Diff for /imach/src/imach.c between versions 1.32 and 1.83

version 1.32, 2002/03/11 14:17:15 version 1.83, 2003/06/10 13:39:11
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.83  2003/06/10 13:39:11  lievre
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.82  2003/06/05 15:57:20  brouard
   first survey ("cross") where individuals from different ages are    Add log in  imach.c and  fullversion number is now printed.
   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  */
   second wave of interviews ("longitudinal") which measure each change  /*
   (if any) in individual health status.  Health expectancies are     Interpolated Markov Chain
   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    Short summary of the programme:
   Maximum Likelihood of the parameters involved in the model.  The    
   simplest model is the multinomial logistic model where pij is the    This program computes Healthy Life Expectancies from
   probabibility to be observed in state j at the second wave    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   conditional to be observed in state i at the first wave. Therefore    first survey ("cross") where individuals from different ages are
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    interviewed on their health status or degree of disability (in the
   'age' is age and 'sex' is a covariate. If you want to have a more    case of a health survey which is our main interest) -2- at least a
   complex model than "constant and age", you should modify the program    second wave of interviews ("longitudinal") which measure each change
   where the markup *Covariates have to be included here again* invites    (if any) in individual health status.  Health expectancies are
   you to do it.  More covariates you add, slower the    computed from the time spent in each health state according to a
   convergence.    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
   The advantage of this computer programme, compared to a simple    simplest model is the multinomial logistic model where pij is the
   multinomial logistic model, is clear when the delay between waves is not    probability to be observed in state j at the second wave
   identical for each individual. Also, if a individual missed an    conditional to be observed in state i at the first wave. Therefore
   intermediate interview, the information is lost, but taken into    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   account using an interpolation or extrapolation.      '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
   hPijx is the probability to be observed in state i at age x+h    where the markup *Covariates have to be included here again* invites
   conditional to the observed state i at age x. The delay 'h' can be    you to do it.  More covariates you add, slower the
   split into an exact number (nh*stepm) of unobserved intermediate    convergence.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    The advantage of this computer programme, compared to a simple
   matrix is simply the matrix product of nh*stepm elementary matrices    multinomial logistic model, is clear when the delay between waves is not
   and the contribution of each individual to the likelihood is simply    identical for each individual. Also, if a individual missed an
   hPijx.    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    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
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    split into an exact number (nh*stepm) of unobserved intermediate
            Institut national d'études démographiques, Paris.    states. This elementary transition (by month, quarter,
   This software have been partly granted by Euro-REVES, a concerted action    semester or year) is modelled as a multinomial logistic.  The hPx
   from the European Union.    matrix is simply the matrix product of nh*stepm elementary matrices
   It is copyrighted identically to a GNU software product, ie programme and    and the contribution of each individual to the likelihood is simply
   software can be distributed freely for non commercial use. Latest version    hPijx.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the stable prevalence. 
 #include <math.h>    
 #include <stdio.h>    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <stdlib.h>             Institut national d'études démographiques, Paris.
 #include <unistd.h>    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 #define MAXLINE 256    It is copyrighted identically to a GNU software product, ie programme and
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    software can be distributed freely for non commercial use. Latest version
 #define FILENAMELENGTH 80    can be accessed at http://euroreves.ined.fr/imach .
 /*#define DEBUG*/  
 #define windows    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    
     **********************************************************************/
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  /*
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    main
     read parameterfile
 #define NINTERVMAX 8    read datafile
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    concatwav
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    if (mle >= 1)
 #define NCOVMAX 8 /* Maximum number of covariates */      mlikeli
 #define MAXN 20000    print results files
 #define YEARM 12. /* Number of months per year */    if mle==1 
 #define AGESUP 130       computes hessian
 #define AGEBASE 40    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
     open gnuplot file
 int erreur; /* Error number */    open html file
 int nvar;    stable prevalence
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;     for age prevalim()
 int npar=NPARMAX;    h Pij x
 int nlstate=2; /* Number of live states */    variance of p varprob
 int ndeath=1; /* Number of dead states */    forecasting if prevfcast==1 prevforecast call prevalence()
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    health expectancies
 int popbased=0;    Variance-covariance of DFLE
     prevalence()
 int *wav; /* Number of waves for this individuual 0 is possible */     movingaverage()
 int maxwav; /* Maxim number of waves */    varevsij() 
 int jmin, jmax; /* min, max spacing between 2 waves */    if popbased==1 varevsij(,popbased)
 int mle, weightopt;    total life expectancies
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Variance of stable prevalence
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */   end
 double jmean; /* Mean space between 2 waves */  */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;   
 FILE *ficreseij;  #include <math.h>
   char filerese[FILENAMELENGTH];  #include <stdio.h>
  FILE  *ficresvij;  #include <stdlib.h>
   char fileresv[FILENAMELENGTH];  #include <unistd.h>
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 #define NR_END 1  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FREE_ARG char*  #define FILENAMELENGTH 80
 #define FTOL 1.0e-10  /*#define DEBUG*/
   #define windows
 #define NRANSI  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define ITMAX 200  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define TOL 2.0e-4  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10  #define NINTERVMAX 8
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define GOLD 1.618034  #define NCOVMAX 8 /* Maximum number of covariates */
 #define GLIMIT 100.0  #define MAXN 20000
 #define TINY 1.0e-20  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 static double maxarg1,maxarg2;  #define AGEBASE 40
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #ifdef windows
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define DIRSEPARATOR '\\'
    #define ODIRSEPARATOR '/'
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #else
 #define rint(a) floor(a+0.5)  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 static double sqrarg;  #endif
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  /* $Id$ */
   /* $State$ */
 int imx;  
 int stepm;  char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 /* Stepm, step in month: minimum step interpolation*/  char fullversion[]="$Revision$ $Date$"; 
   int erreur; /* Error number */
 int m,nb;  int nvar;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int npar=NPARMAX;
 double **pmmij, ***probs, ***mobaverage;  int nlstate=2; /* Number of live states */
 double dateintmean=0;  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double *weight;  int popbased=0;
 int **s; /* Status */  
 double *agedc, **covar, idx;  int *wav; /* Number of waves for this individuual 0 is possible */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int mle, weightopt;
 double ftolhess; /* Tolerance for computing hessian */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 /**************** split *************************/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 {  double jmean; /* Mean space between 2 waves */
    char *s;                             /* pointer */  double **oldm, **newm, **savm; /* Working pointers to matrices */
    int  l1, l2;                         /* length counters */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    l1 = strlen( path );                 /* length of path */  FILE *ficlog, *ficrespow;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #ifdef windows  FILE *ficresprobmorprev;
    s = strrchr( path, '\\' );           /* find last / */  FILE *fichtm; /* Html File */
 #else  FILE *ficreseij;
    s = strrchr( path, '/' );            /* find last / */  char filerese[FILENAMELENGTH];
 #endif  FILE  *ficresvij;
    if ( s == NULL ) {                   /* no directory, so use current */  char fileresv[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  FILE  *ficresvpl;
       extern char       *getwd( );  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
       if ( getwd( dirc ) == NULL ) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #else  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       extern char       *getcwd( );  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char filelog[FILENAMELENGTH]; /* Log file */
 #endif  char filerest[FILENAMELENGTH];
          return( GLOCK_ERROR_GETCWD );  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  #define NR_END 1
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FREE_ARG char*
       strcpy( name, s );                /* save file name */  #define FTOL 1.0e-10
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  #define NRANSI 
    }  #define ITMAX 200 
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  #define TOL 2.0e-4 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  #define CGOLD 0.3819660 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define ZEPS 1.0e-10 
 #endif  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    s = strrchr( name, '.' );            /* find last / */  
    s++;  #define GOLD 1.618034 
    strcpy(ext,s);                       /* save extension */  #define GLIMIT 100.0 
    l1= strlen( name);  #define TINY 1.0e-20 
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);  static double maxarg1,maxarg2;
    finame[l1-l2]= 0;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    return( 0 );                         /* we're done */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /******************************************/  
   static double sqrarg;
 void replace(char *s, char*t)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int i;  
   int lg=20;  int imx; 
   i=0;  int stepm;
   lg=strlen(t);  /* Stepm, step in month: minimum step interpolation*/
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  int estepm;
     if (t[i]== '\\') s[i]='/';  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
 }  int m,nb;
   int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 int nbocc(char *s, char occ)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 {  double **pmmij, ***probs;
   int i,j=0;  double dateintmean=0;
   int lg=20;  
   i=0;  double *weight;
   lg=strlen(s);  int **s; /* Status */
   for(i=0; i<= lg; i++) {  double *agedc, **covar, idx;
   if  (s[i] == occ ) j++;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   }  
   return j;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 void cutv(char *u,char *v, char*t, char occ)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int i,lg,j,p=0;  {
   i=0;    char  *ss;                            /* pointer */
   for(j=0; j<=strlen(t)-1; j++) {    int   l1, l2;                         /* length counters */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   lg=strlen(t);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for(j=0; j<p; j++) {    if ( ss == NULL ) {                   /* no directory, so use current */
     (u[j] = t[j]);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      u[p]='\0';      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
    for(j=0; j<= lg; j++) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     if (j>=(p+1))(v[j-p-1] = t[j]);        return( GLOCK_ERROR_GETCWD );
   }      }
 }      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
 /********************** nrerror ********************/      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 void nrerror(char error_text[])      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   fprintf(stderr,"ERREUR ...\n");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   fprintf(stderr,"%s\n",error_text);      dirc[l1-l2] = 0;                    /* add zero */
   exit(1);    }
 }    l1 = strlen( dirc );                  /* length of directory */
 /*********************** vector *******************/  #ifdef windows
 double *vector(int nl, int nh)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   double *v;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #endif
   if (!v) nrerror("allocation failure in vector");    ss = strrchr( name, '.' );            /* find last / */
   return v-nl+NR_END;    ss++;
 }    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
 /************************ free vector ******************/    l2= strlen(ss)+1;
 void free_vector(double*v, int nl, int nh)    strncpy( finame, name, l1-l2);
 {    finame[l1-l2]= 0;
   free((FREE_ARG)(v+nl-NR_END));    return( 0 );                          /* we're done */
 }  }
   
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /******************************************/
 {  
   int *v;  void replace(char *s, char*t)
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    int i;
   return v-nl+NR_END;    int lg=20;
 }    i=0;
     lg=strlen(t);
 /******************free ivector **************************/    for(i=0; i<= lg; i++) {
 void free_ivector(int *v, long nl, long nh)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   free((FREE_ARG)(v+nl-NR_END));    }
 }  }
   
 /******************* imatrix *******************************/  int nbocc(char *s, char occ)
 int **imatrix(long nrl, long nrh, long ncl, long nch)  {
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    int i,j=0;
 {    int lg=20;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    i=0;
   int **m;    lg=strlen(s);
      for(i=0; i<= lg; i++) {
   /* allocate pointers to rows */    if  (s[i] == occ ) j++;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    }
   if (!m) nrerror("allocation failure 1 in matrix()");    return j;
   m += NR_END;  }
   m -= nrl;  
    void cutv(char *u,char *v, char*t, char occ)
    {
   /* allocate rows and set pointers to them */    /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       gives u="abcedf" and v="ghi2j" */
   m[nrl] += NR_END;    int i,lg,j,p=0;
   m[nrl] -= ncl;    i=0;
      for(j=0; j<=strlen(t)-1; j++) {
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      }
   /* return pointer to array of pointers to rows */  
   return m;    lg=strlen(t);
 }    for(j=0; j<p; j++) {
       (u[j] = t[j]);
 /****************** free_imatrix *************************/    }
 void free_imatrix(m,nrl,nrh,ncl,nch)       u[p]='\0';
       int **m;  
       long nch,ncl,nrh,nrl;     for(j=0; j<= lg; j++) {
      /* free an int matrix allocated by imatrix() */      if (j>=(p+1))(v[j-p-1] = t[j]);
 {    }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  }
   free((FREE_ARG) (m+nrl-NR_END));  
 }  /********************** nrerror ********************/
   
 /******************* matrix *******************************/  void nrerror(char error_text[])
 double **matrix(long nrl, long nrh, long ncl, long nch)  {
 {    fprintf(stderr,"ERREUR ...\n");
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    fprintf(stderr,"%s\n",error_text);
   double **m;    exit(EXIT_FAILURE);
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /*********************** vector *******************/
   if (!m) nrerror("allocation failure 1 in matrix()");  double *vector(int nl, int nh)
   m += NR_END;  {
   m -= nrl;    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!v) nrerror("allocation failure in vector");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return v-nl+NR_END;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /************************ free vector ******************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_vector(double*v, int nl, int nh)
   return m;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /************************ivector *******************************/
 {  char *cvector(long nl,long nh)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    char *v;
 }    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
     if (!v) nrerror("allocation failure in cvector");
 /******************* ma3x *******************************/    return v-nl+NR_END;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  }
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /******************free ivector **************************/
   double ***m;  void free_cvector(char *v, long nl, long nh)
   {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m) nrerror("allocation failure 1 in matrix()");  }
   m += NR_END;  
   m -= nrl;  /************************ivector *******************************/
   int *ivector(long nl,long nh)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int *v;
   m[nrl] += NR_END;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] -= ncl;    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /******************free ivector **************************/
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  void free_ivector(int *v, long nl, long nh)
   m[nrl][ncl] += NR_END;  {
   m[nrl][ncl] -= nll;    free((FREE_ARG)(v+nl-NR_END));
   for (j=ncl+1; j<=nch; j++)  }
     m[nrl][j]=m[nrl][j-1]+nlay;  
    /******************* imatrix *******************************/
   for (i=nrl+1; i<=nrh; i++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for (j=ncl+1; j<=nch; j++)  { 
       m[i][j]=m[i][j-1]+nlay;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   }    int **m; 
   return m;    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /*************************free ma3x ************************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m += NR_END; 
 {    m -= nrl; 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    /* allocate rows and set pointers to them */ 
 }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 /***************** f1dim *************************/    m[nrl] += NR_END; 
 extern int ncom;    m[nrl] -= ncl; 
 extern double *pcom,*xicom;    
 extern double (*nrfunc)(double []);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      
 double f1dim(double x)    /* return pointer to array of pointers to rows */ 
 {    return m; 
   int j;  } 
   double f;  
   double *xt;  /****************** free_imatrix *************************/
    void free_imatrix(m,nrl,nrh,ncl,nch)
   xt=vector(1,ncom);        int **m;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];        long nch,ncl,nrh,nrl; 
   f=(*nrfunc)(xt);       /* free an int matrix allocated by imatrix() */ 
   free_vector(xt,1,ncom);  { 
   return f;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   int iter;  {
   double a,b,d,etemp;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double fu,fv,fw,fx;    double **m;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double e=0.0;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
   a=(ax < cx ? ax : cx);    m -= nrl;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   fw=fv=fx=(*f)(x);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] += NR_END;
     xm=0.5*(a+b);    m[nrl] -= ncl;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     printf(".");fflush(stdout);    return m;
 #ifdef DEBUG    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);     */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /*************************free matrix ************************/
       *xmin=x;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       return fx;  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     ftemp=fu;    free((FREE_ARG)(m+nrl-NR_END));
     if (fabs(e) > tol1) {  }
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  /******************* ma3x *******************************/
       p=(x-v)*q-(x-w)*r;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       q=2.0*(q-r);  {
       if (q > 0.0) p = -p;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       q=fabs(q);    double ***m;
       etemp=e;  
       e=d;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if (!m) nrerror("allocation failure 1 in matrix()");
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m += NR_END;
       else {    m -= nrl;
         d=p/q;  
         u=x+d;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         if (u-a < tol2 || b-u < tol2)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           d=SIGN(tol1,xm-x);    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     fu=(*f)(u);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     if (fu <= fx) {    m[nrl][ncl] += NR_END;
       if (u >= x) a=x; else b=x;    m[nrl][ncl] -= nll;
       SHFT(v,w,x,u)    for (j=ncl+1; j<=nch; j++) 
         SHFT(fv,fw,fx,fu)      m[nrl][j]=m[nrl][j-1]+nlay;
         } else {    
           if (u < x) a=u; else b=u;    for (i=nrl+1; i<=nrh; i++) {
           if (fu <= fw || w == x) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
             v=w;      for (j=ncl+1; j<=nch; j++) 
             w=u;        m[i][j]=m[i][j-1]+nlay;
             fv=fw;    }
             fw=fu;    return m; 
           } else if (fu <= fv || v == x || v == w) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             v=u;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
             fv=fu;    */
           }  }
         }  
   }  /*************************free ma3x ************************/
   nrerror("Too many iterations in brent");  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   *xmin=x;  {
   return fx;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /****************** mnbrak ***********************/  }
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /***************** f1dim *************************/
             double (*func)(double))  extern int ncom; 
 {  extern double *pcom,*xicom;
   double ulim,u,r,q, dum;  extern double (*nrfunc)(double []); 
   double fu;   
    double f1dim(double x) 
   *fa=(*func)(*ax);  { 
   *fb=(*func)(*bx);    int j; 
   if (*fb > *fa) {    double f;
     SHFT(dum,*ax,*bx,dum)    double *xt; 
       SHFT(dum,*fb,*fa,dum)   
       }    xt=vector(1,ncom); 
   *cx=(*bx)+GOLD*(*bx-*ax);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *fc=(*func)(*cx);    f=(*nrfunc)(xt); 
   while (*fb > *fc) {    free_vector(xt,1,ncom); 
     r=(*bx-*ax)*(*fb-*fc);    return f; 
     q=(*bx-*cx)*(*fb-*fa);  } 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /*****************brent *************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if ((*bx-u)*(u-*cx) > 0.0) {  { 
       fu=(*func)(u);    int iter; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double a,b,d,etemp;
       fu=(*func)(u);    double fu,fv,fw,fx;
       if (fu < *fc) {    double ftemp;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    double p,q,r,tol1,tol2,u,v,w,x,xm; 
           SHFT(*fb,*fc,fu,(*func)(u))    double e=0.0; 
           }   
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    a=(ax < cx ? ax : cx); 
       u=ulim;    b=(ax > cx ? ax : cx); 
       fu=(*func)(u);    x=w=v=bx; 
     } else {    fw=fv=fx=(*f)(x); 
       u=(*cx)+GOLD*(*cx-*bx);    for (iter=1;iter<=ITMAX;iter++) { 
       fu=(*func)(u);      xm=0.5*(a+b); 
     }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     SHFT(*ax,*bx,*cx,u)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       SHFT(*fa,*fb,*fc,fu)      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
 }  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /*************** linmin ************************/      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)))) { */
 int ncom;  #endif
 double *pcom,*xicom;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 double (*nrfunc)(double []);        *xmin=x; 
          return fx; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      } 
 {      ftemp=fu;
   double brent(double ax, double bx, double cx,      if (fabs(e) > tol1) { 
                double (*f)(double), double tol, double *xmin);        r=(x-w)*(fx-fv); 
   double f1dim(double x);        q=(x-v)*(fx-fw); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        p=(x-v)*q-(x-w)*r; 
               double *fc, double (*func)(double));        q=2.0*(q-r); 
   int j;        if (q > 0.0) p = -p; 
   double xx,xmin,bx,ax;        q=fabs(q); 
   double fx,fb,fa;        etemp=e; 
          e=d; 
   ncom=n;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   pcom=vector(1,n);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   xicom=vector(1,n);        else { 
   nrfunc=func;          d=p/q; 
   for (j=1;j<=n;j++) {          u=x+d; 
     pcom[j]=p[j];          if (u-a < tol2 || b-u < tol2) 
     xicom[j]=xi[j];            d=SIGN(tol1,xm-x); 
   }        } 
   ax=0.0;      } else { 
   xx=1.0;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      } 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 #ifdef DEBUG      fu=(*f)(u); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      if (fu <= fx) { 
 #endif        if (u >= x) a=x; else b=x; 
   for (j=1;j<=n;j++) {        SHFT(v,w,x,u) 
     xi[j] *= xmin;          SHFT(fv,fw,fx,fu) 
     p[j] += xi[j];          } else { 
   }            if (u < x) a=u; else b=u; 
   free_vector(xicom,1,n);            if (fu <= fw || w == x) { 
   free_vector(pcom,1,n);              v=w; 
 }              w=u; 
               fv=fw; 
 /*************** powell ************************/              fw=fu; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,            } else if (fu <= fv || v == x || v == w) { 
             double (*func)(double []))              v=u; 
 {              fv=fu; 
   void linmin(double p[], double xi[], int n, double *fret,            } 
               double (*func)(double []));          } 
   int i,ibig,j;    } 
   double del,t,*pt,*ptt,*xit;    nrerror("Too many iterations in brent"); 
   double fp,fptt;    *xmin=x; 
   double *xits;    return fx; 
   pt=vector(1,n);  } 
   ptt=vector(1,n);  
   xit=vector(1,n);  /****************** mnbrak ***********************/
   xits=vector(1,n);  
   *fret=(*func)(p);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   for (j=1;j<=n;j++) pt[j]=p[j];              double (*func)(double)) 
   for (*iter=1;;++(*iter)) {  { 
     fp=(*fret);    double ulim,u,r,q, dum;
     ibig=0;    double fu; 
     del=0.0;   
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    *fa=(*func)(*ax); 
     for (i=1;i<=n;i++)    *fb=(*func)(*bx); 
       printf(" %d %.12f",i, p[i]);    if (*fb > *fa) { 
     printf("\n");      SHFT(dum,*ax,*bx,dum) 
     for (i=1;i<=n;i++) {        SHFT(dum,*fb,*fa,dum) 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        } 
       fptt=(*fret);    *cx=(*bx)+GOLD*(*bx-*ax); 
 #ifdef DEBUG    *fc=(*func)(*cx); 
       printf("fret=%lf \n",*fret);    while (*fb > *fc) { 
 #endif      r=(*bx-*ax)*(*fb-*fc); 
       printf("%d",i);fflush(stdout);      q=(*bx-*cx)*(*fb-*fa); 
       linmin(p,xit,n,fret,func);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       if (fabs(fptt-(*fret)) > del) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         del=fabs(fptt-(*fret));      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         ibig=i;      if ((*bx-u)*(u-*cx) > 0.0) { 
       }        fu=(*func)(u); 
 #ifdef DEBUG      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       printf("%d %.12e",i,(*fret));        fu=(*func)(u); 
       for (j=1;j<=n;j++) {        if (fu < *fc) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         printf(" x(%d)=%.12e",j,xit[j]);            SHFT(*fb,*fc,fu,(*func)(u)) 
       }            } 
       for(j=1;j<=n;j++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         printf(" p=%.12e",p[j]);        u=ulim; 
       printf("\n");        fu=(*func)(u); 
 #endif      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        fu=(*func)(u); 
 #ifdef DEBUG      } 
       int k[2],l;      SHFT(*ax,*bx,*cx,u) 
       k[0]=1;        SHFT(*fa,*fb,*fc,fu) 
       k[1]=-1;        } 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /*************** linmin ************************/
       printf("\n");  
       for(l=0;l<=1;l++) {  int ncom; 
         for (j=1;j<=n;j++) {  double *pcom,*xicom;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double (*nrfunc)(double []); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);   
         }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  { 
       }    double brent(double ax, double bx, double cx, 
 #endif                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       free_vector(xit,1,n);                double *fc, double (*func)(double)); 
       free_vector(xits,1,n);    int j; 
       free_vector(ptt,1,n);    double xx,xmin,bx,ax; 
       free_vector(pt,1,n);    double fx,fb,fa;
       return;   
     }    ncom=n; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    pcom=vector(1,n); 
     for (j=1;j<=n;j++) {    xicom=vector(1,n); 
       ptt[j]=2.0*p[j]-pt[j];    nrfunc=func; 
       xit[j]=p[j]-pt[j];    for (j=1;j<=n;j++) { 
       pt[j]=p[j];      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
     fptt=(*func)(ptt);    } 
     if (fptt < fp) {    ax=0.0; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    xx=1.0; 
       if (t < 0.0) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         linmin(p,xit,n,fret,func);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           xi[j][ibig]=xi[j][n];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           xi[j][n]=xit[j];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }  #endif
 #ifdef DEBUG    for (j=1;j<=n;j++) { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      xi[j] *= xmin; 
         for(j=1;j<=n;j++)      p[j] += xi[j]; 
           printf(" %.12e",xit[j]);    } 
         printf("\n");    free_vector(xicom,1,n); 
 #endif    free_vector(pcom,1,n); 
       }  } 
     }  
   }  /*************** powell ************************/
 }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
 /**** Prevalence limit ****************/  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)                double (*func)(double [])); 
 {    int i,ibig,j; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double del,t,*pt,*ptt,*xit;
      matrix by transitions matrix until convergence is reached */    double fp,fptt;
     double *xits;
   int i, ii,j,k;    pt=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    ptt=vector(1,n); 
   double **matprod2();    xit=vector(1,n); 
   double **out, cov[NCOVMAX], **pmij();    xits=vector(1,n); 
   double **newm;    *fret=(*func)(p); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)      fp=(*fret); 
     for (j=1;j<=nlstate+ndeath;j++){      ibig=0; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      del=0.0; 
     }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
    cov[1]=1.;      fprintf(ficrespow,"%d %.12f",*iter,*fret);
        for (i=1;i<=n;i++) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf(" %d %.12f",i, p[i]);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fprintf(ficlog," %d %.12lf",i, p[i]);
     newm=savm;        fprintf(ficrespow," %.12lf", p[i]);
     /* Covariates have to be included here again */      }
      cov[2]=agefin;      printf("\n");
        fprintf(ficlog,"\n");
       for (k=1; k<=cptcovn;k++) {      fprintf(ficrespow,"\n");
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      for (i=1;i<=n;i++) { 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       }        fptt=(*fret); 
       for (k=1; k<=cptcovage;k++)  #ifdef DEBUG
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        printf("fret=%lf \n",*fret);
       for (k=1; k<=cptcovprod;k++)        fprintf(ficlog,"fret=%lf \n",*fret);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #endif
         printf("%d",i);fflush(stdout);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        fprintf(ficlog,"%d",i);fflush(ficlog);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          del=fabs(fptt-(*fret)); 
           ibig=i; 
     savm=oldm;        } 
     oldm=newm;  #ifdef DEBUG
     maxmax=0.;        printf("%d %.12e",i,(*fret));
     for(j=1;j<=nlstate;j++){        fprintf(ficlog,"%d %.12e",i,(*fret));
       min=1.;        for (j=1;j<=n;j++) {
       max=0.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for(i=1; i<=nlstate; i++) {          printf(" x(%d)=%.12e",j,xit[j]);
         sumnew=0;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        }
         prlim[i][j]= newm[i][j]/(1-sumnew);        for(j=1;j<=n;j++) {
         max=FMAX(max,prlim[i][j]);          printf(" p=%.12e",p[j]);
         min=FMIN(min,prlim[i][j]);          fprintf(ficlog," p=%.12e",p[j]);
       }        }
       maxmin=max-min;        printf("\n");
       maxmax=FMAX(maxmax,maxmin);        fprintf(ficlog,"\n");
     }  #endif
     if(maxmax < ftolpl){      } 
       return prlim;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
   }        int k[2],l;
 }        k[0]=1;
         k[1]=-1;
 /*************** transition probabilities ***************/        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        for (j=1;j<=n;j++) {
 {          printf(" %.12e",p[j]);
   double s1, s2;          fprintf(ficlog," %.12e",p[j]);
   /*double t34;*/        }
   int i,j,j1, nc, ii, jj;        printf("\n");
         fprintf(ficlog,"\n");
     for(i=1; i<= nlstate; i++){        for(l=0;l<=1;l++) {
     for(j=1; j<i;j++){          for (j=1;j<=n;j++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         /*s2 += param[i][j][nc]*cov[nc];*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       ps[i][j]=s2;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        }
     }  #endif
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        free_vector(xit,1,n); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        free_vector(xits,1,n); 
       }        free_vector(ptt,1,n); 
       ps[i][j]=s2;        free_vector(pt,1,n); 
     }        return; 
   }      } 
     /*ps[3][2]=1;*/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   for(i=1; i<= nlstate; i++){        ptt[j]=2.0*p[j]-pt[j]; 
      s1=0;        xit[j]=p[j]-pt[j]; 
     for(j=1; j<i; j++)        pt[j]=p[j]; 
       s1+=exp(ps[i][j]);      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      fptt=(*func)(ptt); 
       s1+=exp(ps[i][j]);      if (fptt < fp) { 
     ps[i][i]=1./(s1+1.);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(j=1; j<i; j++)        if (t < 0.0) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          linmin(p,xit,n,fret,func); 
     for(j=i+1; j<=nlstate+ndeath; j++)          for (j=1;j<=n;j++) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];            xi[j][ibig]=xi[j][n]; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */            xi[j][n]=xit[j]; 
   } /* end i */          }
   #ifdef DEBUG
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(jj=1; jj<= nlstate+ndeath; jj++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       ps[ii][jj]=0;          for(j=1;j<=n;j++){
       ps[ii][ii]=1;            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
   }          }
           printf("\n");
           fprintf(ficlog,"\n");
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){        }
      printf("%lf ",ps[ii][jj]);      } 
    }    } 
     printf("\n ");  } 
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /**** Prevalence limit (stable prevalence)  ****************/
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   goto end;*/  {
     return ps;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 }       matrix by transitions matrix until convergence is reached */
   
 /**************** Product of 2 matrices ******************/    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double **matprod2();
 {    double **out, cov[NCOVMAX], **pmij();
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    double **newm;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    double agefin, delaymax=50 ; /* Max number of years to converge */
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns    for (ii=1;ii<=nlstate+ndeath;ii++)
      a pointer to pointers identical to out */      for (j=1;j<=nlstate+ndeath;j++){
   long i, j, k;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=nrl; i<= nrh; i++)      }
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)     cov[1]=1.;
         out[i][k] +=in[i][j]*b[j][k];   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return out;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
        cov[2]=agefin;
 /************* Higher Matrix Product ***************/    
         for (k=1; k<=cptcovn;k++) {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          cov[2+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]]);*/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        }
      duration (i.e. until        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for (k=1; k<=cptcovprod;k++)
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      included manually here.        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   int i, j, d, h, k;      savm=oldm;
   double **out, cov[NCOVMAX];      oldm=newm;
   double **newm;      maxmax=0.;
       for(j=1;j<=nlstate;j++){
   /* Hstepm could be zero and should return the unit matrix */        min=1.;
   for (i=1;i<=nlstate+ndeath;i++)        max=0.;
     for (j=1;j<=nlstate+ndeath;j++){        for(i=1; i<=nlstate; i++) {
       oldm[i][j]=(i==j ? 1.0 : 0.0);          sumnew=0;
       po[i][j][0]=(i==j ? 1.0 : 0.0);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     }          prlim[i][j]= newm[i][j]/(1-sumnew);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          max=FMAX(max,prlim[i][j]);
   for(h=1; h <=nhstepm; h++){          min=FMIN(min,prlim[i][j]);
     for(d=1; d <=hstepm; d++){        }
       newm=savm;        maxmin=max-min;
       /* Covariates have to be included here again */        maxmax=FMAX(maxmax,maxmin);
       cov[1]=1.;      }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      if(maxmax < ftolpl){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        return prlim;
       for (k=1; k<=cptcovage;k++)      }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
       for (k=1; k<=cptcovprod;k++)  }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /*************** transition probabilities ***************/ 
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  {
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double s1, s2;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    /*double t34;*/
       savm=oldm;    int i,j,j1, nc, ii, jj;
       oldm=newm;  
     }      for(i=1; i<= nlstate; i++){
     for(i=1; i<=nlstate+ndeath; i++)      for(j=1; j<i;j++){
       for(j=1;j<=nlstate+ndeath;j++) {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         po[i][j][h]=newm[i][j];          /*s2 += param[i][j][nc]*cov[nc];*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
          */          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
       }        }
   } /* end h */        ps[i][j]=s2;
   return po;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 }      }
       for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 /*************** log-likelihood *************/          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 double func( double *x)          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 {        }
   int i, ii, j, k, mi, d, kk;        ps[i][j]=s2;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      }
   double **out;    }
   double sw; /* Sum of weights */      /*ps[3][2]=1;*/
   double lli; /* Individual log likelihood */  
   long ipmx;    for(i=1; i<= nlstate; i++){
   /*extern weight */       s1=0;
   /* We are differentiating ll according to initial status */      for(j=1; j<i; j++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        s1+=exp(ps[i][j]);
   /*for(i=1;i<imx;i++)      for(j=i+1; j<=nlstate+ndeath; j++)
     printf(" %d\n",s[4][i]);        s1+=exp(ps[i][j]);
   */      ps[i][i]=1./(s1+1.);
   cov[1]=1.;      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for(mi=1; mi<= wav[i]-1; mi++){    } /* end i */
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(d=0; d<dh[mi][i]; d++){      for(jj=1; jj<= nlstate+ndeath; jj++){
         newm=savm;        ps[ii][jj]=0;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        ps[ii][ii]=1;
         for (kk=1; kk<=cptcovage;kk++) {      }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    }
         }  
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      for(jj=1; jj<= nlstate+ndeath; jj++){
         savm=oldm;       printf("%lf ",ps[ii][jj]);
         oldm=newm;     }
              printf("\n ");
              }
       } /* end mult */      printf("\n ");printf("%lf ",cov[2]);*/
        /*
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    goto end;*/
       ipmx +=1;      return ps;
       sw += weight[i];  }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  /**************** Product of 2 matrices ******************/
   } /* end of individual */  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   return -l;    /* in, b, out are matrice of pointers which should have been initialized 
 }       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     long i, j, k;
 /*********** Maximum Likelihood Estimation ***************/    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 {          out[i][k] +=in[i][j]*b[j][k];
   int i,j, iter;  
   double **xi,*delti;    return out;
   double fret;  }
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  /************* Higher Matrix Product ***************/
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   powell(p,xi,npar,ftol,&iter,&fret,func);  {
     /* Computes the transition matrix starting at age 'age' over 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));       'nhstepm*hstepm*stepm' months (i.e. until
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       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 
        (typically every 2 years instead of every month which is too big 
 /**** Computes Hessian and covariance matrix ***/       for the memory).
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))       Model is determined by parameters x and covariates have to be 
 {       included manually here. 
   double  **a,**y,*x,pd;  
   double **hess;       */
   int i, j,jk;  
   int *indx;    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   double hessii(double p[], double delta, int theta, double delti[]);    double **newm;
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* Hstepm could be zero and should return the unit matrix */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   hess=matrix(1,npar,1,npar);        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
   printf("\nCalculation of the hessian matrix. Wait...\n");      }
   for (i=1;i<=npar;i++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     printf("%d",i);fflush(stdout);    for(h=1; h <=nhstepm; h++){
     hess[i][i]=hessii(p,ftolhess,i,delti);      for(d=1; d <=hstepm; d++){
     /*printf(" %f ",p[i]);*/        newm=savm;
     /*printf(" %lf ",hess[i][i]);*/        /* Covariates have to be included here again */
   }        cov[1]=1.;
          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   for (i=1;i<=npar;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (j=1;j<=npar;j++)  {        for (k=1; k<=cptcovage;k++)
       if (j>i) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         printf(".%d%d",i,j);fflush(stdout);        for (k=1; k<=cptcovprod;k++)
         hess[i][j]=hessij(p,delti,i,j);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  
       }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   printf("\n");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        oldm=newm;
        }
   a=matrix(1,npar,1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   y=matrix(1,npar,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   x=vector(1,npar);          po[i][j][h]=newm[i][j];
   indx=ivector(1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   for (i=1;i<=npar;i++)           */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);    } /* end h */
     return po;
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);  /*************** log-likelihood *************/
     for (i=1;i<=npar;i++){  double func( double *x)
       matcov[i][j]=x[i];  {
     }    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   printf("\n#Hessian matrix#\n");    double sw; /* Sum of weights */
   for (i=1;i<=npar;i++) {    double lli; /* Individual log likelihood */
     for (j=1;j<=npar;j++) {    int s1, s2;
       printf("%.3e ",hess[i][j]);    double bbh, survp;
     }    long ipmx;
     printf("\n");    /*extern weight */
   }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /* Recompute Inverse */    /*for(i=1;i<imx;i++) 
   for (i=1;i<=npar;i++)      printf(" %d\n",s[4][i]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    */
   ludcmp(a,npar,indx,&pd);    cov[1]=1.;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   for (j=1;j<=npar;j++) {    if(mle==1){
     for (i=1;i<=npar;i++) x[i]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     x[j]=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     lubksb(a,npar,indx,x);        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<=npar;i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       y[i][j]=x[i];            for (j=1;j<=nlstate+ndeath;j++){
       printf("%.3e ",y[i][j]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n");            }
   }          for(d=0; d<dh[mi][i]; d++){
   */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(a,1,npar,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(y,1,npar,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_vector(x,1,npar);            }
   free_ivector(indx,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_matrix(hess,1,npar,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
 }          } /* end mult */
         
 /*************** hessian matrix ****************/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 double hessii( double x[], double delta, int theta, double delti[])          /* 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 
   int i;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   int l=1, lmax=20;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double k1,k2;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double p2[NPARMAX+1];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double res;           * probability in order to take into account the bias as a fraction of the way
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double fx;           * -stepm/2 to stepm/2 .
   int k=0,kmax=10;           * For stepm=1 the results are the same as for previous versions of Imach.
   double l1;           * For stepm > 1 the results are less biased than in previous versions. 
            */
   fx=func(x);          s1=s[mw[mi][i]][i];
   for (i=1;i<=npar;i++) p2[i]=x[i];          s2=s[mw[mi+1][i]][i];
   for(l=0 ; l <=lmax; l++){          bbh=(double)bh[mi][i]/(double)stepm; 
     l1=pow(10,l);          /* bias is positive if real duration
     delts=delt;           * is higher than the multiple of stepm and negative otherwise.
     for(k=1 ; k <kmax; k=k+1){           */
       delt = delta*(l1*k);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       p2[theta]=x[theta] +delt;          if( s2 > nlstate){ 
       k1=func(p2)-fx;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       p2[theta]=x[theta]-delt;               to the likelihood is the probability to die between last step unit time and current 
       k2=func(p2)-fx;               step unit time, which is also the differences between probability to die before dh 
       /*res= (k1-2.0*fx+k2)/delt/delt; */               and probability to die before dh-stepm . 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */               In version up to 0.92 likelihood was computed
                as if date of death was unknown. Death was treated as any other
 #ifdef DEBUG          health state: the date of the interview describes the actual state
       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);          and not the date of a change in health state. The former idea was
 #endif          to consider that at each interview the state was recorded
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          (healthy, disable or death) and IMaCh was corrected; but when we
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          introduced the exact date of death then we should have modified
         k=kmax;          the contribution of an exact death to the likelihood. This new
       }          contribution is smaller and very dependent of the step unit
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          stepm. It is no more the probability to die between last interview
         k=kmax; l=lmax*10.;          and month of death but the probability to survive from last
       }          interview up to one month before death multiplied by the
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          probability to die within a month. Thanks to Chris
         delts=delt;          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
     }          which slows down the processing. The difference can be up to 10%
   }          lower mortality.
   delti[theta]=delts;            */
   return res;            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
 }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  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 */
 double hessij( double x[], double delti[], int thetai,int thetaj)          } 
 {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int i;          /*if(lli ==000.0)*/
   int l=1, l1, lmax=20;          /*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); */
   double k1,k2,k3,k4,res,fx;          ipmx +=1;
   double p2[NPARMAX+1];          sw += weight[i];
   int k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   fx=func(x);      } /* end of individual */
   for (k=1; k<=2; k++) {    }  else if(mle==2){
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     k1=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]+delti[thetai]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     k2=func(p2)-fx;            }
            for(d=0; d<=dh[mi][i]; d++){
     p2[thetai]=x[thetai]-delti[thetai]/k;            newm=savm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     k3=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetai]=x[thetai]-delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     k4=func(p2)-fx;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            savm=oldm;
 #ifdef DEBUG            oldm=newm;
     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);          } /* end mult */
 #endif        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   return res;          /* 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 
 /************** Inverse of matrix **************/           * the nearest (and in case of equal distance, to the lowest) interval but now
 void ludcmp(double **a, int n, int *indx, double *d)           * 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
   int i,imax,j,k;           * probability in order to take into account the bias as a fraction of the way
   double big,dum,sum,temp;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double *vv;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
   vv=vector(1,n);           * For stepm > 1 the results are less biased than in previous versions. 
   *d=1.0;           */
   for (i=1;i<=n;i++) {          s1=s[mw[mi][i]][i];
     big=0.0;          s2=s[mw[mi+1][i]][i];
     for (j=1;j<=n;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
       if ((temp=fabs(a[i][j])) > big) big=temp;          /* bias is positive if real duration
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");           * is higher than the multiple of stepm and negative otherwise.
     vv[i]=1.0/big;           */
   }          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 */
   for (j=1;j<=n;j++) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for (i=1;i<j;i++) {          /*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 */
       sum=a[i][j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          /*if(lli ==000.0)*/
       a[i][j]=sum;          /*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;
     big=0.0;          sw += weight[i];
     for (i=j;i<=n;i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       sum=a[i][j];        } /* end of wave */
       for (k=1;k<j;k++)      } /* end of individual */
         sum -= a[i][k]*a[k][j];    }  else if(mle==3){  /* exponential inter-extrapolation */
       a[i][j]=sum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         big=dum;        for(mi=1; mi<= wav[i]-1; mi++){
         imax=i;          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != imax) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<=n;k++) {            }
         dum=a[imax][k];          for(d=0; d<dh[mi][i]; d++){
         a[imax][k]=a[j][k];            newm=savm;
         a[j][k]=dum;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       *d = -(*d);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       vv[imax]=vv[j];            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     indx[j]=imax;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if (a[j][j] == 0.0) a[j][j]=TINY;            savm=oldm;
     if (j != n) {            oldm=newm;
       dum=1.0/(a[j][j]);          } /* end mult */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
   free_vector(vv,1,n);  /* Doesn't work */           * 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 
 }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
 void lubksb(double **a, int n, int *indx, double b[])           * (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
   int i,ii=0,ip,j;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double sum;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
   for (i=1;i<=n;i++) {           * For stepm > 1 the results are less biased than in previous versions. 
     ip=indx[i];           */
     sum=b[ip];          s1=s[mw[mi][i]][i];
     b[ip]=b[i];          s2=s[mw[mi+1][i]][i];
     if (ii)          bbh=(double)bh[mi][i]/(double)stepm; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          /* bias is positive if real duration
     else if (sum) ii=i;           * is higher than the multiple of stepm and negative otherwise.
     b[i]=sum;           */
   }          /* 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 */
   for (i=n;i>=1;i--) {          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 */
     sum=b[i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          /*if(lli ==000.0)*/
     b[i]=sum/a[i][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); */
   }          ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************ Frequencies ********************/        } /* end of wave */
 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)      } /* end of individual */
 {  /* Some frequencies */    }else{  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ***freq; /* Frequencies */        for(mi=1; mi<= wav[i]-1; mi++){
   double *pp;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double pos, k2, dateintsum=0,k2cpt=0;            for (j=1;j<=nlstate+ndeath;j++){
   FILE *ficresp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   char fileresp[FILENAMELENGTH];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   pp=vector(1,nlstate);          for(d=0; d<dh[mi][i]; d++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            newm=savm;
   strcpy(fileresp,"p");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   strcat(fileresp,fileres);            for (kk=1; kk<=cptcovage;kk++) {
   if((ficresp=fopen(fileresp,"w"))==NULL) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     printf("Problem with prevalence resultfile: %s\n", fileresp);            }
     exit(0);          
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   j1=0;            savm=oldm;
             oldm=newm;
   j=cptcoveff;          } /* end mult */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for(k1=1; k1<=j;k1++){          ipmx +=1;
    for(i1=1; i1<=ncodemax[k1];i1++){          sw += weight[i];
        j1++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        } /* end of wave */
          scanf("%d", i);*/      } /* end of individual */
         for (i=-1; i<=nlstate+ndeath; i++)      } /* End of if */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            for(m=agemin; m <= agemax+3; m++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              freq[i][jk][m]=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
         dateintsum=0;  }
         k2cpt=0;  
        for (i=1; i<=imx; i++) {  
          bool=1;  /*********** Maximum Likelihood Estimation ***************/
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  {
                bool=0;    int i,j, iter;
          }    double **xi;
          if (bool==1) {    double fret;
            for(m=firstpass; m<=lastpass; m++){    char filerespow[FILENAMELENGTH];
              k2=anint[m][i]+(mint[m][i]/12.);    xi=matrix(1,npar,1,npar);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (i=1;i<=npar;i++)
                if(agev[m][i]==0) agev[m][i]=agemax+1;      for (j=1;j<=npar;j++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;        xi[i][j]=(i==j ? 1.0 : 0.0);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    strcpy(filerespow,"pow"); 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    strcat(filerespow,fileres);
                  dateintsum=dateintsum+k2;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
                  k2cpt++;      printf("Problem with resultfile: %s\n", filerespow);
                }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
              }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
            }    for (i=1;i<=nlstate;i++)
          }      for(j=1;j<=nlstate+ndeath;j++)
        }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
            fprintf(ficrespow,"\n");
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
         if  (cptcovn>0) {    fclose(ficrespow);
          fprintf(ficresp, "\n#********** Variable ");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        fprintf(ficresp, "**********\n#");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         }  
        for(i=1; i<=nlstate;i++)  }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");  /**** Computes Hessian and covariance matrix ***/
          void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   for(i=(int)agemin; i <= (int)agemax+3; i++){  {
     if(i==(int)agemax+3)    double  **a,**y,*x,pd;
       printf("Total");    double **hess;
     else    int i, j,jk;
       printf("Age %d", i);    int *indx;
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double hessii(double p[], double delta, int theta, double delti[]);
         pp[jk] += freq[jk][m][i];    double hessij(double p[], double delti[], int i, int j);
     }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     for(jk=1; jk <=nlstate ; jk++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    hess=matrix(1,npar,1,npar);
       if(pp[jk]>=1.e-10)  
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    printf("\nCalculation of the hessian matrix. Wait...\n");
       else    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for (i=1;i<=npar;i++){
     }      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
      for(jk=1; jk <=nlstate ; jk++){      hess[i][i]=hessii(p,ftolhess,i,delti);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      /*printf(" %f ",p[i]);*/
         pp[jk] += freq[jk][m][i];      /*printf(" %lf ",hess[i][i]);*/
      }    }
     
     for(jk=1,pos=0; jk <=nlstate ; jk++)    for (i=1;i<=npar;i++) {
       pos += pp[jk];      for (j=1;j<=npar;j++)  {
     for(jk=1; jk <=nlstate ; jk++){        if (j>i) { 
       if(pos>=1.e-5)          printf(".%d%d",i,j);fflush(stdout);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       else          hess[i][j]=hessij(p,delti,i,j);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          hess[j][i]=hess[i][j];    
       if( i <= (int) agemax){          /*printf(" %lf ",hess[i][j]);*/
         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;    }
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    printf("\n");
         }    fprintf(ficlog,"\n");
       else  
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    
     for(jk=-1; jk <=nlstate+ndeath; jk++)    a=matrix(1,npar,1,npar);
       for(m=-1; m <=nlstate+ndeath; m++)    y=matrix(1,npar,1,npar);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    x=vector(1,npar);
     if(i <= (int) agemax)    indx=ivector(1,npar);
       fprintf(ficresp,"\n");    for (i=1;i<=npar;i++)
     printf("\n");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     }    ludcmp(a,npar,indx,&pd);
     }  
  }    for (j=1;j<=npar;j++) {
   dateintmean=dateintsum/k2cpt;      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
   fclose(ficresp);      lubksb(a,npar,indx,x);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1;i<=npar;i++){ 
   free_vector(pp,1,nlstate);        matcov[i][j]=x[i];
       }
   /* End of Freq */    }
 }  
     printf("\n#Hessian matrix#\n");
 /************ Prevalence ********************/    fprintf(ficlog,"\n#Hessian matrix#\n");
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    for (i=1;i<=npar;i++) { 
 {  /* Some frequencies */      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double ***freq; /* Frequencies */      }
   double *pp;      printf("\n");
   double pos, k2;      fprintf(ficlog,"\n");
     }
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   j1=0;    ludcmp(a,npar,indx,&pd);
    
   j=cptcoveff;    /*  printf("\n#Hessian matrix recomputed#\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
      for (j=1;j<=npar;j++) {
  for(k1=1; k1<=j;k1++){      for (i=1;i<=npar;i++) x[i]=0;
     for(i1=1; i1<=ncodemax[k1];i1++){      x[j]=1;
       j1++;      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
       for (i=-1; i<=nlstate+ndeath; i++)          y[i][j]=x[i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)          printf("%.3e ",y[i][j]);
           for(m=agemin; m <= agemax+3; m++)        fprintf(ficlog,"%.3e ",y[i][j]);
             freq[i][jk][m]=0;      }
            printf("\n");
       for (i=1; i<=imx; i++) {      fprintf(ficlog,"\n");
         bool=1;    }
         if  (cptcovn>0) {    */
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    free_matrix(a,1,npar,1,npar);
               bool=0;    free_matrix(y,1,npar,1,npar);
         }    free_vector(x,1,npar);
         if (bool==1) {    free_ivector(indx,1,npar);
           for(m=firstpass; m<=lastpass; m++){    free_matrix(hess,1,npar,1,npar);
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  }
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  /*************** hessian matrix ****************/
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  double hessii( double x[], double delta, int theta, double delti[])
             }  {
           }    int i;
         }    int l=1, lmax=20;
       }    double k1,k2;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    double p2[NPARMAX+1];
           for(jk=1; jk <=nlstate ; jk++){    double res;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
               pp[jk] += freq[jk][m][i];    double fx;
           }    int k=0,kmax=10;
           for(jk=1; jk <=nlstate ; jk++){    double l1;
             for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
            for(l=0 ; l <=lmax; l++){
          for(jk=1; jk <=nlstate ; jk++){      l1=pow(10,l);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      delts=delt;
              pp[jk] += freq[jk][m][i];      for(k=1 ; k <kmax; k=k+1){
          }        delt = delta*(l1*k);
                  p2[theta]=x[theta] +delt;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
          for(jk=1; jk <=nlstate ; jk++){                  k2=func(p2)-fx;
            if( i <= (int) agemax){        /*res= (k1-2.0*fx+k2)/delt/delt; */
              if(pos>=1.e-5){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                probs[i][jk][j1]= pp[jk]/pos;        
              }  #ifdef DEBUG
            }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
          }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
            #endif
         }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   }          k=kmax;
          }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          k=kmax; l=lmax*10.;
   free_vector(pp,1,nlstate);        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 }  /* End of Freq */          delts=delt;
         }
 /************* 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)    delti[theta]=delts;
 {    return res; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    
      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  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  double hessij( double x[], double delti[], int thetai,int thetaj)
      and mw[mi+1][i]. dh depends on stepm.  {
      */    int i;
     int l=1, l1, lmax=20;
   int i, mi, m;    double k1,k2,k3,k4,res,fx;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double p2[NPARMAX+1];
      double sum=0., jmean=0.;*/    int k;
   
   int j, k=0,jk, ju, jl;    fx=func(x);
   double sum=0.;    for (k=1; k<=2; k++) {
   jmin=1e+5;      for (i=1;i<=npar;i++) p2[i]=x[i];
   jmax=-1;      p2[thetai]=x[thetai]+delti[thetai]/k;
   jmean=0.;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for(i=1; i<=imx; i++){      k1=func(p2)-fx;
     mi=0;    
     m=firstpass;      p2[thetai]=x[thetai]+delti[thetai]/k;
     while(s[m][i] <= nlstate){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       if(s[m][i]>=1)      k2=func(p2)-fx;
         mw[++mi][i]=m;    
       if(m >=lastpass)      p2[thetai]=x[thetai]-delti[thetai]/k;
         break;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       else      k3=func(p2)-fx;
         m++;    
     }/* end while */      p2[thetai]=x[thetai]-delti[thetai]/k;
     if (s[m][i] > nlstate){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       mi++;     /* Death is another wave */      k4=func(p2)-fx;
       /* if(mi==0)  never been interviewed correctly before death */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
          /* Only death is a correct wave */  #ifdef DEBUG
       mw[mi][i]=m;      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);
   #endif
     wav[i]=mi;    }
     if(mi==0)    return res;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  }
   }  
   /************** Inverse of matrix **************/
   for(i=1; i<=imx; i++){  void ludcmp(double **a, int n, int *indx, double *d) 
     for(mi=1; mi<wav[i];mi++){  { 
       if (stepm <=0)    int i,imax,j,k; 
         dh[mi][i]=1;    double big,dum,sum,temp; 
       else{    double *vv; 
         if (s[mw[mi+1][i]][i] > nlstate) {   
           if (agedc[i] < 2*AGESUP) {    vv=vector(1,n); 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    *d=1.0; 
           if(j==0) j=1;  /* Survives at least one month after exam */    for (i=1;i<=n;i++) { 
           k=k+1;      big=0.0; 
           if (j >= jmax) jmax=j;      for (j=1;j<=n;j++) 
           if (j <= jmin) jmin=j;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           sum=sum+j;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      vv[i]=1.0/big; 
           }    } 
         }    for (j=1;j<=n;j++) { 
         else{      for (i=1;i<j;i++) { 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        sum=a[i][j]; 
           k=k+1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           if (j >= jmax) jmax=j;        a[i][j]=sum; 
           else if (j <= jmin)jmin=j;      } 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      big=0.0; 
           sum=sum+j;      for (i=j;i<=n;i++) { 
         }        sum=a[i][j]; 
         jk= j/stepm;        for (k=1;k<j;k++) 
         jl= j -jk*stepm;          sum -= a[i][k]*a[k][j]; 
         ju= j -(jk+1)*stepm;        a[i][j]=sum; 
         if(jl <= -ju)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           dh[mi][i]=jk;          big=dum; 
         else          imax=i; 
           dh[mi][i]=jk+1;        } 
         if(dh[mi][i]==0)      } 
           dh[mi][i]=1; /* At least one step */      if (j != imax) { 
       }        for (k=1;k<=n;k++) { 
     }          dum=a[imax][k]; 
   }          a[imax][k]=a[j][k]; 
   jmean=sum/k;          a[j][k]=dum; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        } 
  }        *d = -(*d); 
 /*********** Tricode ****************************/        vv[imax]=vv[j]; 
 void tricode(int *Tvar, int **nbcode, int imx)      } 
 {      indx[j]=imax; 
   int Ndum[20],ij=1, k, j, i;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   int cptcode=0;      if (j != n) { 
   cptcoveff=0;        dum=1.0/(a[j][j]); 
          for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for (k=0; k<19; k++) Ndum[k]=0;      } 
   for (k=1; k<=7; k++) ncodemax[k]=0;    } 
     free_vector(vv,1,n);  /* Doesn't work */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  ;
     for (i=1; i<=imx; i++) {  } 
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  void lubksb(double **a, int n, int *indx, double b[]) 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  { 
       if (ij > cptcode) cptcode=ij;    int i,ii=0,ip,j; 
     }    double sum; 
    
     for (i=0; i<=cptcode; i++) {    for (i=1;i<=n;i++) { 
       if(Ndum[i]!=0) ncodemax[j]++;      ip=indx[i]; 
     }      sum=b[ip]; 
     ij=1;      b[ip]=b[i]; 
       if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     for (i=1; i<=ncodemax[j]; i++) {      else if (sum) ii=i; 
       for (k=0; k<=19; k++) {      b[i]=sum; 
         if (Ndum[k] != 0) {    } 
           nbcode[Tvar[j]][ij]=k;    for (i=n;i>=1;i--) { 
           ij++;      sum=b[i]; 
         }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         if (ij > ncodemax[j]) break;      b[i]=sum/a[i][i]; 
       }      } 
     }  } 
   }    
   /************ Frequencies ********************/
  for (k=0; k<19; k++) Ndum[k]=0;  void  freqsummary(char fileres[], int iagemin, int iagemax, 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)
   {  /* Some frequencies */
  for (i=1; i<=ncovmodel-2; i++) {    
       ij=Tvar[i];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       Ndum[ij]++;    int first;
     }    double ***freq; /* Frequencies */
     double *pp, **prop;
  ij=1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
  for (i=1; i<=10; i++) {    FILE *ficresp;
    if((Ndum[i]!=0) && (i<=ncov)){    char fileresp[FILENAMELENGTH];
      Tvaraff[ij]=i;    
      ij++;    pp=vector(1,nlstate);
    }    prop=matrix(1,nlstate,iagemin,iagemax+3);
  }    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
     cptcoveff=ij-1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
 }      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 /*********** Health Expectancies ****************/      exit(0);
     }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
 {    j1=0;
   /* Health expectancies */    
   int i, j, nhstepm, hstepm, h, nstepm, k;    j=cptcoveff;
   double age, agelim,hf;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double ***p3mat;  
      first=1;
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");    for(k1=1; k1<=j;k1++){
   for(i=1; i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
     for(j=1; j<=nlstate;j++)        j1++;
       fprintf(ficreseij," %1d-%1d",i,j);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   fprintf(ficreseij,"\n");          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
   k=1;             /* For example stepm=6 months */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */            for(m=iagemin; m <= iagemax+3; m++)
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */              freq[i][jk][m]=0;
   /* 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 (i=1; i<=nlstate; i++)  
      nstepm is the number of stepm from age to agelin.        for(m=iagemin; m <= iagemax+3; m++)
      Look at hpijx to understand the reason of that which relies in memory size          prop[i][m]=0;
      and note for a fixed period like k years */        
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        dateintsum=0;
      survival function given by stepm (the optimization length). Unfortunately it        k2cpt=0;
      means that if the survival funtion is printed only each two years of age and if        for (i=1; i<=imx; i++) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          bool=1;
      results. So we changed our mind and took the option of the best precision.          if  (cptcovn>0) {
   */            for (z1=1; z1<=cptcoveff; z1++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   agelim=AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          if (bool==1){
     /* nhstepm age range expressed in number of stepm */            for(m=firstpass; m<=lastpass; m++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              k2=anint[m][i]+(mint[m][i]/12.);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     if (stepm >= YEARM) hstepm=1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored                if (m<lastpass) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                }
     for(i=1; i<=nlstate;i++)                
       for(j=1; j<=nlstate;j++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){                  dateintsum=dateintsum+k2;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;                  k2cpt++;
           /* 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(ficreseij,"%3.0f",age );            }
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);         
       }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if  (cptcovn>0) {
   }          fprintf(ficresp, "\n#********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 /************ 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)        for(i=1; i<=nlstate;i++) 
 {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /* Variance of health expectancies */        fprintf(ficresp, "\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        
   double **newm;        for(i=iagemin; i <= iagemax+3; i++){
   double **dnewm,**doldm;          if(i==iagemax+3){
   int i, j, nhstepm, hstepm, h;            fprintf(ficlog,"Total");
   int k, cptcode;          }else{
   double *xp;            if(first==1){
   double **gp, **gm;              first=0;
   double ***gradg, ***trgradg;              printf("See log file for details...\n");
   double ***p3mat;            }
   double age,agelim;            fprintf(ficlog,"Age %d", i);
   int theta;          }
           for(jk=1; jk <=nlstate ; jk++){
    fprintf(ficresvij,"# Covariances of life expectancies\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fprintf(ficresvij,"# Age");              pp[jk] += freq[jk][m][i]; 
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for(m=-1, pos=0; m <=0 ; m++)
   fprintf(ficresvij,"\n");              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
   xp=vector(1,npar);              if(first==1){
   dnewm=matrix(1,nlstate,1,npar);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   doldm=matrix(1,nlstate,1,nlstate);              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   hstepm=1*YEARM; /* Every year of age */            }else{
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              if(first==1)
   agelim = AGESUP;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            }
     if (stepm >= YEARM) hstepm=1;          }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     gp=matrix(0,nhstepm,1,nlstate);              pp[jk] += freq[jk][m][i];
     gm=matrix(0,nhstepm,1,nlstate);          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     for(theta=1; theta <=npar; theta++){            pos += pp[jk];
       for(i=1; i<=npar; i++){ /* Computes gradient */            posprop += prop[jk][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }          for(jk=1; jk <=nlstate ; jk++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              if(pos>=1.e-5){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       if (popbased==1) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(i=1; i<=nlstate;i++)            }else{
           prlim[i][i]=probs[(int)age][i][ij];              if(first==1)
       }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){            if( i <= iagemax){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              if(pos>=1.e-5){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         }                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]);*/
                  }
       for(i=1; i<=npar; i++) /* Computes gradient */              else
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
            
       if (popbased==1) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
         for(i=1; i<=nlstate;i++)            for(m=-1; m <=nlstate+ndeath; m++)
           prlim[i][i]=probs[(int)age][i][ij];              if(freq[jk][m][i] !=0 ) {
       }              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       for(j=1; j<= nlstate; j++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(h=0; h<=nhstepm; h++){              }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          if(i <= iagemax)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            fprintf(ficresp,"\n");
         }          if(first==1)
       }            printf("Others in log...\n");
           fprintf(ficlog,"\n");
       for(j=1; j<= nlstate; j++)        }
         for(h=0; h<=nhstepm; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    }
         }    dateintmean=dateintsum/k2cpt; 
     } /* End theta */   
     fclose(ficresp);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     for(h=0; h<=nhstepm; h++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       for(j=1; j<=nlstate;j++)    /* End of Freq */
         for(theta=1; theta <=npar; theta++)  }
           trgradg[h][j][theta]=gradg[h][theta][j];  
   /************ Prevalence ********************/
     for(i=1;i<=nlstate;i++)  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for(j=1;j<=nlstate;j++)  {  
         vareij[i][j][(int)age] =0.;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     for(h=0;h<=nhstepm;h++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
       for(k=0;k<=nhstepm;k++){       We still use firstpass and lastpass as another selection.
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);   
         for(i=1;i<=nlstate;i++)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           for(j=1;j<=nlstate;j++)    double ***freq; /* Frequencies */
             vareij[i][j][(int)age] += doldm[i][j];    double *pp, **prop;
       }    double pos,posprop; 
     }    double  y2; /* in fractional years */
     h=1;    int iagemin, iagemax;
     if (stepm >= YEARM) h=stepm/YEARM;  
     fprintf(ficresvij,"%.0f ",age );    iagemin= (int) agemin;
     for(i=1; i<=nlstate;i++)    iagemax= (int) agemax;
       for(j=1; j<=nlstate;j++){    /*pp=vector(1,nlstate);*/
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fprintf(ficresvij,"\n");    j1=0;
     free_matrix(gp,0,nhstepm,1,nlstate);    
     free_matrix(gm,0,nhstepm,1,nlstate);    j=cptcoveff;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(k1=1; k1<=j;k1++){
   } /* End age */      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   free_vector(xp,1,npar);        
   free_matrix(doldm,1,nlstate,1,npar);        for (i=1; i<=nlstate; i++)  
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
 }       
         for (i=1; i<=imx; i++) { /* Each individual */
 /************ Variance of prevlim ******************/          bool=1;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          if  (cptcovn>0) {
 {            for (z1=1; z1<=cptcoveff; z1++) 
   /* Variance of prevalence limit */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                bool=0;
   double **newm;          } 
   double **dnewm,**doldm;          if (bool==1) { 
   int i, j, nhstepm, hstepm;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   int k, cptcode;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   double *xp;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   double *gp, *gm;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double **gradg, **trgradg;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double age,agelim;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   int theta;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                      /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   fprintf(ficresvpl,"# Age");                  prop[s[m][i]][iagemax+3] += weight[i]; 
   for(i=1; i<=nlstate;i++)                } 
       fprintf(ficresvpl," %1d-%1d",i,i);              }
   fprintf(ficresvpl,"\n");            } /* end selection of waves */
           }
   xp=vector(1,npar);        }
   dnewm=matrix(1,nlstate,1,npar);        for(i=iagemin; i <= iagemax+3; i++){  
   doldm=matrix(1,nlstate,1,nlstate);          
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   hstepm=1*YEARM; /* Every year of age */            posprop += prop[jk][i]; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          } 
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(jk=1; jk <=nlstate ; jk++){     
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            if( i <=  iagemax){ 
     if (stepm >= YEARM) hstepm=1;              if(posprop>=1.e-5){ 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                probs[i][jk][j1]= prop[jk][i]/posprop;
     gradg=matrix(1,npar,1,nlstate);              } 
     gp=vector(1,nlstate);            } 
     gm=vector(1,nlstate);          }/* end jk */ 
         }/* end i */ 
     for(theta=1; theta <=npar; theta++){      } /* end i1 */
       for(i=1; i<=npar; i++){ /* Computes gradient */    } /* end k1 */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
       }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*free_vector(pp,1,nlstate);*/
       for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         gp[i] = prlim[i][i];  }  /* End of prevalence */
      
       for(i=1; i<=npar; i++) /* Computes gradient */  /************* Waves Concatenation ***************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  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)
       for(i=1;i<=nlstate;i++)  {
         gm[i] = prlim[i][i];    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
       for(i=1;i<=nlstate;i++)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     } /* End theta */       and mw[mi+1][i]. dh depends on stepm.
        */
     trgradg =matrix(1,nlstate,1,npar);  
     int i, mi, m;
     for(j=1; j<=nlstate;j++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for(theta=1; theta <=npar; theta++)       double sum=0., jmean=0.;*/
         trgradg[j][theta]=gradg[theta][j];    int first;
     int j, k=0,jk, ju, jl;
     for(i=1;i<=nlstate;i++)    double sum=0.;
       varpl[i][(int)age] =0.;    first=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    jmin=1e+5;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    jmax=-1;
     for(i=1;i<=nlstate;i++)    jmean=0.;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    for(i=1; i<=imx; i++){
       mi=0;
     fprintf(ficresvpl,"%.0f ",age );      m=firstpass;
     for(i=1; i<=nlstate;i++)      while(s[m][i] <= nlstate){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        if(s[m][i]>=1)
     fprintf(ficresvpl,"\n");          mw[++mi][i]=m;
     free_vector(gp,1,nlstate);        if(m >=lastpass)
     free_vector(gm,1,nlstate);          break;
     free_matrix(gradg,1,npar,1,nlstate);        else
     free_matrix(trgradg,1,nlstate,1,npar);          m++;
   } /* End age */      }/* end while */
       if (s[m][i] > nlstate){
   free_vector(xp,1,npar);        mi++;     /* Death is another wave */
   free_matrix(doldm,1,nlstate,1,npar);        /* if(mi==0)  never been interviewed correctly before death */
   free_matrix(dnewm,1,nlstate,1,nlstate);           /* Only death is a correct wave */
         mw[mi][i]=m;
 }      }
   
 /************ Variance of one-step probabilities  ******************/      wav[i]=mi;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      if(mi==0){
 {        if(first==0){
   int i, j;          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
   int k=0, cptcode;          first=1;
   double **dnewm,**doldm;        }
   double *xp;        if(first==1){
   double *gp, *gm;          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   double **gradg, **trgradg;        }
   double age,agelim, cov[NCOVMAX];      } /* end mi==0 */
   int theta;    } /* End individuals */
   char fileresprob[FILENAMELENGTH];  
     for(i=1; i<=imx; i++){
   strcpy(fileresprob,"prob");      for(mi=1; mi<wav[i];mi++){
   strcat(fileresprob,fileres);        if (stepm <=0)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          dh[mi][i]=1;
     printf("Problem with resultfile: %s\n", fileresprob);        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            if (agedc[i] < 2*AGESUP) {
              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */
   xp=vector(1,npar);            k=k+1;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if (j >= jmax) jmax=j;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            if (j <= jmin) jmin=j;
              sum=sum+j;
   cov[1]=1;            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   for (age=bage; age<=fage; age ++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     cov[2]=age;            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     gradg=matrix(1,npar,1,9);            }
     trgradg=matrix(1,9,1,npar);          }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          else{
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(theta=1; theta <=npar; theta++){            k=k+1;
       for(i=1; i<=npar; i++)            if (j >= jmax) jmax=j;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            else if (j <= jmin)jmin=j;
                  /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       k=0;            sum=sum+j;
       for(i=1; i<= (nlstate+ndeath); i++){          }
         for(j=1; j<=(nlstate+ndeath);j++){          jk= j/stepm;
            k=k+1;          jl= j -jk*stepm;
           gp[k]=pmmij[i][j];          ju= j -(jk+1)*stepm;
         }          if(mle <=1){ 
       }            if(jl==0){
               dh[mi][i]=jk;
       for(i=1; i<=npar; i++)              bh[mi][i]=0;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }else{ /* We want a negative bias in order to only have interpolation ie
                        * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              bh[mi][i]=ju;
       k=0;            }
       for(i=1; i<=(nlstate+ndeath); i++){          }else{
         for(j=1; j<=(nlstate+ndeath);j++){            if(jl <= -ju){
           k=k+1;              dh[mi][i]=jk;
           gm[k]=pmmij[i][j];              bh[mi][i]=jl;       /* bias is positive if real duration
         }                                   * is higher than the multiple of stepm and negative otherwise.
       }                                   */
                  }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            else{
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                dh[mi][i]=jk+1;
     }              bh[mi][i]=ju;
             }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            if(dh[mi][i]==0){
       for(theta=1; theta <=npar; theta++)              dh[mi][i]=1; /* At least one step */
       trgradg[j][theta]=gradg[theta][j];              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);*/
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          }
         } /* end if mle */
      pmij(pmmij,cov,ncovmodel,x,nlstate);      } /* end wave */
     }
      k=0;    jmean=sum/k;
      for(i=1; i<=(nlstate+ndeath); i++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
          k=k+1;   }
          gm[k]=pmmij[i][j];  
         }  /*********** Tricode ****************************/
      }  void tricode(int *Tvar, int **nbcode, int imx)
        {
      /*printf("\n%d ",(int)age);    
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
            int cptcode=0;
     cptcoveff=0; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));   
      }*/    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   fprintf(ficresprob,"\n%d ",(int)age);  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                                 modality*/ 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   }        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                                         Tvar[j]. If V=sex and male is 0 and 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                                         female is 1, then  cptcode=1.*/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      }
 }  
  free_vector(xp,1,npar);      for (i=0; i<=cptcode; i++) {
 fclose(ficresprob);        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 */
       }
 }  
       ij=1; 
 /******************* Printing html file ***********/      for (i=1; i<=ncodemax[j]; i++) {
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){        for (k=0; k<= maxncov; k++) {
   int jj1, k1, i1, cpt;          if (Ndum[k] != 0) {
   FILE *fichtm;            nbcode[Tvar[j]][ij]=k; 
   /*char optionfilehtm[FILENAMELENGTH];*/            /* 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; */
             
   strcpy(optionfilehtm,optionfile);            ij++;
   strcat(optionfilehtm,".htm");          }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          if (ij > ncodemax[j]) break; 
     printf("Problem with %s \n",optionfilehtm), exit(0);        }  
   }      } 
     }  
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
 Total number of observations=%d <br>   for (i=1; i<=ncovmodel-2; i++) { 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 <hr  size=\"2\" color=\"#EC5E5E\">     ij=Tvar[i];
 <li>Outputs files<br><br>\n     Ndum[ij]++;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n   }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>   ij=1;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>   for (i=1; i<= maxncov; i++) {
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>     if((Ndum[i]!=0) && (i<=ncovcol)){
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>       Tvaraff[ij]=i; /*For printing */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>       ij++;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>     }
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>   }
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>   
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>   cptcoveff=ij-1; /*Number of simple covariates*/
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  }
    
 fprintf(fichtm," <li>Graphs</li><p>");  /*********** Health Expectancies ****************/
   
  m=cptcoveff;  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   {
  jj1=0;    /* Health expectancies */
  for(k1=1; k1<=m;k1++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
    for(i1=1; i1<=ncodemax[k1];i1++){    double age, agelim, hf;
        jj1++;    double ***p3mat,***varhe;
        if (cptcovn > 0) {    double **dnewm,**doldm;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double *xp;
          for (cpt=1; cpt<=cptcoveff;cpt++)    double **gp, **gm;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double ***gradg, ***trgradg;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int theta;
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        xp=vector(1,npar);
        for(cpt=1; cpt<nlstate;cpt++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
        }    fprintf(ficreseij,"# Health expectancies\n");
     for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficreseij,"# Age");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    for(i=1; i<=nlstate;i++)
 interval) in state (%d): v%s%d%d.gif <br>      for(j=1; j<=nlstate;j++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          fprintf(ficreseij," %1d-%1d (SE)",i,j);
      }    fprintf(ficreseij,"\n");
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    if(estepm < stepm){
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }    }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    else  hstepm=estepm;   
 health expectancies in states (1) and (2): e%s%d.gif<br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     * This is mainly to measure the difference between two models: for example
 fprintf(fichtm,"\n</body>");     * 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 
    }     * progression in between and thus overestimating or underestimating according
 fclose(fichtm);     * to the curvature of the survival function. If, for the same date, we 
 }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
 /******************* Gnuplot file **************/     * hypothesis. A more precise result, taking into account a more precise
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){     * curvature will be obtained if estepm is as small as stepm. */
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    /* 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. 
   strcpy(optionfilegnuplot,optionfilefiname);       nhstepm is the number of hstepm from age to agelim 
   strcat(optionfilegnuplot,".plt");       nstepm is the number of stepm from age to agelin. 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       Look at hpijx to understand the reason of that which relies in memory size
     printf("Problem with file %s",optionfilegnuplot);       and note for a fixed period like estepm months */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
 #ifdef windows       means that if the survival funtion is printed only each two years of age and if
     fprintf(ficgp,"cd \"%s\" \n",pathc);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 #endif       results. So we changed our mind and took the option of the best precision.
 m=pow(2,cptcoveff);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {    agelim=AGESUP;
    for (k1=1; k1<= m ; k1 ++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
 #ifdef windows      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 #endif      /* if (stepm >= YEARM) hstepm=1;*/
 #ifdef unix      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       gp=matrix(0,nhstepm,1,nlstate*nlstate);
 for (i=1; i<= nlstate ; i ++) {      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     for (i=1; i<= nlstate ; i ++) {   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* Computing Variances of health expectancies */
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       for(theta=1; theta <=npar; theta++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=npar; i++){ 
 }            xp[i] = x[i] + (i==theta ?delti[theta]:0);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fprintf(ficgp,"\nset ter gif small size 400,300");    
 #endif        cptj=0;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<= nlstate; j++){
    }          for(i=1; i<=nlstate; i++){
   }            cptj=cptj+1;
   /*2 eme*/            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   for (k1=1; k1<= m ; k1 ++) {            }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          }
            }
     for (i=1; i<= nlstate+1 ; i ++) {       
       k=2*i;       
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for(i=1; i<=npar; i++) 
       for (j=1; j<= nlstate+1 ; j ++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        
 }          cptj=0;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(j=1; j<= nlstate; j++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(i=1;i<=nlstate;i++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            cptj=cptj+1;
       for (j=1; j<= nlstate+1 ; j ++) {            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 }              }
       fprintf(ficgp,"\" t\"\" w l 0,");          }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=1; j<= nlstate*nlstate; j++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(h=0; h<=nhstepm-1; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 }            }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");       } 
       else fprintf(ficgp,"\" t\"\" w l 0,");     
     }  /* End theta */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    
   /*3eme*/       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   for (k1=1; k1<= m ; k1 ++) {          for(theta=1; theta <=npar; theta++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {            trgradg[h][j][theta]=gradg[h][theta][j];
       k=2+nlstate*(cpt-1);       
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {       for(i=1;i<=nlstate*nlstate;i++)
         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);        for(j=1;j<=nlstate*nlstate;j++)
       }          varhe[i][j][(int)age] =0.;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }       printf("%d|",(int)age);fflush(stdout);
     }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
   /* CV preval stat */        for(k=0;k<=nhstepm-1;k++){
     for (k1=1; k1<= m ; k1 ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     for (cpt=1; cpt<nlstate ; cpt ++) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       k=3;          for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       for (i=1; i< nlstate ; i ++)        }
         fprintf(ficgp,"+$%d",k+i+1);      }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      /* Computing expectancies */
            for(i=1; i<=nlstate;i++)
       l=3+(nlstate+ndeath)*cpt;        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for (i=1; i< nlstate ; i ++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         l=3+(nlstate+ndeath)*cpt;            
         fprintf(ficgp,"+$%d",l+i+1);  /* 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(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }      fprintf(ficreseij,"%3.0f",age );
   }        cptj=0;
        for(i=1; i<=nlstate;i++)
   /* proba elementaires */        for(j=1; j<=nlstate;j++){
    for(i=1,jk=1; i <=nlstate; i++){          cptj++;
     for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){      fprintf(ficreseij,"\n");
             
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           jk++;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficgp,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    }
     }    printf("\n");
     fprintf(ficlog,"\n");
     for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    free_vector(xp,1,npar);
    i=1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      k3=i;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      for(k=1; k<=(nlstate+ndeath); k++) {  }
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  /************ Variance ******************/
 ij=1;  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(j=3; j <=ncovmodel; j++) {  {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Variance of health expectancies */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
             ij++;    /* double **newm;*/
           }    double **dnewm,**doldm;
           else    double **dnewmp,**doldmp;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int i, j, nhstepm, hstepm, h, nstepm ;
         }    int k, cptcode;
           fprintf(ficgp,")/(1");    double *xp;
            double **gp, **gm;  /* for var eij */
         for(k1=1; k1 <=nlstate; k1++){      double ***gradg, ***trgradg; /*for var eij */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double **gradgp, **trgradgp; /* for var p point j */
 ij=1;    double *gpp, *gmp; /* for var p point j */
           for(j=3; j <=ncovmodel; j++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double ***p3mat;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double age,agelim, hf;
             ij++;    double ***mobaverage;
           }    int theta;
           else    char digit[4];
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    char digitp[25];
           }  
           fprintf(ficgp,")");    char fileresprobmorprev[FILENAMELENGTH];
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    if(popbased==1){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      if(mobilav!=0)
         i=i+ncovmodel;        strcpy(digitp,"-populbased-mobilav-");
        }      else strcpy(digitp,"-populbased-nomobil-");
      }    }
    }    else 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      strcpy(digitp,"-stablbased-");
    }  
        if (mobilav!=0) {
   fclose(ficgp);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 }  /* end gnuplot */      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);
 /*************** Moving average **************/      }
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){    }
   
   int i, cpt, cptcod;    strcpy(fileresprobmorprev,"prmorprev"); 
     for (agedeb=agemin; agedeb<=fage; agedeb++)    sprintf(digit,"%-d",ij);
       for (i=1; i<=nlstate;i++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           mobaverage[(int)agedeb][i][cptcod]=0.;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        strcat(fileresprobmorprev,fileres);
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for (i=1; i<=nlstate;i++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           for (cpt=0;cpt<=4;cpt++){    }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    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);
       }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     }      fprintf(ficresprobmorprev," p.%-d SE",j);
          for(i=1; i<=nlstate;i++)
 }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
 /************** Forecasting ******************/    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      exit(0);
   int *popage;    }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    else{
   double *popeffectif,*popcount;      fprintf(ficgp,"\n# Routine varevsij");
   double ***p3mat;    }
   char fileresf[FILENAMELENGTH];    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
  agelim=AGESUP;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      exit(0);
     }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    else{
        fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
        fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   strcpy(fileresf,"f");    }
   strcat(fileresf,fileres);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   }    fprintf(ficresvij,"# Age");
   printf("Computing forecasting: result on file '%s' \n", fileresf);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    xp=vector(1,npar);
     movingaverage(agedeb, fage, agemin, mobaverage);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (stepm<=12) stepsize=1;  
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   agelim=AGESUP;    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
   hstepm=1;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   hstepm=hstepm/stepm;    
   yp1=modf(dateintmean,&yp);    if(estepm < stepm){
   anprojmean=yp;      printf ("Problem %d lower than %d\n",estepm, stepm);
   yp2=modf((yp1*12),&yp);    }
   mprojmean=yp;    else  hstepm=estepm;   
   yp1=modf((yp2*30.5),&yp);    /* For example we decided to compute the life expectancy with the smallest unit */
   jprojmean=yp;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if(jprojmean==0) jprojmean=1;       nhstepm is the number of hstepm from age to agelim 
   if(mprojmean==0) jprojmean=1;       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       and note for a fixed period like k years */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for(cptcov=1;cptcov<=i2;cptcov++){       survival function given by stepm (the optimization length). Unfortunately it
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       means that if the survival funtion is printed every two years of age and if
       k=k+1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficresf,"\n#******");       results. So we changed our mind and took the option of the best precision.
       for(j=1;j<=cptcoveff;j++) {    */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }    agelim = AGESUP;
       fprintf(ficresf,"******\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresf,"# StartingAge FinalAge");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      gp=matrix(0,nhstepm,1,nlstate);
         fprintf(ficresf,"\n");      gm=matrix(0,nhstepm,1,nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      for(theta=1; theta <=npar; theta++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           nhstepm = nhstepm/hstepm;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           oldm=oldms;savm=savms;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                if (popbased==1) {
           for (h=0; h<=nhstepm; h++){          if(mobilav ==0){
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);              prlim[i][i]=probs[(int)age][i][ij];
             }          }else{ /* mobilav */ 
             for(j=1; j<=nlstate+ndeath;j++) {            for(i=1; i<=nlstate;i++)
               kk1=0.;kk2=0;              prlim[i][i]=mobaverage[(int)age][i][ij];
               for(i=1; i<=nlstate;i++) {                        }
                 if (mobilav==1)        }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    
                 else {        for(j=1; j<= nlstate; j++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for(h=0; h<=nhstepm; h++){
                 }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
               }          }
               if (h==(int)(calagedate+12*cpt)){        }
                 fprintf(ficresf," %.3f", kk1);        /* This for computing probability of death (h=1 means
                                   computed over hstepm matrices product = hstepm*stepm months) 
               }           as a weighted average of prlim.
             }        */
           }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       }        }    
     }        /* end probability of death */
   }  
                for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fclose(ficresf);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 }   
 /************** Forecasting ******************/        if (popbased==1) {
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              prlim[i][i]=probs[(int)age][i][ij];
   int *popage;          }else{ /* mobilav */ 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for(i=1; i<=nlstate;i++)
   double *popeffectif,*popcount;              prlim[i][i]=mobaverage[(int)age][i][ij];
   double ***p3mat,***tabpop,***tabpopprev;          }
   char filerespop[FILENAMELENGTH];        }
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<= nlstate; j++){
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(h=0; h<=nhstepm; h++){
   agelim=AGESUP;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
          /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
   strcpy(filerespop,"pop");           as a weighted average of prlim.
   strcat(filerespop,fileres);        */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     printf("Problem with forecast resultfile: %s\n", filerespop);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   printf("Computing forecasting: result on file '%s' \n", filerespop);        }    
         /* end probability of death */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
         for(j=1; j<= nlstate; j++) /* vareij */
   if (mobilav==1) {          for(h=0; h<=nhstepm; h++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     movingaverage(agedeb, fage, agemin, mobaverage);          }
   }  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   if (stepm<=12) stepsize=1;        }
    
   agelim=AGESUP;      } /* End theta */
    
   hstepm=1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   hstepm=hstepm/stepm;  
        for(h=0; h<=nhstepm; h++) /* veij */
   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[h][j][theta]=gradg[h][theta][j];
     }  
     popage=ivector(0,AGESUP);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     popeffectif=vector(0,AGESUP);        for(theta=1; theta <=npar; theta++)
     popcount=vector(0,AGESUP);          trgradgp[j][theta]=gradgp[theta][j];
        
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          for(i=1;i<=nlstate;i++)
     imx=i;        for(j=1;j<=nlstate;j++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          vareij[i][j][(int)age] =0.;
   }  
       for(h=0;h<=nhstepm;h++){
   for(cptcov=1;cptcov<=i2;cptcov++){        for(k=0;k<=nhstepm;k++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       k=k+1;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficrespop,"\n#******");          for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {            for(j=1;j<=nlstate;j++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficrespop,"******\n");      }
       fprintf(ficrespop,"# Age");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      /* pptj */
       if (popforecast==1)  fprintf(ficrespop," [Population]");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for (cpt=0; cpt<=0;cpt++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for(i=nlstate+1;i<=nlstate+ndeath;i++)
                  varppt[j][i]=doldmp[j][i];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      /* end ppptj */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /*  x centered again */
           nhstepm = nhstepm/hstepm;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
           oldm=oldms;savm=savms;      if (popbased==1) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if(mobilav ==0){
                  for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){            prlim[i][i]=probs[(int)age][i][ij];
             if (h==(int) (calagedate+YEARM*cpt)) {        }else{ /* mobilav */ 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=mobaverage[(int)age][i][ij];
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;      }
               for(i=1; i<=nlstate;i++) {                             
                 if (mobilav==1)      /* This for computing probability of death (h=1 means
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                 else {         as a weighted average of prlim.
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      */
                 }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
               }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
               if (h==(int)(calagedate+12*cpt)){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      }    
                   /*fprintf(ficrespop," %.3f", kk1);      /* end probability of death */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             for(i=1; i<=nlstate;i++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
               kk1=0.;        for(i=1; i<=nlstate;i++){
                 for(j=1; j<=nlstate;j++){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        }
                 }      } 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      fprintf(ficresprobmorprev,"\n");
             }  
       fprintf(ficresvij,"%.0f ",age );
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for(i=1; i<=nlstate;i++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(j=1; j<=nlstate;j++){
           }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }      fprintf(ficresvij,"\n");
       }      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   /******/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      } /* End age */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    free_vector(gpp,nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(gmp,nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           oldm=oldms;savm=savms;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           for (h=0; h<=nhstepm; h++){  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
             if (h==(int) (calagedate+YEARM*cpt)) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
             }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
               kk1=0.;kk2=0;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
               for(i=1; i<=nlstate;i++) {                  fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
               }    /*  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);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  */
             }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,nlstate);
       }    free_matrix(dnewm,1,nlstate,1,npar);
    }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
   if (popforecast==1) {    fclose(ficgp);
     free_ivector(popage,0,AGESUP);    fclose(fichtm);
     free_vector(popeffectif,0,AGESUP);  }  
     free_vector(popcount,0,AGESUP);  
   }  /************ Variance of prevlim ******************/
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  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)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   fclose(ficrespop);    /* Variance of prevalence limit */
 }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
 /***********************************************/    double **dnewm,**doldm;
 /**************** Main Program *****************/    int i, j, nhstepm, hstepm;
 /***********************************************/    int k, cptcode;
     double *xp;
 int main(int argc, char *argv[])    double *gp, *gm;
 {    double **gradg, **trgradg;
     double age,agelim;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int theta;
   double agedeb, agefin,hf;     
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
   double fret;    for(i=1; i<=nlstate;i++)
   double **xi,tmp,delta;        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   double dum; /* Dummy variable */  
   double ***p3mat;    xp=vector(1,npar);
   int *indx;    dnewm=matrix(1,nlstate,1,npar);
   char line[MAXLINE], linepar[MAXLINE];    doldm=matrix(1,nlstate,1,nlstate);
   char title[MAXLINE];    
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    hstepm=1*YEARM; /* Every year of age */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char filerest[FILENAMELENGTH];      if (stepm >= YEARM) hstepm=1;
   char fileregp[FILENAMELENGTH];      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   char popfile[FILENAMELENGTH];      gradg=matrix(1,npar,1,nlstate);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      gp=vector(1,nlstate);
   int firstobs=1, lastobs=10;      gm=vector(1,nlstate);
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;      for(theta=1; theta <=npar; theta++){
   int ju,jl, mi;        for(i=1; i<=npar; i++){ /* Computes gradient */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        }
   int mobilav=0,popforecast=0;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   int hstepm, nhstepm;        for(i=1;i<=nlstate;i++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          gp[i] = prlim[i][i];
       
   double bage, fage, age, agelim, agebase;        for(i=1; i<=npar; i++) /* Computes gradient */
   double ftolpl=FTOL;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double **prlim;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double *severity;        for(i=1;i<=nlstate;i++)
   double ***param; /* Matrix of parameters */          gm[i] = prlim[i][i];
   double  *p;  
   double **matcov; /* Matrix of covariance */        for(i=1;i<=nlstate;i++)
   double ***delti3; /* Scale */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   double *delti; /* Scale */      } /* End theta */
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */      trgradg =matrix(1,nlstate,1,npar);
   double *epj, vepp;  
   double kk1, kk2;      for(j=1; j<=nlstate;j++)
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        for(theta=1; theta <=npar; theta++)
            trgradg[j][theta]=gradg[theta][j];
   
   char version[80]="Imach version 0.71c, March 2002, INED-EUROREVES ";      for(i=1;i<=nlstate;i++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   char z[1]="c", occ;      for(i=1;i<=nlstate;i++)
 #include <sys/time.h>        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      fprintf(ficresvpl,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   /* long total_usecs;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   struct timeval start_time, end_time;      fprintf(ficresvpl,"\n");
        free_vector(gp,1,nlstate);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
   printf("\n%s",version);    } /* End age */
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    free_vector(xp,1,npar);
     scanf("%s",pathtot);    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   else{  
     strcpy(pathtot,argv[1]);  }
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  /************ Variance of one-step probabilities  ******************/
   /*cygwin_split_path(pathtot,path,optionfile);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  {
   /* cutv(path,optionfile,pathtot,'\\');*/    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    int k=0,l, cptcode;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    int first=1, first1;
   chdir(path);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   replace(pathc,path);    double **dnewm,**doldm;
     double *xp;
 /*-------- arguments in the command line --------*/    double *gp, *gm;
     double **gradg, **trgradg;
   strcpy(fileres,"r");    double **mu;
   strcat(fileres, optionfilefiname);    double age,agelim, cov[NCOVMAX];
   strcat(fileres,".txt");    /* Other files have txt extension */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   /*---------arguments file --------*/    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    char fileresprobcor[FILENAMELENGTH];
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    double ***varpij;
   }  
     strcpy(fileresprob,"prob"); 
   strcpy(filereso,"o");    strcat(fileresprob,fileres);
   strcat(filereso,fileres);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if((ficparo=fopen(filereso,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprob);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
     strcpy(fileresprobcov,"probcov"); 
   /* Reads comments: lines beginning with '#' */    strcat(fileresprobcov,fileres);
   while((c=getc(ficpar))=='#' && c!= EOF){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprobcov);
     fgets(line, MAXLINE, ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     puts(line);    }
     fputs(line,ficparo);    strcpy(fileresprobcor,"probcor"); 
   }    strcat(fileresprobcor,fileres);
   ungetc(c,ficpar);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     ungetc(c,ficpar);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     puts(line);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fputs(line,ficparo);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    
   ungetc(c,ficpar);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
        fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficresprobcov,"# Age");
   cptcovn=0;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficresprobcov,"# Age");
   
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
   /* Read guess parameters */        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   /* Reads comments: lines beginning with '#' */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     ungetc(c,ficpar);      }  
     fgets(line, MAXLINE, ficpar);   /* fprintf(ficresprob,"\n");
     puts(line);    fprintf(ficresprobcov,"\n");
     fputs(line,ficparo);    fprintf(ficresprobcor,"\n");
   }   */
   ungetc(c,ficpar);   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     for(i=1; i <=nlstate; i++)    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     for(j=1; j <=nlstate+ndeath-1; j++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    first=1;
       fprintf(ficparo,"%1d%1d",i1,j1);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("%1d%1d",i,j);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       for(k=1; k<=ncovmodel;k++){      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         fscanf(ficpar," %lf",&param[i][j][k]);      exit(0);
         printf(" %lf",param[i][j][k]);    }
         fprintf(ficparo," %lf",param[i][j][k]);    else{
       }      fprintf(ficgp,"\n# Routine varprob");
       fscanf(ficpar,"\n");    }
       printf("\n");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       fprintf(ficparo,"\n");      printf("Problem with html file: %s\n", optionfilehtm);
     }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        exit(0);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    }
     else{
   p=param[1][1];      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     ungetc(c,ficpar);      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fgets(line, MAXLINE, ficpar);      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");
     puts(line);  
     fputs(line,ficparo);    }
   }  
   ungetc(c,ficpar);    cov[1]=1;
     tj=cptcoveff;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    j1=0;
   for(i=1; i <=nlstate; i++){    for(t=1; t<=tj;t++){
     for(j=1; j <=nlstate+ndeath-1; j++){      for(i1=1; i1<=ncodemax[t];i1++){ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);        j1++;
       printf("%1d%1d",i,j);        if  (cptcovn>0) {
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficresprob, "\n#********** Variable "); 
       for(k=1; k<=ncovmodel;k++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          fprintf(ficresprob, "**********\n#\n");
         printf(" %le",delti3[i][j][k]);          fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficparo," %le",delti3[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcov, "**********\n#\n");
       fscanf(ficpar,"\n");          
       printf("\n");          fprintf(ficgp, "\n#********** Variable "); 
       fprintf(ficparo,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficgp, "**********\n#\n");
   }          
   delti=delti3[1][1];          
            fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor, "\n#********** Variable ");    
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficresprobcor, "**********\n#");    
   }        }
   ungetc(c,ficpar);        
          for (age=bage; age<=fage; age ++){ 
   matcov=matrix(1,npar,1,npar);          cov[2]=age;
   for(i=1; i <=npar; i++){          for (k=1; k<=cptcovn;k++) {
     fscanf(ficpar,"%s",&str);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     printf("%s",str);          }
     fprintf(ficparo,"%s",str);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(j=1; j <=i; j++){          for (k=1; k<=cptcovprod;k++)
       fscanf(ficpar," %le",&matcov[i][j]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf(" %.5le",matcov[i][j]);          
       fprintf(ficparo," %.5le",matcov[i][j]);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fscanf(ficpar,"\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
     printf("\n");          gm=vector(1,(nlstate)*(nlstate+ndeath));
     fprintf(ficparo,"\n");      
   }          for(theta=1; theta <=npar; theta++){
   for(i=1; i <=npar; i++)            for(i=1; i<=npar; i++)
     for(j=i+1;j<=npar;j++)              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       matcov[i][j]=matcov[j][i];            
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
   printf("\n");            
             k=0;
             for(i=1; i<= (nlstate); i++){
     /*-------- Rewriting paramater file ----------*/              for(j=1; j<=(nlstate+ndeath);j++){
      strcpy(rfileres,"r");    /* "Rparameterfile */                k=k+1;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                gp[k]=pmmij[i][j];
      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;            for(i=1; i<=npar; i++)
     }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     fprintf(ficres,"#%s\n",version);      
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
     /*-------- data file ----------*/            k=0;
     if((fic=fopen(datafile,"r"))==NULL)    {            for(i=1; i<=(nlstate); i++){
       printf("Problem with datafile: %s\n", datafile);goto end;              for(j=1; j<=(nlstate+ndeath);j++){
     }                k=k+1;
                 gm[k]=pmmij[i][j];
     n= lastobs;              }
     severity = vector(1,maxwav);            }
     outcome=imatrix(1,maxwav+1,1,n);       
     num=ivector(1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     moisnais=vector(1,n);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     annais=vector(1,n);          }
     moisdc=vector(1,n);  
     andc=vector(1,n);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     agedc=vector(1,n);            for(theta=1; theta <=npar; theta++)
     cod=ivector(1,n);              trgradg[j][theta]=gradg[theta][j];
     weight=vector(1,n);          
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     mint=matrix(1,maxwav,1,n);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     anint=matrix(1,maxwav,1,n);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     s=imatrix(1,maxwav+1,1,n);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     adl=imatrix(1,maxwav+1,1,n);              free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     tab=ivector(1,NCOVMAX);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     ncodemax=ivector(1,8);  
           pmij(pmmij,cov,ncovmodel,x,nlstate);
     i=1;          
     while (fgets(line, MAXLINE, fic) != NULL)    {          k=0;
       if ((i >= firstobs) && (i <=lastobs)) {          for(i=1; i<=(nlstate); i++){
                    for(j=1; j<=(nlstate+ndeath);j++){
         for (j=maxwav;j>=1;j--){              k=k+1;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              mu[k][(int) age]=pmmij[i][j];
           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);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                      varpij[i][j][(int)age] = doldm[i][j];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){          fprintf(ficresprob,"\n%d ",(int)age);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresprobcov,"\n%d ",(int)age);
         }          fprintf(ficresprobcor,"\n%d ",(int)age);
         num[i]=atol(stra);  
                  for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         i=i+1;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       }          }
     }          i=0;
     /* printf("ii=%d", ij);          for (k=1; k<=(nlstate);k++){
        scanf("%d",i);*/            for (l=1; l<=(nlstate+ndeath);l++){ 
   imx=i-1; /* Number of individuals */              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   /* for (i=1; i<=imx; i++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              for (j=1; j<=i;j++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     }              }
             }
     for (i=1; i<=imx; i++)          }/* end of loop for state */
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        } /* end of loop for age */
   
   /* Calculation of the number of parameter from char model*/        /* Confidence intervalle of pij  */
   Tvar=ivector(1,15);        /*
   Tprod=ivector(1,15);          fprintf(ficgp,"\nset noparametric;unset label");
   Tvaraff=ivector(1,15);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   Tvard=imatrix(1,15,1,2);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   Tage=ivector(1,15);                fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
              fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   if (strlen(model) >1){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     j=0, j1=0, k1=1, k2=1;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     j=nbocc(model,'+');        */
     j1=nbocc(model,'*');  
     cptcovn=j+1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     cptcovprod=j1;        first1=1;
            for (k2=1; k2<=(nlstate);k2++){
              for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     strcpy(modelsav,model);            if(l2==k2) continue;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            j=(k2-1)*(nlstate+ndeath)+l2;
       printf("Error. Non available option model=%s ",model);            for (k1=1; k1<=(nlstate);k1++){
       goto end;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     }                if(l1==k1) continue;
                    i=(k1-1)*(nlstate+ndeath)+l1;
     for(i=(j+1); i>=1;i--){                if(i<=j) continue;
       cutv(stra,strb,modelsav,'+');                for (age=bage; age<=fage; age ++){ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                  if ((int)age %5==0){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       /*scanf("%d",i);*/                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       if (strchr(strb,'*')) {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         cutv(strd,strc,strb,'*');                    mu1=mu[i][(int) age]/stepm*YEARM ;
         if (strcmp(strc,"age")==0) {                    mu2=mu[j][(int) age]/stepm*YEARM;
           cptcovprod--;                    c12=cv12/sqrt(v1*v2);
           cutv(strb,stre,strd,'V');                    /* Computing eigen value of matrix of covariance */
           Tvar[i]=atoi(stre);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           cptcovage++;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             Tage[cptcovage]=i;                    /* Eigen vectors */
             /*printf("stre=%s ", stre);*/                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         }                    /*v21=sqrt(1.-v11*v11); *//* error */
         else if (strcmp(strd,"age")==0) {                    v21=(lc1-v1)/cv12*v11;
           cptcovprod--;                    v12=-v21;
           cutv(strb,stre,strc,'V');                    v22=v11;
           Tvar[i]=atoi(stre);                    tnalp=v21/v11;
           cptcovage++;                    if(first1==1){
           Tage[cptcovage]=i;                      first1=0;
         }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         else {                    }
           cutv(strb,stre,strc,'V');                    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);
           Tvar[i]=ncov+k1;                    /*printf(fignu*/
           cutv(strb,strc,strd,'V');                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           Tprod[k1]=i;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           Tvard[k1][1]=atoi(strc);                    if(first==1){
           Tvard[k1][2]=atoi(stre);                      first=0;
           Tvar[cptcovn+k2]=Tvard[k1][1];                      fprintf(ficgp,"\nset parametric;unset label");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                      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);
           for (k=1; k<=lastobs;k++)                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                      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);
           k1++;                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
           k2=k2+2;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
         }                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       else {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                      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",\
        /*  scanf("%d",i);*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       cutv(strd,strc,strb,'V');                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       Tvar[i]=atoi(strc);                    }else{
       }                      first=0;
       strcpy(modelsav,stra);                        fprintf(fichtm," %d (%.3f),",(int) age, c12);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         scanf("%d",i);*/                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
 }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                    }/* if first */
   printf("cptcovprod=%d ", cptcovprod);                  } /* age mod 5 */
   scanf("%d ",i);*/                } /* end loop age */
     fclose(fic);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
     /*  if(mle==1){*/              } /*l12 */
     if (weightopt != 1) { /* Maximisation without weights*/            } /* k12 */
       for(i=1;i<=n;i++) weight[i]=1.0;          } /*l1 */
     }        }/* k1 */
     /*-calculation of age at interview from date of interview and age at death -*/      } /* loop covariates */
     agev=matrix(1,maxwav,1,imx);    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    for (i=1; i<=imx; i++)    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      for(m=2; (m<= maxwav); m++)    free_vector(xp,1,npar);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fclose(ficresprob);
          anint[m][i]=9999;    fclose(ficresprobcov);
          s[m][i]=-1;    fclose(ficresprobcor);
        }    fclose(ficgp);
        fclose(fichtm);
     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){  /******************* Printing html file ***********/
           if (s[m][i] == nlstate+1) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             if(agedc[i]>0)                    int lastpass, int stepm, int weightopt, char model[],\
               if(moisdc[i]!=99 && andc[i]!=9999)                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
               agev[m][i]=agedc[i];                    int popforecast, int estepm ,\
             else {                    double jprev1, double mprev1,double anprev1, \
               if (andc[i]!=9999){                    double jprev2, double mprev2,double anprev2){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int jj1, k1, i1, cpt;
               agev[m][i]=-1;    /*char optionfilehtm[FILENAMELENGTH];*/
               }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
             }      printf("Problem with %s \n",optionfilehtm), exit(0);
           }      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
           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)     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
               agev[m][i]=1;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
             else if(agev[m][i] <agemin){   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
               agemin=agev[m][i];   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   - Life expectancies by age and initial health status (estepm=%2d months): 
             }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
             else if(agev[m][i] >agemax){    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/   m=cptcoveff;
             /*   agev[m][i] = age[i]+2*m;*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           }  
           else { /* =9 */   jj1=0;
             agev[m][i]=1;   for(k1=1; k1<=m;k1++){
             s[m][i]=-1;     for(i1=1; i1<=ncodemax[k1];i1++){
           }       jj1++;
         }       if (cptcovn > 0) {
         else /*= 0 Unknown */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           agev[m][i]=1;         for (cpt=1; cpt<=cptcoveff;cpt++) 
       }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     }       }
     for (i=1; i<=imx; i++)  {       /* Pij */
       for(m=1; (m<= maxwav); m++){       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>
         if (s[m][i] > (nlstate+ndeath)) {  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           printf("Error: Wrong value in nlstate or ndeath\n");         /* Quasi-incidences */
           goto end;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
         }  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
       }         /* Stable prevalence in each health state */
     }         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
     free_vector(severity,1,maxwav);       for(cpt=1; cpt<=nlstate;cpt++) {
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     free_vector(moisnais,1,n);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     free_vector(annais,1,n);       }
     /* free_matrix(mint,1,maxwav,1,n);       fprintf(fichtm,"\n<br>- Total life expectancy by age and
        free_matrix(anint,1,maxwav,1,n);*/  health expectancies in states (1) and (2): e%s%d.png<br>
     free_vector(moisdc,1,n);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     free_vector(andc,1,n);     } /* end i1 */
    }/* End k1 */
       fprintf(fichtm,"</ul>");
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     /* Concatenates waves */   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
       Tcode=ivector(1,100);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   - 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);
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  /*  if(popforecast==1) fprintf(fichtm,"\n */
        /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    codtab=imatrix(1,100,1,10);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    h=0;  /*      <br>",fileres,fileres,fileres,fileres); */
    m=pow(2,cptcoveff);  /*  else  */
    /*    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); */
    for(k=1;k<=cptcoveff; k++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){   m=cptcoveff;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
            h++;  
            if (h>m) h=1;codtab[h][k]=j;   jj1=0;
          }   for(k1=1; k1<=m;k1++){
        }     for(i1=1; i1<=ncodemax[k1];i1++){
      }       jj1++;
    }       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
    /*for(i=1; i <=m ;i++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      for(k=1; k <=cptcovn; k++){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);       }
      }       for(cpt=1; cpt<=nlstate;cpt++) {
      printf("\n");         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
    }  interval) in state (%d): v%s%d%d.png <br>
    scanf("%d",i);*/  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           }
    /* Calculates basic frequencies. Computes observed prevalence at single age     } /* end i1 */
        and prints on file fileres'p'. */   }/* End k1 */
    fprintf(fichtm,"</ul>");
      fclose(fichtm);
      }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /******************* Gnuplot file **************/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
          int ng;
     /* For Powell, parameters are in a vector p[] starting at p[1]    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      printf("Problem with file %s",optionfilegnuplot);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    /*#ifdef windows */
     }      fprintf(ficgp,"cd \"%s\" \n",pathc);
          /*#endif */
     /*--------- results files --------------*/  m=pow(2,cptcoveff);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    
     /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
    jk=1;     for (k1=1; k1<= m ; k1 ++) {
    fprintf(ficres,"# Parameters\n");       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    printf("# Parameters\n");       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){       for (i=1; i<= nlstate ; i ++) {
        if (k != i)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          {         else fprintf(ficgp," \%%*lf (\%%*lf)");
            printf("%d%d ",i,k);       }
            fprintf(ficres,"%1d%1d ",i,k);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
            for(j=1; j <=ncovmodel; j++){       for (i=1; i<= nlstate ; i ++) {
              printf("%f ",p[jk]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
              fprintf(ficres,"%f ",p[jk]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
              jk++;       } 
            }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
            printf("\n");       for (i=1; i<= nlstate ; i ++) {
            fprintf(ficres,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          }         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }  
    }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
  if(mle==1){     }
     /* Computing hessian and covariance matrix */    }
     ftolhess=ftol; /* Usually correct */    /*2 eme*/
     hesscov(matcov, p, npar, delti, ftolhess, func);    
  }    for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficres,"# Scales\n");      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     printf("# Scales\n");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
      for(i=1,jk=1; i <=nlstate; i++){      
       for(j=1; j <=nlstate+ndeath; j++){      for (i=1; i<= nlstate+1 ; i ++) {
         if (j!=i) {        k=2*i;
           fprintf(ficres,"%1d%1d",i,j);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
           printf("%1d%1d",i,j);        for (j=1; j<= nlstate+1 ; j ++) {
           for(k=1; k<=ncovmodel;k++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             printf(" %.5e",delti[jk]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
             fprintf(ficres," %.5e",delti[jk]);        }   
             jk++;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           printf("\n");        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           fprintf(ficres,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
         }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
      }        }   
            fprintf(ficgp,"\" t\"\" w l 0,");
     k=1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     fprintf(ficres,"# Covariance\n");        for (j=1; j<= nlstate+1 ; j ++) {
     printf("# Covariance\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     for(i=1;i<=npar;i++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
       /*  if (k>nlstate) k=1;        }   
       i1=(i-1)/(ncovmodel*nlstate)+1;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        else fprintf(ficgp,"\" t\"\" w l 0,");
       printf("%s%d%d",alph[k],i1,tab[i]);*/      }
       fprintf(ficres,"%3d",i);    }
       printf("%3d",i);    
       for(j=1; j<=i;j++){    /*3eme*/
         fprintf(ficres," %.5e",matcov[i][j]);    
         printf(" %.5e",matcov[i][j]);    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<= nlstate ; cpt ++) {
       fprintf(ficres,"\n");        k=2+nlstate*(2*cpt-2);
       printf("\n");        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       k++;        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
     }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       ungetc(c,ficpar);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fgets(line, MAXLINE, ficpar);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       puts(line);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       fputs(line,ficparo);          
     }        */
     ungetc(c,ficpar);        for (i=1; i< nlstate ; i ++) {
            fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);          
            } 
     if (fage <= 2) {      }
       bage = agemin;    }
       fage = agemaxpar;    
     }    /* CV preval stable (period) */
        for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for (cpt=1; cpt<=nlstate ; cpt ++) {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        k=3;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        for (i=1; i< nlstate ; i ++)
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"+$%d",k+i+1);
     puts(line);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     fputs(line,ficparo);        
   }        l=3+(nlstate+ndeath)*cpt;
   ungetc(c,ficpar);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
          for (i=1; i< nlstate ; i ++) {
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          l=3+(nlstate+ndeath)*cpt;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"+$%d",l+i+1);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
              fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   while((c=getc(ficpar))=='#' && c!= EOF){      } 
     ungetc(c,ficpar);    }  
     fgets(line, MAXLINE, ficpar);    
     puts(line);    /* proba elementaires */
     fputs(line,ficparo);    for(i=1,jk=1; i <=nlstate; i++){
   }      for(k=1; k <=(nlstate+ndeath); k++){
   ungetc(c,ficpar);        if (k != i) {
            for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            jk++; 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            fprintf(ficgp,"\n");
           }
   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){     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     ungetc(c,ficpar);       for(jk=1; jk <=m; jk++) {
     fgets(line, MAXLINE, ficpar);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     puts(line);         if (ng==2)
     fputs(line,ficparo);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   }         else
   ungetc(c,ficpar);           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);
   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);         i=1;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);         for(k2=1; k2<=nlstate; k2++) {
 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);           k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
 while((c=getc(ficpar))=='#' && c!= EOF){               if(ng==2)
     ungetc(c,ficpar);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     fgets(line, MAXLINE, ficpar);               else
     puts(line);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     fputs(line,ficparo);               ij=1;
   }               for(j=3; j <=ncovmodel; j++) {
   ungetc(c,ficpar);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                   ij++;
   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);                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);               }
                fprintf(ficgp,")/(1");
 /*------------ gnuplot -------------*/               
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);               for(k1=1; k1 <=nlstate; k1++){   
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 /*------------ free_vector  -------------*/                 ij=1;
  chdir(path);                 for(j=3; j <=ncovmodel; j++){
                     if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  free_ivector(wav,1,imx);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                     ij++;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                     }
  free_ivector(num,1,n);                   else
  free_vector(agedc,1,n);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                 }
  fclose(ficparo);                 fprintf(ficgp,")");
  fclose(ficres);               }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 /*--------- index.htm --------*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);             }
            } /* end k */
           } /* end k2 */
   /*--------------- Prevalence limit --------------*/       } /* end jk */
       } /* end ng */
   strcpy(filerespl,"pl");     fclose(ficgp); 
   strcat(filerespl,fileres);  }  /* end gnuplot */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }  /*************** Moving average **************/
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    int i, cpt, cptcod;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int modcovmax =1;
   fprintf(ficrespl,"\n");    int mobilavrange, mob;
      double age;
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                             a covariate has 2 modalities */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   k=0;      if(mobilav==1) mobilavrange=5; /* default */
   agebase=agemin;      else mobilavrange=mobilav;
   agelim=agemaxpar;      for (age=bage; age<=fage; age++)
   ftolpl=1.e-10;        for (i=1; i<=nlstate;i++)
   i1=cptcoveff;          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   if (cptcovn < 1){i1=1;}            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
   for(cptcov=1;cptcov<=i1;cptcov++){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         we use a 5 terms etc. until the borders are no more concerned. 
         k=k+1;      */ 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      for (mob=3;mob <=mobilavrange;mob=mob+2){
         fprintf(ficrespl,"\n#******");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
         for(j=1;j<=cptcoveff;j++)          for (i=1; i<=nlstate;i++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
         fprintf(ficrespl,"******\n");              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                        for (cpt=1;cpt<=(mob-1)/2;cpt++){
         for (age=agebase; age<=agelim; age++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
           fprintf(ficrespl,"%.0f",age );                }
           for(i=1; i<=nlstate;i++)              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
           fprintf(ficrespl," %.5f", prlim[i][i]);            }
           fprintf(ficrespl,"\n");          }
         }        }/* end age */
       }      }/* end mob */
     }    }else return -1;
   fclose(ficrespl);    return 0;
   }/* End movingaverage */
   /*------------- h Pij x at various ages ------------*/  
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  /************** Forecasting ******************/
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* proj1, year, month, day of starting projection 
   }       agemin, agemax range of age
   printf("Computing pij: result on file '%s' \n", filerespij);       dateprev1 dateprev2 range of dates during which prevalence is computed
         anproj2 year of en of projection (same day and month as proj1).
   stepsize=(int) (stepm+YEARM-1)/YEARM;    */
   /*if (stepm<=24) stepsize=2;*/    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
   agelim=AGESUP;    double agec; /* generic age */
   hstepm=stepsize*YEARM; /* Every year of age */    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double *popeffectif,*popcount;
      double ***p3mat;
   k=0;    double ***mobaverage;
   for(cptcov=1;cptcov<=i1;cptcov++){    char fileresf[FILENAMELENGTH];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    agelim=AGESUP;
         fprintf(ficrespij,"\n#****** ");    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
         for(j=1;j<=cptcoveff;j++)   
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(fileresf,"f"); 
         fprintf(ficrespij,"******\n");    strcat(fileresf,fileres);
            if((ficresf=fopen(fileresf,"w"))==NULL) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      printf("Problem with forecast resultfile: %s\n", fileresf);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("Computing forecasting: result on file '%s' \n", fileresf);
           oldm=oldms;savm=savms;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    if (mobilav!=0) {
               fprintf(ficrespij," %1d-%1d",i,j);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespij,"\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           for (h=0; h<=nhstepm; h++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
           }    if (stepm<=12) stepsize=1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if(estepm < stepm){
           fprintf(ficrespij,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
     }    else  hstepm=estepm;   
   }  
     hstepm=hstepm/stepm; 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
   fclose(ficrespij);    anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
   /*---------- Forecasting ------------------*/    yp1=modf((yp2*30.5),&yp);
   if((stepm == 1) && (strcmp(model,".")==0)){    jprojmean=yp;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    if(jprojmean==0) jprojmean=1;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    if(mprojmean==0) jprojmean=1;
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    i1=cptcoveff;
     free_vector(weight,1,n);}    if (cptcovn < 1){i1=1;}
   else{    
     erreur=108;    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     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(ficresf,"#****** Routine prevforecast **\n");
    
   /*            if (h==(int)(YEARM*yearp)){ */
   /*---------- Health expectancies and variances ------------*/    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   strcpy(filerest,"t");        k=k+1;
   strcat(filerest,fileres);        fprintf(ficresf,"\n#******");
   if((ficrest=fopen(filerest,"w"))==NULL) {        for(j=1;j<=cptcoveff;j++) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   }        }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
   strcpy(filerese,"e");          for(i=1; i<=nlstate;i++)              
   strcat(filerese,fileres);            fprintf(ficresf," p%d%d",i,j);
   if((ficreseij=fopen(filerese,"w"))==NULL) {          fprintf(ficresf," p.%d",j);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        }
   }        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            nhstepm = nhstepm/hstepm; 
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
   k=0;          
   for(cptcov=1;cptcov<=i1;cptcov++){            for (h=0; h<=nhstepm; h++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              if (h*hstepm/YEARM*stepm ==yearp) {
       k=k+1;                fprintf(ficresf,"\n");
       fprintf(ficrest,"\n#****** ");                for(j=1;j<=cptcoveff;j++) 
       for(j=1;j<=cptcoveff;j++)                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       fprintf(ficrest,"******\n");              } 
               for(j=1; j<=nlstate+ndeath;j++) {
       fprintf(ficreseij,"\n#****** ");                ppij=0.;
       for(j=1;j<=cptcoveff;j++)                for(i=1; i<=nlstate;i++) {
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                  if (mobilav==1) 
       fprintf(ficreseij,"******\n");                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
       fprintf(ficresvij,"\n#****** ");                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       for(j=1;j<=cptcoveff;j++)                  }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                  if (h*hstepm/YEARM*stepm== yearp) {
       fprintf(ficresvij,"******\n");                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                } /* end i */
       oldm=oldms;savm=savms;                if (h*hstepm/YEARM*stepm==yearp) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                    fprintf(ficresf," %.3f", ppij);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                }
       oldm=oldms;savm=savms;              }/* end j */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            } /* end h */
                free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
          } /* end yearp */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      } /* end cptcod */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    } /* end  cptcov */
       fprintf(ficrest,"\n");         
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    fclose(ficresf);
       epj=vector(1,nlstate+1);  }
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  /************** Forecasting *****not tested NB*************/
         if (popbased==1) {  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++)    
             prlim[i][i]=probs[(int)age][i][k];    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
         }    int *popage;
            double calagedatem, agelim, kk1, kk2;
         fprintf(ficrest," %.0f",age);    double *popeffectif,*popcount;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double ***p3mat,***tabpop,***tabpopprev;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double ***mobaverage;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    char filerespop[FILENAMELENGTH];
           }  
           epj[nlstate+1] +=epj[j];    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(i=1, vepp=0.;i <=nlstate;i++)    agelim=AGESUP;
           for(j=1;j <=nlstate;j++)    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
             vepp += vareij[i][j][(int)age];    
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
         for(j=1;j <=nlstate;j++){    
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    
         }    strcpy(filerespop,"pop"); 
         fprintf(ficrest,"\n");    strcat(filerespop,fileres);
       }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     }      printf("Problem with forecast resultfile: %s\n", filerespop);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
   fclose(ficreseij);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   fclose(ficresvij);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   fclose(ficrest);  
   fclose(ficpar);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   free_vector(epj,1,nlstate+1);  
      if (mobilav!=0) {
   /*------- Variance limit prevalence------*/        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   strcpy(fileresvpl,"vpl");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(fileresvpl,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    }
     exit(0);  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    if (stepm<=12) stepsize=1;
     
   k=0;    agelim=AGESUP;
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    hstepm=1;
       k=k+1;    hstepm=hstepm/stepm; 
       fprintf(ficresvpl,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    if (popforecast==1) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if((ficpop=fopen(popfile,"r"))==NULL) {
       fprintf(ficresvpl,"******\n");        printf("Problem with population file : %s\n",popfile);exit(0);
              fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      } 
       oldm=oldms;savm=savms;      popage=ivector(0,AGESUP);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      popeffectif=vector(0,AGESUP);
     }      popcount=vector(0,AGESUP);
  }      
       i=1;   
   fclose(ficresvpl);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
   /*---------- End : free ----------------*/      imx=i;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          k=k+1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficrespop,"\n#******");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1;j<=cptcoveff;j++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
          fprintf(ficrespop,"******\n");
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficrespop,"# Age");
   free_vector(delti,1,npar);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   free_matrix(agev,1,maxwav,1,imx);        if (popforecast==1)  fprintf(ficrespop," [Population]");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        
         for (cpt=0; cpt<=0;cpt++) { 
   if(erreur >0)          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     printf("End of Imach with error %d\n",erreur);          
   else   printf("End of Imach\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
   /* 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);*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*------ End -----------*/            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
  end:            for (h=0; h<=nhstepm; h++){
 #ifdef windows              if (h==(int) (calagedatem+YEARM*cpt)) {
   /* chdir(pathcd);*/                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 #endif              } 
  /*system("wgnuplot graph.plt");*/              for(j=1; j<=nlstate+ndeath;j++) {
  /*system("../gp37mgw/wgnuplot graph.plt");*/                kk1=0.;kk2=0;
  /*system("cd ../gp37mgw");*/                for(i=1; i<=nlstate;i++) {              
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                  if (mobilav==1) 
  strcpy(plotcmd,GNUPLOTPROGRAM);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
  strcat(plotcmd," ");                  else {
  strcat(plotcmd,optionfilegnuplot);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
  system(plotcmd);                  }
                 }
 #ifdef windows                if (h==(int)(calagedatem+12*cpt)){
   while (z[0] != 'q') {                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     chdir(path);                    /*fprintf(ficrespop," %.3f", kk1);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     scanf("%s",z);                }
     if (z[0] == 'c') system("./imach");              }
     else if (z[0] == 'e') {              for(i=1; i<=nlstate;i++){
       chdir(path);                kk1=0.;
       system(optionfilehtm);                  for(j=1; j<=nlstate;j++){
     }                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     else if (z[0] == 'q') exit(0);                  }
   }                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
 #endif              }
 }  
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*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];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* 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]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* 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 (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)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){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)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=firstpass; (m<=lastpass); 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;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     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);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"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+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/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,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year 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);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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
   Youngest age at first (selected) pass %.2f, oldest age %.2f<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,agemin,agemax,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(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           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*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     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,"# Cov Agex agex+h hpijx with i,j=");
           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 %3.f %3.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, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (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);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     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_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     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_ma3x(probs,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);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     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 graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#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.1.32  
changed lines
  Added in v.1.83


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>