      }
      }
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {    strcpy(fileresprobmorprev,"prmorprev"); 
    for (k1=1; k1<= m ; k1 ++) {    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 #ifdef windows    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 #endif    strcat(fileresprobmorprev,fileres);
 #ifdef unix    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
 #endif      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
 for (i=1; i<= nlstate ; i ++) {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
 }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     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=nlstate+1; j<=(nlstate+ndeath);j++){
     for (i=1; i<= nlstate ; i ++) {      fprintf(ficresprobmorprev," p.%-d SE",j);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 }    }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresprobmorprev,"\n");
      for (i=1; i<= nlstate ; i ++) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 }        exit(0);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    }
 #ifdef unix    else{
 fprintf(ficgp,"\nset ter gif small size 400,300");      fprintf(ficgp,"\n# Routine varevsij");
 #endif    }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    }      printf("Problem with html file: %s\n", optionfilehtm);
   }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   /*2 eme*/      exit(0);
     }
   for (k1=1; k1<= m ; k1 ++) {    else{
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
          fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
     for (i=1; i<= nlstate+1 ; i ++) {    }
       k=2*i;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    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");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresvij,"# Age");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=nlstate;j++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficresvij,"\n");
     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 ++) {    xp=vector(1,npar);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    dnewm=matrix(1,nlstate,1,npar);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    doldm=matrix(1,nlstate,1,nlstate);
 }      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       fprintf(ficgp,"\" t\"\" w l 0,");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      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 ++) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    gpp=vector(nlstate+1,nlstate+ndeath);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    gmp=vector(nlstate+1,nlstate+ndeath);
 }      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    
       else fprintf(ficgp,"\" t\"\" w l 0,");    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    }
   }    else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
   /*3eme*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   for (k1=1; k1<= m ; k1 ++) {       nstepm is the number of stepm from age to agelin. 
     for (cpt=1; cpt<= nlstate ; cpt ++) {       Look at hpijx to understand the reason of that which relies in memory size
       k=2+nlstate*(cpt-1);       and note for a fixed period like k years */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for (i=1; i< nlstate ; i ++) {       survival function given by stepm (the optimization length). Unfortunately it
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);       means that if the survival funtion is printed every two years of age and if
       }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       results. So we changed our mind and took the option of the best precision.
     }    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
   /* CV preval stat */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for (k1=1; k1<= m ; k1 ++) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for (cpt=1; cpt<nlstate ; cpt ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       k=3;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       for (i=1; i< nlstate ; i ++)      gm=matrix(0,nhstepm,1,nlstate);
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
            for(theta=1; theta <=npar; theta++){
       l=3+(nlstate+ndeath)*cpt;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (i=1; i< nlstate ; i ++) {        }
         l=3+(nlstate+ndeath)*cpt;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficgp,"+$%d",l+i+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          if (popbased==1) {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          if(mobilav ==0){
     }            for(i=1; i<=nlstate;i++)
   }                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   /* proba elementaires */            for(i=1; i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){              prlim[i][i]=mobaverage[(int)age][i][ij];
     for(k=1; k <=(nlstate+ndeath); k++){          }
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){    
                for(j=1; j<= nlstate; j++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          for(h=0; h<=nhstepm; h++){
           jk++;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           fprintf(ficgp,"\n");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
     }        /* This for computing probability of death (h=1 means
     }           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
     for(jk=1; jk <=m; jk++) {        */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
    i=1;          for(i=1; i<= nlstate; i++)
    for(k2=1; k2<=nlstate; k2++) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
      k3=i;        }    
      for(k=1; k<=(nlstate+ndeath); k++) {        /* end probability of death */
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 ij=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for(j=3; j <=ncovmodel; j++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);   
             ij++;        if (popbased==1) {
           }          if(mobilav ==0){
           else            for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              prlim[i][i]=probs[(int)age][i][ij];
         }          }else{ /* mobilav */ 
           fprintf(ficgp,")/(1");            for(i=1; i<=nlstate;i++)
                      prlim[i][i]=mobaverage[(int)age][i][ij];
         for(k1=1; k1 <=nlstate; k1++){            }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        }
 ij=1;  
           for(j=3; j <=ncovmodel; j++){        for(j=1; j<= nlstate; j++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for(h=0; h<=nhstepm; h++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             ij++;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }          }
           else        }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        /* This for computing probability of death (h=1 means
           }           computed over hstepm matrices product = hstepm*stepm months) 
           fprintf(ficgp,")");           as a weighted average of prlim.
         }        */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for(i=1; i<= nlstate; i++)
         i=i+ncovmodel;            gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }        }    
      }        /* end probability of death */
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        for(j=1; j<= nlstate; j++) /* vareij */
    }          for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   fclose(ficgp);          }
 }  /* end gnuplot */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      } /* End theta */
   
   int i, cpt, cptcod;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)      for(h=0; h<=nhstepm; h++) /* veij */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        for(j=1; j<=nlstate;j++)
           mobaverage[(int)agedeb][i][cptcod]=0.;          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(theta=1; theta <=npar; theta++)
           for (cpt=0;cpt<=4;cpt++){          trgradgp[j][theta]=gradgp[theta][j];
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      for(i=1;i<=nlstate;i++)
         }        for(j=1;j<=nlstate;j++)
       }          vareij[i][j][(int)age] =0.;
     }  
          for(h=0;h<=nhstepm;h++){
 }        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 /************** Forecasting ******************/          for(i=1;i<=nlstate;i++)
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;      }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;      /* pptj */
   double ***p3mat;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   char fileresf[FILENAMELENGTH];      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
  agelim=AGESUP;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      /*  x centered again */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   strcpy(fileresf,"f");   
   strcat(fileresf,fileres);      if (popbased==1) {
   if((ficresf=fopen(fileresf,"w"))==NULL) {        if(mobilav ==0){
     printf("Problem with forecast resultfile: %s\n", fileresf);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=probs[(int)age][i][ij];
   printf("Computing forecasting: result on file '%s' \n", fileresf);        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
   if (mobilav==1) {      }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      
     movingaverage(agedeb, fage, ageminpar, mobaverage);      /* This for computing probability of death (h=1 means
   }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
   stepsize=(int) (stepm+YEARM-1)/YEARM;      */
   if (stepm<=12) stepsize=1;      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
          for(i=1; i<= nlstate; i++)
   agelim=AGESUP;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
   hstepm=1;      /* end probability of death */
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   anprojmean=yp;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   yp2=modf((yp1*12),&yp);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   mprojmean=yp;        for(i=1; i<=nlstate;i++){
   yp1=modf((yp2*30.5),&yp);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   jprojmean=yp;        }
   if(jprojmean==0) jprojmean=1;      } 
   if(mprojmean==0) jprojmean=1;      fprintf(ficresprobmorprev,"\n");
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i2;cptcov++){        for(j=1; j<=nlstate;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       k=k+1;        }
       fprintf(ficresf,"\n#******");      fprintf(ficresvij,"\n");
       for(j=1;j<=cptcoveff;j++) {      free_matrix(gp,0,nhstepm,1,nlstate);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      free_matrix(gm,0,nhstepm,1,nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficresf,"******\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       fprintf(ficresf,"# StartingAge FinalAge");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    } /* End age */
          free_vector(gpp,nlstate+1,nlstate+ndeath);
          free_vector(gmp,nlstate+1,nlstate+ndeath);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficresf,"\n");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
           nhstepm = nhstepm/hstepm;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
              fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
           oldm=oldms;savm=savms;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", estepm,digitp,digit);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*  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);
          */
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    free_vector(xp,1,npar);
             }    free_matrix(doldm,1,nlstate,1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {    free_matrix(dnewm,1,nlstate,1,npar);
               kk1=0.;kk2=0;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               for(i=1; i<=nlstate;i++) {                  free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                 if (mobilav==1)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 else {    fclose(ficresprobmorprev);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fclose(ficgp);
                 }    fclose(fichtm);
                  }
               }  
               if (h==(int)(calagedate+12*cpt)){  /************ Variance of prevlim ******************/
                 fprintf(ficresf," %.3f", kk1);  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)
                          {
               }    /* Variance of prevalence limit */
             }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           }    double **newm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
       }    int k, cptcode;
     }    double *xp;
   }    double *gp, *gm;
            double **gradg, **trgradg;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age,agelim;
     int theta;
   fclose(ficresf);     
 }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
 /************** Forecasting ******************/    fprintf(ficresvpl,"# Age");
 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){    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(ficresvpl,"\n");
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    xp=vector(1,npar);
   double *popeffectif,*popcount;    dnewm=matrix(1,nlstate,1,npar);
   double ***p3mat,***tabpop,***tabpopprev;    doldm=matrix(1,nlstate,1,nlstate);
   char filerespop[FILENAMELENGTH];    
     hstepm=1*YEARM; /* Every year of age */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    agelim = AGESUP;
   agelim=AGESUP;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        if (stepm >= YEARM) hstepm=1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
        gp=vector(1,nlstate);
   strcpy(filerespop,"pop");      gm=vector(1,nlstate);
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      for(theta=1; theta <=npar; theta++){
     printf("Problem with forecast resultfile: %s\n", filerespop);        for(i=1; i<=npar; i++){ /* Computes gradient */
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   printf("Computing forecasting: result on file '%s' \n", filerespop);        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
   if (mobilav==1) {      
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1; i<=npar; i++) /* Computes gradient */
     movingaverage(agedeb, fage, ageminpar, mobaverage);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;          gm[i] = prlim[i][i];
   if (stepm<=12) stepsize=1;  
          for(i=1;i<=nlstate;i++)
   agelim=AGESUP;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
   hstepm=1;  
   hstepm=hstepm/stepm;      trgradg =matrix(1,nlstate,1,npar);
    
   if (popforecast==1) {      for(j=1; j<=nlstate;j++)
     if((ficpop=fopen(popfile,"r"))==NULL) {        for(theta=1; theta <=npar; theta++)
       printf("Problem with population file : %s\n",popfile);exit(0);          trgradg[j][theta]=gradg[theta][j];
     }  
     popage=ivector(0,AGESUP);      for(i=1;i<=nlstate;i++)
     popeffectif=vector(0,AGESUP);        varpl[i][(int)age] =0.;
     popcount=vector(0,AGESUP);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     i=1;        for(i=1;i<=nlstate;i++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
     imx=i;      fprintf(ficresvpl,"%.0f ",age );
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){      free_vector(gp,1,nlstate);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      free_vector(gm,1,nlstate);
       k=k+1;      free_matrix(gradg,1,npar,1,nlstate);
       fprintf(ficrespop,"\n#******");      free_matrix(trgradg,1,nlstate,1,npar);
       for(j=1;j<=cptcoveff;j++) {    } /* End age */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    free_vector(xp,1,npar);
       fprintf(ficrespop,"******\n");    free_matrix(doldm,1,nlstate,1,npar);
       fprintf(ficrespop,"# Age");    free_matrix(dnewm,1,nlstate,1,nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");  }
        
       for (cpt=0; cpt<=0;cpt++) {  /************ Variance of one-step probabilities  ******************/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    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 (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int i, j=0,  i1, k1, l1, t, tj;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int k2, l2, j1,  z1;
           nhstepm = nhstepm/hstepm;    int k=0,l, cptcode;
              int first=1, first1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           oldm=oldms;savm=savms;    double **dnewm,**doldm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double *xp;
            double *gp, *gm;
           for (h=0; h<=nhstepm; h++){    double **gradg, **trgradg;
             if (h==(int) (calagedate+YEARM*cpt)) {    double **mu;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double age,agelim, cov[NCOVMAX];
             }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
             for(j=1; j<=nlstate+ndeath;j++) {    int theta;
               kk1=0.;kk2=0;    char fileresprob[FILENAMELENGTH];
               for(i=1; i<=nlstate;i++) {                  char fileresprobcov[FILENAMELENGTH];
                 if (mobilav==1)    char fileresprobcor[FILENAMELENGTH];
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    double ***varpij;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }    strcpy(fileresprob,"prob"); 
               }    strcat(fileresprob,fileres);
               if (h==(int)(calagedate+12*cpt)){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      printf("Problem with resultfile: %s\n", fileresprob);
                   /*fprintf(ficrespop," %.3f", kk1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    }
               }    strcpy(fileresprobcov,"probcov"); 
             }    strcat(fileresprobcov,fileres);
             for(i=1; i<=nlstate;i++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
               kk1=0.;      printf("Problem with resultfile: %s\n", fileresprobcov);
                 for(j=1; j<=nlstate;j++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    }
                 }    strcpy(fileresprobcor,"probcor"); 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    strcat(fileresprobcor,fileres);
             }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    }
           }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       }    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   /******/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficresprob,"# Age");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprobcov,"# Age");
           nhstepm = nhstepm/hstepm;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
              fprintf(ficresprobcov,"# Age");
           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(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){      for(j=1; j<=(nlstate+ndeath);j++){
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
             }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             for(j=1; j<=nlstate+ndeath;j++) {      }  
               kk1=0.;kk2=0;    fprintf(ficresprob,"\n");
               for(i=1; i<=nlstate;i++) {                  fprintf(ficresprobcov,"\n");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fprintf(ficresprobcor,"\n");
               }    xp=vector(1,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         }    first=1;
       }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
    }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        exit(0);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     else{
   if (popforecast==1) {      fprintf(ficgp,"\n# Routine varprob");
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     free_vector(popcount,0,AGESUP);      printf("Problem with html file: %s\n", optionfilehtm);
   }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      exit(0);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   fclose(ficrespop);    else{
 }      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
 /***********************************************/  
 /**************** Main Program *****************/      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
 /***********************************************/      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 int main(int argc, char *argv[])  
 {    }
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    cov[1]=1;
   double agedeb, agefin,hf;    tj=cptcoveff;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   double fret;    for(t=1; t<=tj;t++){
   double **xi,tmp,delta;      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
   double dum; /* Dummy variable */        if  (cptcovn>0) {
   double ***p3mat;          fprintf(ficresprob, "\n#********** Variable "); 
   int *indx;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   char line[MAXLINE], linepar[MAXLINE];          fprintf(ficresprob, "**********\n#");
   char title[MAXLINE];          fprintf(ficresprobcov, "\n#********** Variable "); 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          fprintf(ficresprobcov, "**********\n#");
            
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   char filerest[FILENAMELENGTH];          fprintf(ficgp, "**********\n#");
   char fileregp[FILENAMELENGTH];          
   char popfile[FILENAMELENGTH];          
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   int firstobs=1, lastobs=10;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int sdeb, sfin; /* Status at beginning and end */          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   int c,  h , cpt,l;          
   int ju,jl, mi;          fprintf(ficresprobcor, "\n#********** Variable ");    
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          fprintf(ficgp, "**********\n#");    
   int mobilav=0,popforecast=0;        }
   int hstepm, nhstepm;        
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   double bage, fage, age, agelim, agebase;          for (k=1; k<=cptcovn;k++) {
   double ftolpl=FTOL;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   double **prlim;          }
   double *severity;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double ***param; /* Matrix of parameters */          for (k=1; k<=cptcovprod;k++)
   double  *p;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double **matcov; /* Matrix of covariance */          
   double ***delti3; /* Scale */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   double *delti; /* Scale */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   double ***eij, ***vareij;          gp=vector(1,(nlstate)*(nlstate+ndeath));
   double **varpl; /* Variances of prevalence limits by age */          gm=vector(1,(nlstate)*(nlstate+ndeath));
   double *epj, vepp;      
   double kk1, kk2;          for(theta=1; theta <=npar; theta++){
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            for(i=1; i<=npar; i++)
                xp[i] = x[i] + (i==theta ?delti[theta]:0);
             
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   char *alph[]={"a","a","b","c","d","e"}, str[4];            
             k=0;
             for(i=1; i<= (nlstate); i++){
   char z[1]="c", occ;              for(j=1; j<=(nlstate+ndeath);j++){
 #include <sys/time.h>                k=k+1;
 #include <time.h>                gp[k]=pmmij[i][j];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              }
              }
   /* long total_usecs;            
   struct timeval start_time, end_time;            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:0);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      
   getcwd(pathcd, size);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   printf("\n%s",version);            for(i=1; i<=(nlstate); i++){
   if(argc <=1){              for(j=1; j<=(nlstate+ndeath);j++){
     printf("\nEnter the parameter file name: ");                k=k+1;
     scanf("%s",pathtot);                gm[k]=pmmij[i][j];
   }              }
   else{            }
     strcpy(pathtot,argv[1]);       
   }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
   /*cygwin_split_path(pathtot,path,optionfile);          }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              trgradg[j][theta]=gradg[theta][j];
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          
   chdir(path);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   replace(pathc,path);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 /*-------- arguments in the command line --------*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   strcpy(fileres,"r");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */          pmij(pmmij,cov,ncovmodel,x,nlstate);
           
   /*---------arguments file --------*/          k=0;
           for(i=1; i<=(nlstate); i++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            for(j=1; j<=(nlstate+ndeath);j++){
     printf("Problem with optionfile %s\n",optionfile);              k=k+1;
     goto end;              mu[k][(int) age]=pmmij[i][j];
   }            }
           }
   strcpy(filereso,"o");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   strcat(filereso,fileres);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   if((ficparo=fopen(filereso,"w"))==NULL) {              varpij[i][j][(int)age] = doldm[i][j];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /* Reads comments: lines beginning with '#' */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     ungetc(c,ficpar);            }*/
     fgets(line, MAXLINE, ficpar);  
     puts(line);          fprintf(ficresprob,"\n%d ",(int)age);
     fputs(line,ficparo);          fprintf(ficresprobcov,"\n%d ",(int)age);
   }          fprintf(ficresprobcor,"\n%d ",(int)age);
   ungetc(c,ficpar);  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   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);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   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<=(nlstate)*(nlstate+ndeath);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);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          i=0;
     puts(line);          for (k=1; k<=(nlstate);k++){
     fputs(line,ficparo);            for (l=1; l<=(nlstate+ndeath);l++){ 
   }              i=i++;
   ungetc(c,ficpar);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                  for (j=1; j<=i;j++){
   covar=matrix(0,NCOVMAX,1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   cptcovn=0;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              }
             }
   ncovmodel=2+cptcovn;          }/* end of loop for state */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        } /* end of loop for age */
    
   /* Read guess parameters */        /* Confidence intervalle of pij  */
   /* Reads comments: lines beginning with '#' */        /*
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"\nset noparametric;unset label");
     ungetc(c,ficpar);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     puts(line);          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);
     fputs(line,ficparo);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   ungetc(c,ficpar);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
          */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     for(j=1; j <=nlstate+ndeath-1; j++){        first1=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for (k2=1; k2<=(nlstate);k2++){
       fprintf(ficparo,"%1d%1d",i1,j1);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       printf("%1d%1d",i,j);            if(l2==k2) continue;
       for(k=1; k<=ncovmodel;k++){            j=(k2-1)*(nlstate+ndeath)+l2;
         fscanf(ficpar," %lf",&param[i][j][k]);            for (k1=1; k1<=(nlstate);k1++){
         printf(" %lf",param[i][j][k]);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         fprintf(ficparo," %lf",param[i][j][k]);                if(l1==k1) continue;
       }                i=(k1-1)*(nlstate+ndeath)+l1;
       fscanf(ficpar,"\n");                if(i<=j) continue;
       printf("\n");                for (age=bage; age<=fage; age ++){ 
       fprintf(ficparo,"\n");                  if ((int)age %5==0){
     }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
   p=param[1][1];                    mu2=mu[j][(int) age]/stepm*YEARM;
                      c12=cv12/sqrt(v1*v2);
   /* Reads comments: lines beginning with '#' */                    /* Computing eigen value of matrix of covariance */
   while((c=getc(ficpar))=='#' && c!= EOF){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ungetc(c,ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fgets(line, MAXLINE, ficpar);                    /* Eigen vectors */
     puts(line);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     fputs(line,ficparo);                    /*v21=sqrt(1.-v11*v11); *//* error */
   }                    v21=(lc1-v1)/cv12*v11;
   ungetc(c,ficpar);                    v12=-v21;
                     v22=v11;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                    tnalp=v21/v11;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                    if(first1==1){
   for(i=1; i <=nlstate; i++){                      first1=0;
     for(j=1; j <=nlstate+ndeath-1; j++){                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
       fscanf(ficpar,"%1d%1d",&i1,&j1);                    }
       printf("%1d%1d",i,j);                    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);
       fprintf(ficparo,"%1d%1d",i1,j1);                    /*printf(fignu*/
       for(k=1; k<=ncovmodel;k++){                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         fscanf(ficpar,"%le",&delti3[i][j][k]);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         printf(" %le",delti3[i][j][k]);                    if(first==1){
         fprintf(ficparo," %le",delti3[i][j][k]);                      first=0;
       }                      fprintf(ficgp,"\nset parametric;unset label");
       fscanf(ficpar,"\n");                      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);
       printf("\n");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(ficparo,"\n");                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
     }                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   }                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   delti=delti3[1][1];                      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);
   /* Reads comments: lines beginning with '#' */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      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",\
     ungetc(c,ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fgets(line, MAXLINE, ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     puts(line);                    }else{
     fputs(line,ficparo);                      first=0;
   }                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   ungetc(c,ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   matcov=matrix(1,npar,1,npar);                      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",\
   for(i=1; i <=npar; i++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fscanf(ficpar,"%s",&str);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     printf("%s",str);                    }/* if first */
     fprintf(ficparo,"%s",str);                  } /* age mod 5 */
     for(j=1; j <=i; j++){                } /* end loop age */
       fscanf(ficpar," %le",&matcov[i][j]);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
       printf(" %.5le",matcov[i][j]);                first=1;
       fprintf(ficparo," %.5le",matcov[i][j]);              } /*l12 */
     }            } /* k12 */
     fscanf(ficpar,"\n");          } /*l1 */
     printf("\n");        }/* k1 */
     fprintf(ficparo,"\n");      } /* loop covariates */
   }    }
   for(i=1; i <=npar; i++)    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     for(j=i+1;j<=npar;j++)    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       matcov[i][j]=matcov[j][i];    free_vector(xp,1,npar);
        fclose(ficresprob);
   printf("\n");    fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     /*-------- Rewriting paramater file ----------*/    fclose(fichtm);
      strcpy(rfileres,"r");    /* "Rparameterfile */  }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  /******************* Printing html file ***********/
     if((ficres =fopen(rfileres,"w"))==NULL) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                    int lastpass, int stepm, int weightopt, char model[],\
     }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fprintf(ficres,"#%s\n",version);                    int popforecast, int estepm ,\
                        double jprev1, double mprev1,double anprev1, \
     /*-------- data file ----------*/                    double jprev2, double mprev2,double anprev2){
     if((fic=fopen(datafile,"r"))==NULL)    {    int jj1, k1, i1, cpt;
       printf("Problem with datafile: %s\n", datafile);goto end;    /*char optionfilehtm[FILENAMELENGTH];*/
     }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     n= lastobs;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
     severity = vector(1,maxwav);    }
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
     moisnais=vector(1,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
     annais=vector(1,n);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     moisdc=vector(1,n);   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     andc=vector(1,n);   - Life expectancies by age and initial health status (estepm=%2d months): 
     agedc=vector(1,n);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     cod=ivector(1,n);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);   m=cptcoveff;
     s=imatrix(1,maxwav+1,1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);   jj1=0;
     ncodemax=ivector(1,8);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
     i=1;       jj1++;
     while (fgets(line, MAXLINE, fic) != NULL)    {       if (cptcovn > 0) {
       if ((i >= firstobs) && (i <=lastobs)) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                 for (cpt=1; cpt<=cptcoveff;cpt++) 
         for (j=maxwav;j>=1;j--){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           strcpy(line,stra);       }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       /* Pij */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
         }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
               /* Quasi-incidences */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       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>
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);         for(cpt=1; cpt<nlstate;cpt++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);           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);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);         }
         for (j=ncovcol;j>=1;j--){       for(cpt=1; cpt<=nlstate;cpt++) {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
         }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
         num[i]=atol(stra);       }
               fprintf(fichtm,"\n<br>- Total life expectancy by age and
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  health expectancies in states (1) and (2): e%s%d.png<br>
           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;}*/  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
         i=i+1;   }/* End k1 */
       }   fprintf(fichtm,"</ul>");
     }  
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   imx=i-1; /* Number of individuals */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   /* for (i=1; i<=imx; i++){   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     }*/   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
    
   /* for (i=1; i<=imx; i++){   if(popforecast==1) fprintf(fichtm,"\n
      if (s[4][i]==9)  s[4][i]=-1;   - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
      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]));}   - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
   */          <br>",fileres,fileres,fileres,fileres);
     else 
   /* Calculation of the number of parameter from char model*/     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);
   Tvar=ivector(1,15);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);   m=cptcoveff;
   Tvard=imatrix(1,15,1,2);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   Tage=ivector(1,15);        
       jj1=0;
   if (strlen(model) >1){   for(k1=1; k1<=m;k1++){
     j=0, j1=0, k1=1, k2=1;     for(i1=1; i1<=ncodemax[k1];i1++){
     j=nbocc(model,'+');       jj1++;
     j1=nbocc(model,'*');       if (cptcovn > 0) {
     cptcovn=j+1;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     cptcovprod=j1;         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     strcpy(modelsav,model);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       }
       printf("Error. Non available option model=%s ",model);       for(cpt=1; cpt<=nlstate;cpt++) {
       goto end;         fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
     }  interval) in state (%d): v%s%d%d.png <br>
      <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
     for(i=(j+1); i>=1;i--){       }
       cutv(stra,strb,modelsav,'+');     } /* end i1 */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   }/* End k1 */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/   fprintf(fichtm,"</ul>");
       /*scanf("%d",i);*/  fclose(fichtm);
       if (strchr(strb,'*')) {  }
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  /******************* Gnuplot file **************/
           cptcovprod--;  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           cptcovage++;    int ng;
             Tage[cptcovage]=i;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
             /*printf("stre=%s ", stre);*/      printf("Problem with file %s",optionfilegnuplot);
         }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
         else if (strcmp(strd,"age")==0) {    }
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    /*#ifdef windows */
           Tvar[i]=atoi(stre);      fprintf(ficgp,"cd \"%s\" \n",pathc);
           cptcovage++;      /*#endif */
           Tage[cptcovage]=i;  m=pow(2,cptcoveff);
         }    
         else {   /* 1eme*/
           cutv(strb,stre,strc,'V');    for (cpt=1; cpt<= nlstate ; cpt ++) {
           Tvar[i]=ncovcol+k1;     for (k1=1; k1<= m ; k1 ++) {
           cutv(strb,strc,strd,'V');       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           Tprod[k1]=i;       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);
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);       for (i=1; i<= nlstate ; i ++) {
           Tvar[cptcovn+k2]=Tvard[k1][1];         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];         else fprintf(ficgp," \%%*lf (\%%*lf)");
           for (k=1; k<=lastobs;k++)       }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
           k1++;       for (i=1; i<= nlstate ; i ++) {
           k2=k2+2;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         }         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       } 
       else {       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       for (i=1; i<= nlstate ; i ++) {
        /*  scanf("%d",i);*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       cutv(strd,strc,strb,'V');         else fprintf(ficgp," \%%*lf (\%%*lf)");
       Tvar[i]=atoi(strc);       }  
       }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       strcpy(modelsav,stra);       }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    }
         scanf("%d",i);*/    /*2 eme*/
     }    
 }    for (k1=1; k1<= m ; k1 ++) { 
        fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   printf("cptcovprod=%d ", cptcovprod);      
   scanf("%d ",i);*/      for (i=1; i<= nlstate+1 ; i ++) {
     fclose(fic);        k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
     /*  if(mle==1){*/        for (j=1; j<= nlstate+1 ; j ++) {
     if (weightopt != 1) { /* Maximisation without weights*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       for(i=1;i<=n;i++) weight[i]=1.0;          else fprintf(ficgp," \%%*lf (\%%*lf)");
     }        }   
     /*-calculation of age at interview from date of interview and age at death -*/        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     agev=matrix(1,maxwav,1,imx);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
     for (i=1; i<=imx; i++) {        for (j=1; j<= nlstate+1 ; j ++) {
       for(m=2; (m<= maxwav); m++) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          else fprintf(ficgp," \%%*lf (\%%*lf)");
          anint[m][i]=9999;        }   
          s[m][i]=-1;        fprintf(ficgp,"\" t\"\" w l 0,");
        }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        for (j=1; j<= nlstate+1 ; j ++) {
       }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
     for (i=1; i<=imx; i++)  {        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        else fprintf(ficgp,"\" t\"\" w l 0,");
       for(m=1; (m<= maxwav); m++){      }
         if(s[m][i] >0){    }
           if (s[m][i] >= nlstate+1) {    
             if(agedc[i]>0)    /*3eme*/
               if(moisdc[i]!=99 && andc[i]!=9999)    
                 agev[m][i]=agedc[i];    for (k1=1; k1<= m ; k1 ++) { 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      for (cpt=1; cpt<= nlstate ; cpt ++) {
            else {        k=2+nlstate*(2*cpt-2);
               if (andc[i]!=9999){        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
               agev[m][i]=-1;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
               }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           else if(s[m][i] !=9){ /* Should no more exist */          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             if(mint[m][i]==99 || anint[m][i]==9999)          
               agev[m][i]=1;        */
             else if(agev[m][i] <agemin){        for (i=1; i< nlstate ; i ++) {
               agemin=agev[m][i];          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          
             }        } 
             else if(agev[m][i] >agemax){      }
               agemax=agev[m][i];    }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    
             }    /* CV preval stat */
             /*agev[m][i]=anint[m][i]-annais[i];*/    for (k1=1; k1<= m ; k1 ++) { 
             /*   agev[m][i] = age[i]+2*m;*/      for (cpt=1; cpt<nlstate ; cpt ++) {
           }        k=3;
           else { /* =9 */        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
             agev[m][i]=1;        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
             s[m][i]=-1;        
           }        for (i=1; i< nlstate ; i ++)
         }          fprintf(ficgp,"+$%d",k+i+1);
         else /*= 0 Unknown */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           agev[m][i]=1;        
       }        l=3+(nlstate+ndeath)*cpt;
            fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     }        for (i=1; i< nlstate ; i ++) {
     for (i=1; i<=imx; i++)  {          l=3+(nlstate+ndeath)*cpt;
       for(m=1; (m<= maxwav); m++){          fprintf(ficgp,"+$%d",l+i+1);
         if (s[m][i] > (nlstate+ndeath)) {        }
           printf("Error: Wrong value in nlstate or ndeath\n");          fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
           goto end;      } 
         }    }  
       }    
     }    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
     free_vector(severity,1,maxwav);          for(j=1; j <=ncovmodel; j++){
     free_imatrix(outcome,1,maxwav+1,1,n);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     free_vector(moisnais,1,n);            jk++; 
     free_vector(annais,1,n);            fprintf(ficgp,"\n");
     /* free_matrix(mint,1,maxwav,1,n);          }
        free_matrix(anint,1,maxwav,1,n);*/        }
     free_vector(moisdc,1,n);      }
     free_vector(andc,1,n);     }
   
         for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     wav=ivector(1,imx);       for(jk=1; jk <=m; jk++) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);         if (ng==2)
               fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     /* Concatenates waves */         else
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);           fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
       Tcode=ivector(1,100);         for(k2=1; k2<=nlstate; k2++) {
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);           k3=i;
       ncodemax[1]=1;           for(k=1; k<=(nlstate+ndeath); k++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);             if (k != k2){
                     if(ng==2)
    codtab=imatrix(1,100,1,10);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
    h=0;               else
    m=pow(2,cptcoveff);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
    for(k=1;k<=cptcoveff; k++){               for(j=3; j <=ncovmodel; j++) {
      for(i=1; i <=(m/pow(2,k));i++){                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
        for(j=1; j <= ncodemax[k]; j++){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                   ij++;
            h++;                 }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                 else
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                   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++){   
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       codtab[1][2]=1;codtab[2][2]=2; */                 ij=1;
    /* for(i=1; i <=m ;i++){                 for(j=3; j <=ncovmodel; j++){
       for(k=1; k <=cptcovn; k++){                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       }                     ij++;
       printf("\n");                   }
       }                   else
       scanf("%d",i);*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                     }
    /* Calculates basic frequencies. Computes observed prevalence at single age                 fprintf(ficgp,")");
        and prints on file fileres'p'. */               }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                   if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   i=i+ncovmodel;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */             }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           } /* end k */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         } /* end k2 */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       } /* end jk */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     } /* end ng */
           fclose(ficgp); 
     /* For Powell, parameters are in a vector p[] starting at p[1]  }  /* end gnuplot */
        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) */  
   /*************** Moving average **************/
     if(mle==1){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    int i, cpt, cptcod;
        int modcovmax =1;
     /*--------- results files --------------*/    int mobilavrange, mob;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);    double age;
    
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
    jk=1;                             a covariate has 2 modalities */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
      for(k=1; k <=(nlstate+ndeath); k++){      if(mobilav==1) mobilavrange=5; /* default */
        if (k != i)      else mobilavrange=mobilav;
          {      for (age=bage; age<=fage; age++)
            printf("%d%d ",i,k);        for (i=1; i<=nlstate;i++)
            fprintf(ficres,"%1d%1d ",i,k);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
            for(j=1; j <=ncovmodel; j++){            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
              printf("%f ",p[jk]);      /* We keep the original values on the extreme ages bage, fage and for 
              fprintf(ficres,"%f ",p[jk]);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
              jk++;         we use a 5 terms etc. until the borders are no more concerned. 
            }      */ 
            printf("\n");      for (mob=3;mob <=mobilavrange;mob=mob+2){
            fprintf(ficres,"\n");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
          }          for (i=1; i<=nlstate;i++){
      }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
    }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  if(mle==1){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     /* Computing hessian and covariance matrix */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     ftolhess=ftol; /* Usually correct */                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     hesscov(matcov, p, npar, delti, ftolhess, func);                }
  }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            }
     printf("# Scales (for hessian or gradient estimation)\n");          }
      for(i=1,jk=1; i <=nlstate; i++){        }/* end age */
       for(j=1; j <=nlstate+ndeath; j++){      }/* end mob */
         if (j!=i) {    }else return -1;
           fprintf(ficres,"%1d%1d",i,j);    return 0;
           printf("%1d%1d",i,j);  }/* End movingaverage */
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);  /************** Forecasting ******************/
             jk++;  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){
           }    
           printf("\n");    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
           fprintf(ficres,"\n");    int *popage;
         }    double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       }    double *popeffectif,*popcount;
      }    double ***p3mat;
        double ***mobaverage;
     k=1;    char fileresf[FILENAMELENGTH];
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  
     printf("# 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");   agelim=AGESUP;
     for(i=1;i<=npar;i++){   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   
       printf("%s%d%d",alph[k],i1,tab[i]);*/   
       fprintf(ficres,"%3d",i);    strcpy(fileresf,"f"); 
       printf("%3d",i);    strcat(fileresf,fileres);
       for(j=1; j<=i;j++){    if((ficresf=fopen(fileresf,"w"))==NULL) {
         fprintf(ficres," %.5e",matcov[i][j]);      printf("Problem with forecast resultfile: %s\n", fileresf);
         printf(" %.5e",matcov[i][j]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
       }    }
       fprintf(ficres,"\n");    printf("Computing forecasting: result on file '%s' \n", fileresf);
       printf("\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
       k++;  
     }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
      
     while((c=getc(ficpar))=='#' && c!= EOF){    if (mobilav!=0) {
       ungetc(c,ficpar);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fgets(line, MAXLINE, ficpar);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       puts(line);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fputs(line,ficparo);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     }      }
     ungetc(c,ficpar);    }
     estepm=0;  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (estepm==0 || estepm < stepm) estepm=stepm;    if (stepm<=12) stepsize=1;
     if (fage <= 2) {    
       bage = ageminpar;    agelim=AGESUP;
       fage = agemaxpar;    
     }    hstepm=1;
        hstepm=hstepm/stepm; 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    yp1=modf(dateintmean,&yp);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    anprojmean=yp;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    yp2=modf((yp1*12),&yp);
      mprojmean=yp;
     while((c=getc(ficpar))=='#' && c!= EOF){    yp1=modf((yp2*30.5),&yp);
     ungetc(c,ficpar);    jprojmean=yp;
     fgets(line, MAXLINE, ficpar);    if(jprojmean==0) jprojmean=1;
     puts(line);    if(mprojmean==0) jprojmean=1;
     fputs(line,ficparo);    
   }    fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
   ungetc(c,ficpar);    
      for(cptcov=1;cptcov<=i2;cptcov++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        k=k+1;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficresf,"\n#******");
              for(j=1;j<=cptcoveff;j++) {
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        fprintf(ficresf,"******\n");
     puts(line);        fprintf(ficresf,"# StartingAge FinalAge");
     fputs(line,ficparo);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
   }        
   ungetc(c,ficpar);        
          for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
           fprintf(ficresf,"\n");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
   fscanf(ficpar,"pop_based=%d\n",&popbased);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   fprintf(ficparo,"pop_based=%d\n",popbased);              nhstepm = nhstepm/hstepm; 
   fprintf(ficres,"pop_based=%d\n",popbased);              
              p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   while((c=getc(ficpar))=='#' && c!= EOF){            oldm=oldms;savm=savms;
     ungetc(c,ficpar);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     fgets(line, MAXLINE, ficpar);          
     puts(line);            for (h=0; h<=nhstepm; h++){
     fputs(line,ficparo);              if (h==(int) (calagedate+YEARM*cpt)) {
   }                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
   ungetc(c,ficpar);              } 
               for(j=1; j<=nlstate+ndeath;j++) {
   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);                kk1=0.;kk2=0;
 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<=nlstate;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 (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
 while((c=getc(ficpar))=='#' && c!= EOF){                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     ungetc(c,ficpar);                  }
     fgets(line, MAXLINE, ficpar);                  
     puts(line);                }
     fputs(line,ficparo);                if (h==(int)(calagedate+12*cpt)){
   }                  fprintf(ficresf," %.3f", kk1);
   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);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
       }
 /*------------ gnuplot -------------*/    }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);         
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /*------------ free_vector  -------------*/  
  chdir(path);    fclose(ficresf);
    }
  free_ivector(wav,1,imx);  /************** Forecasting ******************/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  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){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      
  free_ivector(num,1,n);    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
  free_vector(agedc,1,n);    int *popage;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    double calagedate, agelim, kk1, kk2;
  fclose(ficparo);    double *popeffectif,*popcount;
  fclose(ficres);    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
 /*--------- index.htm --------*/    char filerespop[FILENAMELENGTH];
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      agelim=AGESUP;
   /*--------------- Prevalence limit --------------*/    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
      
   strcpy(filerespl,"pl");    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   strcat(filerespl,fileres);    
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    strcpy(filerespop,"pop"); 
   }    strcat(filerespop,fileres);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   fprintf(ficrespl,"#Prevalence limit\n");      printf("Problem with forecast resultfile: %s\n", filerespop);
   fprintf(ficrespl,"#Age ");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    printf("Computing forecasting: result on file '%s' \n", filerespop);
      fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (mobilav!=0) {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   k=0;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   agebase=ageminpar;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   agelim=agemaxpar;      }
   ftolpl=1.e-10;    }
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    agelim=AGESUP;
         k=k+1;    
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    hstepm=1;
         fprintf(ficrespl,"\n#******");    hstepm=hstepm/stepm; 
         for(j=1;j<=cptcoveff;j++)    
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (popforecast==1) {
         fprintf(ficrespl,"******\n");      if((ficpop=fopen(popfile,"r"))==NULL) {
                printf("Problem with population file : %s\n",popfile);exit(0);
         for (age=agebase; age<=agelim; age++){        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      } 
           fprintf(ficrespl,"%.0f",age );      popage=ivector(0,AGESUP);
           for(i=1; i<=nlstate;i++)      popeffectif=vector(0,AGESUP);
           fprintf(ficrespl," %.5f", prlim[i][i]);      popcount=vector(0,AGESUP);
           fprintf(ficrespl,"\n");      
         }      i=1;   
       }      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     }     
   fclose(ficrespl);      imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   /*------------- h Pij x at various ages ------------*/    }
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for(cptcov=1;cptcov<=i2;cptcov++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        k=k+1;
   }        fprintf(ficrespop,"\n#******");
   printf("Computing pij: result on file '%s' \n", filerespij);        for(j=1;j<=cptcoveff;j++) {
            fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   /*if (stepm<=24) stepsize=2;*/        fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
   agelim=AGESUP;        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   hstepm=stepsize*YEARM; /* Every year of age */        if (popforecast==1)  fprintf(ficrespop," [Population]");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        
          for (cpt=0; cpt<=0;cpt++) { 
   k=0;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   for(cptcov=1;cptcov<=i1;cptcov++){          
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
       k=k+1;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         fprintf(ficrespij,"\n#****** ");            nhstepm = nhstepm/hstepm; 
         for(j=1;j<=cptcoveff;j++)            
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespij,"******\n");            oldm=oldms;savm=savms;
                    hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (h=0; h<=nhstepm; h++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              if (h==(int) (calagedate+YEARM*cpt)) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           oldm=oldms;savm=savms;              } 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                for(j=1; j<=nlstate+ndeath;j++) {
           fprintf(ficrespij,"# Age");                kk1=0.;kk2=0;
           for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++) {              
             for(j=1; j<=nlstate+ndeath;j++)                  if (mobilav==1) 
               fprintf(ficrespij," %1d-%1d",i,j);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
           fprintf(ficrespij,"\n");                  else {
           for (h=0; h<=nhstepm; h++){                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                  }
             for(i=1; i<=nlstate;i++)                }
               for(j=1; j<=nlstate+ndeath;j++)                if (h==(int)(calagedate+12*cpt)){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
             fprintf(ficrespij,"\n");                    /*fprintf(ficrespop," %.3f", kk1);
           }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                }
           fprintf(ficrespij,"\n");              }
         }              for(i=1; i<=nlstate;i++){
     }                kk1=0.;
   }                  for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                  }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
   fclose(ficrespij);              }
   
               if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
   /*---------- Forecasting ------------------*/                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   if((stepm == 1) && (strcmp(model,".")==0)){            }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          }
     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);}    /******/
   else{  
     erreur=108;        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     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(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   }          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
   /*---------- Health expectancies and variances ------------*/            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(filerest,"t");            oldm=oldms;savm=savms;
   strcat(filerest,fileres);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   if((ficrest=fopen(filerest,"w"))==NULL) {            for (h=0; h<=nhstepm; h++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              if (h==(int) (calagedate+YEARM*cpt)) {
   }                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
   strcpy(filerese,"e");                for(i=1; i<=nlstate;i++) {              
   strcat(filerese,fileres);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   if((ficreseij=fopen(filerese,"w"))==NULL) {                }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
   }              }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  strcpy(fileresv,"v");          }
   strcat(fileresv,fileres);        }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {     } 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }   
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   k=0;    if (popforecast==1) {
   for(cptcov=1;cptcov<=i1;cptcov++){      free_ivector(popage,0,AGESUP);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_vector(popeffectif,0,AGESUP);
       k=k+1;      free_vector(popcount,0,AGESUP);
       fprintf(ficrest,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficrest,"******\n");    fclose(ficrespop);
   }
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /***********************************************/
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /**************** Main Program *****************/
       fprintf(ficreseij,"******\n");  /***********************************************/
   
       fprintf(ficresvij,"\n#****** ");  int main(int argc, char *argv[])
       for(j=1;j<=cptcoveff;j++)  {
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
       fprintf(ficresvij,"******\n");    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
     double agedeb, agefin,hf;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);      double fret;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double **xi,tmp,delta;
       oldm=oldms;savm=savms;  
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    double dum; /* Dummy variable */
        double ***p3mat;
     double ***mobaverage;
      int *indx;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    char line[MAXLINE], linepar[MAXLINE];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
       fprintf(ficrest,"\n");    int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
       epj=vector(1,nlstate+1);    int c,  h , cpt,l;
       for(age=bage; age <=fage ;age++){    int ju,jl, mi;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
         if (popbased==1) {    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
           for(i=1; i<=nlstate;i++)    int mobilav=0,popforecast=0;
             prlim[i][i]=probs[(int)age][i][k];    int hstepm, nhstepm;
         }    double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
          
         fprintf(ficrest," %4.0f",age);    double bage, fage, age, agelim, agebase;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double ftolpl=FTOL;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double **prlim;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    double *severity;
           }    double ***param; /* Matrix of parameters */
           epj[nlstate+1] +=epj[j];    double  *p;
         }    double **matcov; /* Matrix of covariance */
         for(i=1, vepp=0.;i <=nlstate;i++)    double ***delti3; /* Scale */
           for(j=1;j <=nlstate;j++)    double *delti; /* Scale */
             vepp += vareij[i][j][(int)age];    double ***eij, ***vareij;
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    double **varpl; /* Variances of prevalence limits by age */
         for(j=1;j <=nlstate;j++){    double *epj, vepp;
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));    double kk1, kk2;
         }    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
         fprintf(ficrest,"\n");  
       }    char *alph[]={"a","a","b","c","d","e"}, str[4];
     }  
   }  
     char z[1]="c", occ;
   fclose(ficreseij);  #include <sys/time.h>
   fclose(ficresvij);  #include <time.h>
   fclose(ficrest);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   fclose(ficpar);   
   free_vector(epj,1,nlstate+1);    /* long total_usecs;
         struct timeval start_time, end_time;
   /*------- Variance limit prevalence------*/      
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   strcpy(fileresvpl,"vpl");    getcwd(pathcd, size);
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    printf("\n%s",version);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    if(argc <=1){
     exit(0);      printf("\nEnter the parameter file name: ");
   }      scanf("%s",pathtot);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
     else{
   k=0;      strcpy(pathtot,argv[1]);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
       k=k+1;    /*cygwin_split_path(pathtot,path,optionfile);
       fprintf(ficresvpl,"\n#****** ");      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
       for(j=1;j<=cptcoveff;j++)    /* cutv(path,optionfile,pathtot,'\\');*/
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
          printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    chdir(path);
       oldm=oldms;savm=savms;    replace(pathc,path);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
     }    /*-------- arguments in the command line --------*/
  }  
     /* Log file */
   fclose(ficresvpl);    strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
   /*---------- End : free ----------------*/    if((ficlog=fopen(filelog,"w"))==NULL)    {
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      printf("Problem with logfile %s\n",filelog);
        goto end;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"Log filename:%s\n",filelog);
      fprintf(ficlog,"\n%s",version);
      fprintf(ficlog,"\nEnter the parameter file name: ");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    fflush(ficlog);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* */
      strcpy(fileres,"r");
   free_matrix(matcov,1,npar,1,npar);    strcat(fileres, optionfilefiname);
   free_vector(delti,1,npar);    strcat(fileres,".txt");    /* Other files have txt extension */
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    /*---------arguments file --------*/
   
   if(erreur >0)    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("End of Imach with error or warning %d\n",erreur);      printf("Problem with optionfile %s\n",optionfile);
   else   printf("End of Imach\n");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      goto end;
      }
   /* 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);*/    strcpy(filereso,"o");
   /*------ End -----------*/    strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
  end:      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
 #ifdef windows      goto end;
   /* chdir(pathcd);*/    }
 #endif  
  /*system("wgnuplot graph.plt");*/    /* Reads comments: lines beginning with '#' */
  /*system("../gp37mgw/wgnuplot graph.plt");*/    while((c=getc(ficpar))=='#' && c!= EOF){
  /*system("cd ../gp37mgw");*/      ungetc(c,ficpar);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fgets(line, MAXLINE, ficpar);
  strcpy(plotcmd,GNUPLOTPROGRAM);      puts(line);
  strcat(plotcmd," ");      fputs(line,ficparo);
  strcat(plotcmd,optionfilegnuplot);    }
  system(plotcmd);    ungetc(c,ficpar);
   
 #ifdef windows    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);
   while (z[0] != 'q') {    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);
     /* chdir(path); */    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);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    while((c=getc(ficpar))=='#' && c!= EOF){
     scanf("%s",z);      ungetc(c,ficpar);
     if (z[0] == 'c') system("./imach");      fgets(line, MAXLINE, ficpar);
     else if (z[0] == 'e') system(optionfilehtm);      puts(line);
     else if (z[0] == 'g') system(plotcmd);      fputs(line,ficparo);
     else if (z[0] == 'q') exit(0);    }
   }    ungetc(c,ficpar);
 #endif    
 }     
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if (andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Should no more exist */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if(mint[m][i]==99 || anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=1; (m<= maxwav); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+mprev1/12.+jprev1/365.;
     dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
     fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
     fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,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,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;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*/
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Age");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     } 
     else{
       erreur=108;
       printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
       fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     calagedate=-1;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;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);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     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(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting: %s\n",plotcmd);fflush(stdout);
     system(plotcmd);
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.36  
changed lines
  Added in v.1.66


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