Diff for /imach/src/imach.c between versions 1.30 and 1.80

version 1.30, 2002/03/08 16:17:18 version 1.80, 2003/06/05 15:34:14
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probabibility to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    read datafile
 #define FILENAMELENGTH 80    concatwav
 /*#define DEBUG*/    if (mle >= 1)
 #define windows      mlikeli
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    print results files
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    if mle==1 
        computes hessian
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */        begin-prev-date,...
     open gnuplot file
 #define NINTERVMAX 8    open html file
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    stable prevalence
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */     for age prevalim()
 #define NCOVMAX 8 /* Maximum number of covariates */    h Pij x
 #define MAXN 20000    variance of p varprob
 #define YEARM 12. /* Number of months per year */    forecasting if prevfcast==1 prevforecast call prevalence()
 #define AGESUP 130    health expectancies
 #define AGEBASE 40    Variance-covariance of DFLE
     prevalence()
      movingaverage()
 int erreur; /* Error number */    varevsij() 
 int nvar;    if popbased==1 varevsij(,popbased)
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    total life expectancies
 int npar=NPARMAX;    Variance of stable prevalence
 int nlstate=2; /* Number of live states */   end
 int ndeath=1; /* Number of dead states */  */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  
   
 int *wav; /* Number of waves for this individuual 0 is possible */   
 int maxwav; /* Maxim number of waves */  #include <math.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdio.h>
 int mle, weightopt;  #include <stdlib.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #include <unistd.h>
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */  #define MAXLINE 256
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #define FILENAMELENGTH 80
 FILE *ficgp,*ficresprob,*ficpop;  /*#define DEBUG*/
 FILE *ficreseij;  #define windows
   char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  FILE  *ficresvij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   char fileresvpl[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NR_END 1  #define NINTERVMAX 8
 #define FREE_ARG char*  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define FTOL 1.0e-10  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 #define NRANSI  #define MAXN 20000
 #define ITMAX 200  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 #define TOL 2.0e-4  #define AGEBASE 40
   #ifdef windows
 #define CGOLD 0.3819660  #define DIRSEPARATOR '\\'
 #define ZEPS 1.0e-10  #define ODIRSEPARATOR '/'
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #else
   #define DIRSEPARATOR '/'
 #define GOLD 1.618034  #define ODIRSEPARATOR '\\'
 #define GLIMIT 100.0  #endif
 #define TINY 1.0e-20  
   /* $Id$ */
 static double maxarg1,maxarg2;  /* $Log$
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   * Revision 1.80  2003/06/05 15:34:14  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))   * Trying to add the true revision is the program and log
     *
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  /* Revision 1.79  2003/06/05 15:17:23  brouard
 #define rint(a) floor(a+0.5)  /* *** empty log message ***
   /* */
 static double sqrarg;  /* $Revision$ */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  /* $Date$ */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  /* $State$ */
   
 int imx;  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 int stepm;  int erreur; /* Error number */
 /* Stepm, step in month: minimum step interpolation*/  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int m,nb;  int npar=NPARMAX;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int nlstate=2; /* Number of live states */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int ndeath=1; /* Number of dead states */
 double **pmmij, ***probs, ***mobaverage;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double dateintmean=0;  int popbased=0;
   
 double *weight;  int *wav; /* Number of waves for this individuual 0 is possible */
 int **s; /* Status */  int maxwav; /* Maxim number of waves */
 double *agedc, **covar, idx;  int jmin, jmax; /* min, max spacing between 2 waves */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double ftolhess; /* Tolerance for computing hessian */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /**************** split *************************/  double jmean; /* Mean space between 2 waves */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    char *s;                             /* pointer */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    int  l1, l2;                         /* length counters */  FILE *ficlog, *ficrespow;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    l1 = strlen( path );                 /* length of path */  FILE *ficresprobmorprev;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *fichtm; /* Html File */
 #ifdef windows  FILE *ficreseij;
    s = strrchr( path, '\\' );           /* find last / */  char filerese[FILENAMELENGTH];
 #else  FILE  *ficresvij;
    s = strrchr( path, '/' );            /* find last / */  char fileresv[FILENAMELENGTH];
 #endif  FILE  *ficresvpl;
    if ( s == NULL ) {                   /* no directory, so use current */  char fileresvpl[FILENAMELENGTH];
 #if     defined(__bsd__)                /* get current working directory */  char title[MAXLINE];
       extern char       *getwd( );  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
       if ( getwd( dirc ) == NULL ) {  
 #else  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       extern char       *getcwd( );  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char fileregp[FILENAMELENGTH];
 #endif  char popfile[FILENAMELENGTH];
          return( GLOCK_ERROR_GETCWD );  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  #define NR_END 1
       s++;                              /* after this, the filename */  #define FREE_ARG char*
       l2 = strlen( s );                 /* length of filename */  #define FTOL 1.0e-10
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  #define NRANSI 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define ITMAX 200 
       dirc[l1-l2] = 0;                  /* add zero */  
    }  #define TOL 2.0e-4 
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  #define CGOLD 0.3819660 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define ZEPS 1.0e-10 
 #else  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  #define GOLD 1.618034 
    s = strrchr( name, '.' );            /* find last / */  #define GLIMIT 100.0 
    s++;  #define TINY 1.0e-20 
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  static double maxarg1,maxarg2;
    l2= strlen( s)+1;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    strncpy( finame, name, l1-l2);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    finame[l1-l2]= 0;    
    return( 0 );                         /* we're done */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
   static double sqrarg;
 /******************************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void replace(char *s, char*t)  
 {  int imx; 
   int i;  int stepm;
   int lg=20;  /* Stepm, step in month: minimum step interpolation*/
   i=0;  
   lg=strlen(t);  int estepm;
   for(i=0; i<= lg; i++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  int m,nb;
   }  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 int nbocc(char *s, char occ)  double dateintmean=0;
 {  
   int i,j=0;  double *weight;
   int lg=20;  int **s; /* Status */
   i=0;  double *agedc, **covar, idx;
   lg=strlen(s);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   }  double ftolhess; /* Tolerance for computing hessian */
   return j;  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void cutv(char *u,char *v, char*t, char occ)  {
 {    char  *ss;                            /* pointer */
   int i,lg,j,p=0;    int   l1, l2;                         /* length counters */
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    l1 = strlen(path );                   /* length of path */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
   lg=strlen(t);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for(j=0; j<p; j++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     (u[j] = t[j]);      /* get current working directory */
   }      /*    extern  char* getcwd ( char *buf , int len);*/
      u[p]='\0';      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
    for(j=0; j<= lg; j++) {      }
     if (j>=(p+1))(v[j-p-1] = t[j]);      strcpy( name, path );               /* we've got it */
   }    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /********************** nrerror ********************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 void nrerror(char error_text[])      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   fprintf(stderr,"ERREUR ...\n");    }
   fprintf(stderr,"%s\n",error_text);    l1 = strlen( dirc );                  /* length of directory */
   exit(1);  #ifdef windows
 }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 /*********************** vector *******************/  #else
 double *vector(int nl, int nh)    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 {  #endif
   double *v;    ss = strrchr( name, '.' );            /* find last / */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    ss++;
   if (!v) nrerror("allocation failure in vector");    strcpy(ext,ss);                       /* save extension */
   return v-nl+NR_END;    l1= strlen( name);
 }    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
 /************************ free vector ******************/    finame[l1-l2]= 0;
 void free_vector(double*v, int nl, int nh)    return( 0 );                          /* we're done */
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  
   /******************************************/
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  void replace(char *s, char*t)
 {  {
   int *v;    int i;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    int lg=20;
   if (!v) nrerror("allocation failure in ivector");    i=0;
   return v-nl+NR_END;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /******************free ivector **************************/      if (t[i]== '\\') s[i]='/';
 void free_ivector(int *v, long nl, long nh)    }
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  int nbocc(char *s, char occ)
   {
 /******************* imatrix *******************************/    int i,j=0;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    int lg=20;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    i=0;
 {    lg=strlen(s);
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    for(i=0; i<= lg; i++) {
   int **m;    if  (s[i] == occ ) j++;
      }
   /* allocate pointers to rows */    return j;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  void cutv(char *u,char *v, char*t, char occ)
   m -= nrl;  {
      /* cuts string t into u and v where u is ended by char occ excluding it
         and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   /* allocate rows and set pointers to them */       gives u="abcedf" and v="ghi2j" */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    int i,lg,j,p=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    i=0;
   m[nrl] += NR_END;    for(j=0; j<=strlen(t)-1; j++) {
   m[nrl] -= ncl;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      }
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      lg=strlen(t);
   /* return pointer to array of pointers to rows */    for(j=0; j<p; j++) {
   return m;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)     for(j=0; j<= lg; j++) {
       int **m;      if (j>=(p+1))(v[j-p-1] = t[j]);
       long nch,ncl,nrh,nrl;    }
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /********************** nrerror ********************/
   free((FREE_ARG) (m+nrl-NR_END));  
 }  void nrerror(char error_text[])
   {
 /******************* matrix *******************************/    fprintf(stderr,"ERREUR ...\n");
 double **matrix(long nrl, long nrh, long ncl, long nch)    fprintf(stderr,"%s\n",error_text);
 {    exit(EXIT_FAILURE);
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  }
   double **m;  /*********************** vector *******************/
   double *vector(int nl, int nh)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    double *v;
   m += NR_END;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m -= nrl;    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /************************ free vector ******************/
   m[nrl] -= ncl;  void free_vector(double*v, int nl, int nh)
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    free((FREE_ARG)(v+nl-NR_END));
   return m;  }
 }  
   /************************ivector *******************************/
 /*************************free matrix ************************/  char *cvector(long nl,long nh)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  {
 {    char *v;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!v) nrerror("allocation failure in cvector");
 }    return v-nl+NR_END;
   }
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /******************free ivector **************************/
 {  void free_cvector(char *v, long nl, long nh)
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  {
   double ***m;    free((FREE_ARG)(v+nl-NR_END));
   }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
     int *v;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m[nrl][ncl] += NR_END;  }
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /******************* imatrix *******************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (i=nrl+1; i<=nrh; i++) {  { 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     for (j=ncl+1; j<=nch; j++)    int **m; 
       m[i][j]=m[i][j-1]+nlay;    
   }    /* allocate pointers to rows */ 
   return m;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 /*************************free ma3x ************************/    m -= nrl; 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    /* allocate rows and set pointers to them */ 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   free((FREE_ARG)(m+nrl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 }    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 /***************** f1dim *************************/    
 extern int ncom;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 extern double *pcom,*xicom;    
 extern double (*nrfunc)(double []);    /* return pointer to array of pointers to rows */ 
      return m; 
 double f1dim(double x)  } 
 {  
   int j;  /****************** free_imatrix *************************/
   double f;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double *xt;        int **m;
          long nch,ncl,nrh,nrl; 
   xt=vector(1,ncom);       /* free an int matrix allocated by imatrix() */ 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  { 
   f=(*nrfunc)(xt);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free_vector(xt,1,ncom);    free((FREE_ARG) (m+nrl-NR_END)); 
   return f;  } 
 }  
   /******************* matrix *******************************/
 /*****************brent *************************/  double **matrix(long nrl, long nrh, long ncl, long nch)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   int iter;    double **m;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ftemp;    if (!m) nrerror("allocation failure 1 in matrix()");
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m += NR_END;
   double e=0.0;    m -= nrl;
    
   a=(ax < cx ? ax : cx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   b=(ax > cx ? ax : cx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   x=w=v=bx;    m[nrl] += NR_END;
   fw=fv=fx=(*f)(x);    m[nrl] -= ncl;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    return m;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
     printf(".");fflush(stdout);     */
 #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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  /*************************free matrix ************************/
 #endif  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  {
       *xmin=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       return fx;    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /******************* ma3x *******************************/
       r=(x-w)*(fx-fv);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       q=2.0*(q-r);    double ***m;
       if (q > 0.0) p = -p;  
       q=fabs(q);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       etemp=e;    if (!m) nrerror("allocation failure 1 in matrix()");
       e=d;    m += NR_END;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m -= nrl;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         d=p/q;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         u=x+d;    m[nrl] += NR_END;
         if (u-a < tol2 || b-u < tol2)    m[nrl] -= ncl;
           d=SIGN(tol1,xm-x);  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl][ncl] += NR_END;
     fu=(*f)(u);    m[nrl][ncl] -= nll;
     if (fu <= fx) {    for (j=ncl+1; j<=nch; j++) 
       if (u >= x) a=x; else b=x;      m[nrl][j]=m[nrl][j-1]+nlay;
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    for (i=nrl+1; i<=nrh; i++) {
         } else {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           if (u < x) a=u; else b=u;      for (j=ncl+1; j<=nch; j++) 
           if (fu <= fw || w == x) {        m[i][j]=m[i][j-1]+nlay;
             v=w;    }
             w=u;    return m; 
             fv=fw;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             fw=fu;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           } else if (fu <= fv || v == x || v == w) {    */
             v=u;  }
             fv=fu;  
           }  /*************************free ma3x ************************/
         }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
   nrerror("Too many iterations in brent");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   *xmin=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return fx;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /****************** mnbrak ***********************/  /***************** f1dim *************************/
   extern int ncom; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  extern double *pcom,*xicom;
             double (*func)(double))  extern double (*nrfunc)(double []); 
 {   
   double ulim,u,r,q, dum;  double f1dim(double x) 
   double fu;  { 
      int j; 
   *fa=(*func)(*ax);    double f;
   *fb=(*func)(*bx);    double *xt; 
   if (*fb > *fa) {   
     SHFT(dum,*ax,*bx,dum)    xt=vector(1,ncom); 
       SHFT(dum,*fb,*fa,dum)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
   *cx=(*bx)+GOLD*(*bx-*ax);    free_vector(xt,1,ncom); 
   *fc=(*func)(*cx);    return f; 
   while (*fb > *fc) {  } 
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /*****************brent *************************/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    int iter; 
     if ((*bx-u)*(u-*cx) > 0.0) {    double a,b,d,etemp;
       fu=(*func)(u);    double fu,fv,fw,fx;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double ftemp;
       fu=(*func)(u);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       if (fu < *fc) {    double e=0.0; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))   
           SHFT(*fb,*fc,fu,(*func)(u))    a=(ax < cx ? ax : cx); 
           }    b=(ax > cx ? ax : cx); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    x=w=v=bx; 
       u=ulim;    fw=fv=fx=(*f)(x); 
       fu=(*func)(u);    for (iter=1;iter<=ITMAX;iter++) { 
     } else {      xm=0.5*(a+b); 
       u=(*cx)+GOLD*(*cx-*bx);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       fu=(*func)(u);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
     SHFT(*ax,*bx,*cx,u)      fprintf(ficlog,".");fflush(ficlog);
       SHFT(*fa,*fb,*fc,fu)  #ifdef DEBUG
       }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 /*************** linmin ************************/  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 int ncom;        *xmin=x; 
 double *pcom,*xicom;        return fx; 
 double (*nrfunc)(double []);      } 
        ftemp=fu;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if (fabs(e) > tol1) { 
 {        r=(x-w)*(fx-fv); 
   double brent(double ax, double bx, double cx,        q=(x-v)*(fx-fw); 
                double (*f)(double), double tol, double *xmin);        p=(x-v)*q-(x-w)*r; 
   double f1dim(double x);        q=2.0*(q-r); 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (q > 0.0) p = -p; 
               double *fc, double (*func)(double));        q=fabs(q); 
   int j;        etemp=e; 
   double xx,xmin,bx,ax;        e=d; 
   double fx,fb,fa;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
            d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   ncom=n;        else { 
   pcom=vector(1,n);          d=p/q; 
   xicom=vector(1,n);          u=x+d; 
   nrfunc=func;          if (u-a < tol2 || b-u < tol2) 
   for (j=1;j<=n;j++) {            d=SIGN(tol1,xm-x); 
     pcom[j]=p[j];        } 
     xicom[j]=xi[j];      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   ax=0.0;      } 
   xx=1.0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      fu=(*f)(u); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      if (fu <= fx) { 
 #ifdef DEBUG        if (u >= x) a=x; else b=x; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        SHFT(v,w,x,u) 
 #endif          SHFT(fv,fw,fx,fu) 
   for (j=1;j<=n;j++) {          } else { 
     xi[j] *= xmin;            if (u < x) a=u; else b=u; 
     p[j] += xi[j];            if (fu <= fw || w == x) { 
   }              v=w; 
   free_vector(xicom,1,n);              w=u; 
   free_vector(pcom,1,n);              fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /*************** powell ************************/              v=u; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,              fv=fu; 
             double (*func)(double []))            } 
 {          } 
   void linmin(double p[], double xi[], int n, double *fret,    } 
               double (*func)(double []));    nrerror("Too many iterations in brent"); 
   int i,ibig,j;    *xmin=x; 
   double del,t,*pt,*ptt,*xit;    return fx; 
   double fp,fptt;  } 
   double *xits;  
   pt=vector(1,n);  /****************** mnbrak ***********************/
   ptt=vector(1,n);  
   xit=vector(1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   xits=vector(1,n);              double (*func)(double)) 
   *fret=(*func)(p);  { 
   for (j=1;j<=n;j++) pt[j]=p[j];    double ulim,u,r,q, dum;
   for (*iter=1;;++(*iter)) {    double fu; 
     fp=(*fret);   
     ibig=0;    *fa=(*func)(*ax); 
     del=0.0;    *fb=(*func)(*bx); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if (*fb > *fa) { 
     for (i=1;i<=n;i++)      SHFT(dum,*ax,*bx,dum) 
       printf(" %d %.12f",i, p[i]);        SHFT(dum,*fb,*fa,dum) 
     printf("\n");        } 
     for (i=1;i<=n;i++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    *fc=(*func)(*cx); 
       fptt=(*fret);    while (*fb > *fc) { 
 #ifdef DEBUG      r=(*bx-*ax)*(*fb-*fc); 
       printf("fret=%lf \n",*fret);      q=(*bx-*cx)*(*fb-*fa); 
 #endif      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       printf("%d",i);fflush(stdout);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       linmin(p,xit,n,fret,func);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if (fabs(fptt-(*fret)) > del) {      if ((*bx-u)*(u-*cx) > 0.0) { 
         del=fabs(fptt-(*fret));        fu=(*func)(u); 
         ibig=i;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       }        fu=(*func)(u); 
 #ifdef DEBUG        if (fu < *fc) { 
       printf("%d %.12e",i,(*fret));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (j=1;j<=n;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);            } 
         printf(" x(%d)=%.12e",j,xit[j]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       }        u=ulim; 
       for(j=1;j<=n;j++)        fu=(*func)(u); 
         printf(" p=%.12e",p[j]);      } else { 
       printf("\n");        u=(*cx)+GOLD*(*cx-*bx); 
 #endif        fu=(*func)(u); 
     }      } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      SHFT(*ax,*bx,*cx,u) 
 #ifdef DEBUG        SHFT(*fa,*fb,*fc,fu) 
       int k[2],l;        } 
       k[0]=1;  } 
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /*************** linmin ************************/
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  int ncom; 
       printf("\n");  double *pcom,*xicom;
       for(l=0;l<=1;l++) {  double (*nrfunc)(double []); 
         for (j=1;j<=n;j++) {   
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    double brent(double ax, double bx, double cx, 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));                 double (*f)(double), double tol, double *xmin); 
       }    double f1dim(double x); 
 #endif    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
     int j; 
       free_vector(xit,1,n);    double xx,xmin,bx,ax; 
       free_vector(xits,1,n);    double fx,fb,fa;
       free_vector(ptt,1,n);   
       free_vector(pt,1,n);    ncom=n; 
       return;    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    nrfunc=func; 
     for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
       ptt[j]=2.0*p[j]-pt[j];      pcom[j]=p[j]; 
       xit[j]=p[j]-pt[j];      xicom[j]=xi[j]; 
       pt[j]=p[j];    } 
     }    ax=0.0; 
     fptt=(*func)(ptt);    xx=1.0; 
     if (fptt < fp) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       if (t < 0.0) {  #ifdef DEBUG
         linmin(p,xit,n,fret,func);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (j=1;j<=n;j++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           xi[j][ibig]=xi[j][n];  #endif
           xi[j][n]=xit[j];    for (j=1;j<=n;j++) { 
         }      xi[j] *= xmin; 
 #ifdef DEBUG      p[j] += xi[j]; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    } 
         for(j=1;j<=n;j++)    free_vector(xicom,1,n); 
           printf(" %.12e",xit[j]);    free_vector(pcom,1,n); 
         printf("\n");  } 
 #endif  
       }  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
 }  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 /**** Prevalence limit ****************/                double (*func)(double [])); 
     int i,ibig,j; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double del,t,*pt,*ptt,*xit;
 {    double fp,fptt;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double *xits;
      matrix by transitions matrix until convergence is reached */    pt=vector(1,n); 
     ptt=vector(1,n); 
   int i, ii,j,k;    xit=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    xits=vector(1,n); 
   double **matprod2();    *fret=(*func)(p); 
   double **out, cov[NCOVMAX], **pmij();    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **newm;    for (*iter=1;;++(*iter)) { 
   double agefin, delaymax=50 ; /* Max number of years to converge */      fp=(*fret); 
       ibig=0; 
   for (ii=1;ii<=nlstate+ndeath;ii++)      del=0.0; 
     for (j=1;j<=nlstate+ndeath;j++){      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
    cov[1]=1.;        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficrespow," %.12lf", p[i]);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      }
     newm=savm;      printf("\n");
     /* Covariates have to be included here again */      fprintf(ficlog,"\n");
      cov[2]=agefin;      fprintf(ficrespow,"\n");
        for (i=1;i<=n;i++) { 
       for (k=1; k<=cptcovn;k++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fptt=(*fret); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  #ifdef DEBUG
       }        printf("fret=%lf \n",*fret);
       for (k=1; k<=cptcovage;k++)        fprintf(ficlog,"fret=%lf \n",*fret);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #endif
       for (k=1; k<=cptcovprod;k++)        printf("%d",i);fflush(stdout);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        if (fabs(fptt-(*fret)) > del) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          del=fabs(fptt-(*fret)); 
           ibig=i; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        } 
   #ifdef DEBUG
     savm=oldm;        printf("%d %.12e",i,(*fret));
     oldm=newm;        fprintf(ficlog,"%d %.12e",i,(*fret));
     maxmax=0.;        for (j=1;j<=n;j++) {
     for(j=1;j<=nlstate;j++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       min=1.;          printf(" x(%d)=%.12e",j,xit[j]);
       max=0.;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for(i=1; i<=nlstate; i++) {        }
         sumnew=0;        for(j=1;j<=n;j++) {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf(" p=%.12e",p[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog," p=%.12e",p[j]);
         max=FMAX(max,prlim[i][j]);        }
         min=FMIN(min,prlim[i][j]);        printf("\n");
       }        fprintf(ficlog,"\n");
       maxmin=max-min;  #endif
       maxmax=FMAX(maxmax,maxmin);      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     if(maxmax < ftolpl){  #ifdef DEBUG
       return prlim;        int k[2],l;
     }        k[0]=1;
   }        k[1]=-1;
 }        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
 /*************** transition probabilities ***************/        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          fprintf(ficlog," %.12e",p[j]);
 {        }
   double s1, s2;        printf("\n");
   /*double t34;*/        fprintf(ficlog,"\n");
   int i,j,j1, nc, ii, jj;        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
     for(i=1; i<= nlstate; i++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for(j=1; j<i;j++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; 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]);
         /*s2 += param[i][j][nc]*cov[nc];*/          }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }        }
       ps[i][j]=s2;  #endif
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){        free_vector(xit,1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        free_vector(xits,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        free_vector(ptt,1,n); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        free_vector(pt,1,n); 
       }        return; 
       ps[i][j]=s2;      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   }      for (j=1;j<=n;j++) { 
     /*ps[3][2]=1;*/        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
   for(i=1; i<= nlstate; i++){        pt[j]=p[j]; 
      s1=0;      } 
     for(j=1; j<i; j++)      fptt=(*func)(ptt); 
       s1+=exp(ps[i][j]);      if (fptt < fp) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       s1+=exp(ps[i][j]);        if (t < 0.0) { 
     ps[i][i]=1./(s1+1.);          linmin(p,xit,n,fret,func); 
     for(j=1; j<i; j++)          for (j=1;j<=n;j++) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];            xi[j][ibig]=xi[j][n]; 
     for(j=i+1; j<=nlstate+ndeath; j++)            xi[j][n]=xit[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          for(j=1;j<=n;j++){
     for(jj=1; jj<= nlstate+ndeath; jj++){            printf(" %.12e",xit[j]);
       ps[ii][jj]=0;            fprintf(ficlog," %.12e",xit[j]);
       ps[ii][ii]=1;          }
     }          printf("\n");
   }          fprintf(ficlog,"\n");
   #endif
         }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      } 
     for(jj=1; jj<= nlstate+ndeath; jj++){    } 
      printf("%lf ",ps[ii][jj]);  } 
    }  
     printf("\n ");  /**** Prevalence limit (stable prevalence)  ****************/
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 /*  {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   goto end;*/       matrix by transitions matrix until convergence is reached */
     return ps;  
 }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 /**************** Product of 2 matrices ******************/    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double **newm;
 {    double agefin, delaymax=50 ; /* Max number of years to converge */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    for (ii=1;ii<=nlstate+ndeath;ii++)
   /* in, b, out are matrice of pointers which should have been initialized      for (j=1;j<=nlstate+ndeath;j++){
      before: only the contents of out is modified. The function returns        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      a pointer to pointers identical to out */      }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)     cov[1]=1.;
     for(k=ncolol; k<=ncoloh; k++)   
       for(j=ncl,out[i][k]=0.; j<=nch; j++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         out[i][k] +=in[i][j]*b[j][k];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
   return out;      /* Covariates have to be included here again */
 }       cov[2]=agefin;
     
         for (k=1; k<=cptcovn;k++) {
 /************* Higher Matrix Product ***************/          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]]);*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        }
 {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        for (k=1; k<=cptcovprod;k++)
      duration (i.e. until          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      (typically every 2 years instead of every month which is too big).        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      Model is determined by parameters x and covariates have to be        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      included manually here.      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
      */      savm=oldm;
       oldm=newm;
   int i, j, d, h, k;      maxmax=0.;
   double **out, cov[NCOVMAX];      for(j=1;j<=nlstate;j++){
   double **newm;        min=1.;
         max=0.;
   /* Hstepm could be zero and should return the unit matrix */        for(i=1; i<=nlstate; i++) {
   for (i=1;i<=nlstate+ndeath;i++)          sumnew=0;
     for (j=1;j<=nlstate+ndeath;j++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       oldm[i][j]=(i==j ? 1.0 : 0.0);          prlim[i][j]= newm[i][j]/(1-sumnew);
       po[i][j][0]=(i==j ? 1.0 : 0.0);          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        }
   for(h=1; h <=nhstepm; h++){        maxmin=max-min;
     for(d=1; d <=hstepm; d++){        maxmax=FMAX(maxmax,maxmin);
       newm=savm;      }
       /* Covariates have to be included here again */      if(maxmax < ftolpl){
       cov[1]=1.;        return prlim;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    }
       for (k=1; k<=cptcovage;k++)  }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /*************** transition probabilities ***************/ 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double s1, s2;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    /*double t34;*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    int i,j,j1, nc, ii, jj;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;      for(i=1; i<= nlstate; i++){
       oldm=newm;      for(j=1; j<i;j++){
     }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(i=1; i<=nlstate+ndeath; i++)          /*s2 += param[i][j][nc]*cov[nc];*/
       for(j=1;j<=nlstate+ndeath;j++) {          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         po[i][j][h]=newm[i][j];          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        }
          */        ps[i][j]=s2;
       }        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   } /* end h */      }
   return po;      for(j=i+1; j<=nlstate+ndeath;j++){
 }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 /*************** log-likelihood *************/        }
 double func( double *x)        ps[i][j]=s2;
 {      }
   int i, ii, j, k, mi, d, kk;    }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      /*ps[3][2]=1;*/
   double **out;  
   double sw; /* Sum of weights */    for(i=1; i<= nlstate; i++){
   double lli; /* Individual log likelihood */       s1=0;
   long ipmx;      for(j=1; j<i; j++)
   /*extern weight */        s1+=exp(ps[i][j]);
   /* We are differentiating ll according to initial status */      for(j=i+1; j<=nlstate+ndeath; j++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        s1+=exp(ps[i][j]);
   /*for(i=1;i<imx;i++)      ps[i][i]=1./(s1+1.);
     printf(" %d\n",s[4][i]);      for(j=1; j<i; j++)
   */        ps[i][j]= exp(ps[i][j])*ps[i][i];
   cov[1]=1.;      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(k=1; k<=nlstate; k++) ll[k]=0.;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    } /* end i */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(jj=1; jj<= nlstate+ndeath; jj++){
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        ps[ii][jj]=0;
       for(d=0; d<dh[mi][i]; d++){        ps[ii][ii]=1;
         newm=savm;      }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    }
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
              for(jj=1; jj<= nlstate+ndeath; jj++){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       printf("%lf ",ps[ii][jj]);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));     }
         savm=oldm;      printf("\n ");
         oldm=newm;      }
              printf("\n ");printf("%lf ",cov[2]);*/
          /*
       } /* end mult */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      return ps;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  }
       ipmx +=1;  
       sw += weight[i];  /**************** Product of 2 matrices ******************/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   } /* end of individual */  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* in, b, out are matrice of pointers which should have been initialized 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */       before: only the contents of out is modified. The function returns
   return -l;       a pointer to pointers identical to out */
 }    long i, j, k;
     for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
 /*********** Maximum Likelihood Estimation ***************/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {    return out;
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  
   xi=matrix(1,npar,1,npar);  /************* Higher Matrix Product ***************/
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       xi[i][j]=(i==j ? 1.0 : 0.0);  {
   printf("Powell\n");    /* Computes the transition matrix starting at age 'age' over 
   powell(p,xi,npar,ftol,&iter,&fret,func);       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));       nhstepm*hstepm matrices. 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 }       for the memory).
        Model is determined by parameters x and covariates have to be 
 /**** Computes Hessian and covariance matrix ***/       included manually here. 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {       */
   double  **a,**y,*x,pd;  
   double **hess;    int i, j, d, h, k;
   int i, j,jk;    double **out, cov[NCOVMAX];
   int *indx;    double **newm;
   
   double hessii(double p[], double delta, int theta, double delti[]);    /* Hstepm could be zero and should return the unit matrix */
   double hessij(double p[], double delti[], int i, int j);    for (i=1;i<=nlstate+ndeath;i++)
   void lubksb(double **a, int npar, int *indx, double b[]) ;      for (j=1;j<=nlstate+ndeath;j++){
   void ludcmp(double **a, int npar, int *indx, double *d) ;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
   hess=matrix(1,npar,1,npar);      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   printf("\nCalculation of the hessian matrix. Wait...\n");    for(h=1; h <=nhstepm; h++){
   for (i=1;i<=npar;i++){      for(d=1; d <=hstepm; d++){
     printf("%d",i);fflush(stdout);        newm=savm;
     hess[i][i]=hessii(p,ftolhess,i,delti);        /* Covariates have to be included here again */
     /*printf(" %f ",p[i]);*/        cov[1]=1.;
     /*printf(" %lf ",hess[i][i]);*/        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          for (k=1; k<=cptcovage;k++)
   for (i=1;i<=npar;i++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=npar;j++)  {        for (k=1; k<=cptcovprod;k++)
       if (j>i) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];            /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf(" %lf ",hess[i][j]);*/        /*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, 
     }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   }        savm=oldm;
   printf("\n");        oldm=newm;
       }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
   a=matrix(1,npar,1,npar);          po[i][j][h]=newm[i][j];
   y=matrix(1,npar,1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   x=vector(1,npar);           */
   indx=ivector(1,npar);        }
   for (i=1;i<=npar;i++)    } /* end h */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    return po;
   ludcmp(a,npar,indx,&pd);  }
   
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /*************** log-likelihood *************/
     x[j]=1;  double func( double *x)
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    int i, ii, j, k, mi, d, kk;
       matcov[i][j]=x[i];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     }    double **out;
   }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   printf("\n#Hessian matrix#\n");    int s1, s2;
   for (i=1;i<=npar;i++) {    double bbh, survp;
     for (j=1;j<=npar;j++) {    long ipmx;
       printf("%.3e ",hess[i][j]);    /*extern weight */
     }    /* We are differentiating ll according to initial status */
     printf("\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   /* Recompute Inverse */    */
   for (i=1;i<=npar;i++)    cov[1]=1.;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (j=1;j<=npar;j++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=1;i<=npar;i++) x[i]=0;        for(mi=1; mi<= wav[i]-1; mi++){
     x[j]=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     lubksb(a,npar,indx,x);            for (j=1;j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       y[i][j]=x[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%.3e ",y[i][j]);            }
     }          for(d=0; d<dh[mi][i]; d++){
     printf("\n");            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(a,1,npar,1,npar);            }
   free_matrix(y,1,npar,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(x,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_ivector(indx,1,npar);            savm=oldm;
   free_matrix(hess,1,npar,1,npar);            oldm=newm;
           } /* end mult */
         
 }          /*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.
 /*************** hessian matrix ****************/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 double hessii( double x[], double delta, int theta, double delti[])           * (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
   int i;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int l=1, lmax=20;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   double k1,k2;           * probability in order to take into account the bias as a fraction of the way
   double p2[NPARMAX+1];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double res;           * -stepm/2 to stepm/2 .
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * For stepm=1 the results are the same as for previous versions of Imach.
   double fx;           * For stepm > 1 the results are less biased than in previous versions. 
   int k=0,kmax=10;           */
   double l1;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   fx=func(x);          bbh=(double)bh[mi][i]/(double)stepm; 
   for (i=1;i<=npar;i++) p2[i]=x[i];          /* bias is positive if real duration
   for(l=0 ; l <=lmax; l++){           * is higher than the multiple of stepm and negative otherwise.
     l1=pow(10,l);           */
     delts=delt;          /* 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(k=1 ; k <kmax; k=k+1){          if( s2 > nlstate){ 
       delt = delta*(l1*k);            /* 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 
       k1=func(p2)-fx;               step unit time, which is also the differences between probability to die before dh 
       p2[theta]=x[theta]-delt;               and probability to die before dh-stepm . 
       k2=func(p2)-fx;               In version up to 0.92 likelihood was computed
       /*res= (k1-2.0*fx+k2)/delt/delt; */          as if date of death was unknown. Death was treated as any other
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          health state: the date of the interview describes the actual state
                and not the date of a change in health state. The former idea was
 #ifdef DEBUG          to consider that at each interview the state was recorded
       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);          (healthy, disable or death) and IMaCh was corrected; but when we
 #endif          introduced the exact date of death then we should have modified
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          the contribution of an exact death to the likelihood. This new
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          contribution is smaller and very dependent of the step unit
         k=kmax;          stepm. It is no more the probability to die between last interview
       }          and month of death but the probability to survive from last
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          interview up to one month before death multiplied by the
         k=kmax; l=lmax*10.;          probability to die within a month. Thanks to Chris
       }          Jackson for correcting this bug.  Former versions increased
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          mortality artificially. The bad side is that we add another loop
         delts=delt;          which slows down the processing. The difference can be up to 10%
       }          lower mortality.
     }            */
   }            lli=log(out[s1][s2] - savm[s1][s2]);
   delti[theta]=delts;          }else{
   return res;            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 */
 }          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 double hessij( double x[], double delti[], int thetai,int thetaj)          /*if(lli ==000.0)*/
 {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int i;          ipmx +=1;
   int l=1, l1, lmax=20;          sw += weight[i];
   double k1,k2,k3,k4,res,fx;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double p2[NPARMAX+1];        } /* end of wave */
   int k;      } /* end of individual */
     }  else if(mle==2){
   fx=func(x);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (k=1; k<=2; k++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=1;i<=npar;i++) p2[i]=x[i];        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetai]=x[thetai]+delti[thetai]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            for (j=1;j<=nlstate+ndeath;j++){
     k1=func(p2)-fx;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for(d=0; d<=dh[mi][i]; d++){
     k2=func(p2)-fx;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetai]=x[thetai]-delti[thetai]/k;            for (kk=1; kk<=cptcovage;kk++) {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     k3=func(p2)-fx;            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetai]=x[thetai]-delti[thetai]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            savm=oldm;
     k4=func(p2)-fx;            oldm=newm;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          } /* end mult */
 #ifdef DEBUG        
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 #endif          /* 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 
   return res;           * (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
 /************** Inverse of matrix **************/           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 void ludcmp(double **a, int n, int *indx, double *d)           * probability in order to take into account the bias as a fraction of the way
 {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int i,imax,j,k;           * -stepm/2 to stepm/2 .
   double big,dum,sum,temp;           * For stepm=1 the results are the same as for previous versions of Imach.
   double *vv;           * For stepm > 1 the results are less biased than in previous versions. 
             */
   vv=vector(1,n);          s1=s[mw[mi][i]][i];
   *d=1.0;          s2=s[mw[mi+1][i]][i];
   for (i=1;i<=n;i++) {          bbh=(double)bh[mi][i]/(double)stepm; 
     big=0.0;          /* bias is positive if real duration
     for (j=1;j<=n;j++)           * is higher than the multiple of stepm and negative otherwise.
       if ((temp=fabs(a[i][j])) > big) big=temp;           */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          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 */
     vv[i]=1.0/big;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   }          /*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 */
   for (j=1;j<=n;j++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for (i=1;i<j;i++) {          /*if(lli ==000.0)*/
       sum=a[i][j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          ipmx +=1;
       a[i][j]=sum;          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     big=0.0;        } /* end of wave */
     for (i=j;i<=n;i++) {      } /* end of individual */
       sum=a[i][j];    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (k=1;k<j;k++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       a[i][j]=sum;        for(mi=1; mi<= wav[i]-1; mi++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         big=dum;            for (j=1;j<=nlstate+ndeath;j++){
         imax=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     if (j != imax) {          for(d=0; d<dh[mi][i]; d++){
       for (k=1;k<=n;k++) {            newm=savm;
         dum=a[imax][k];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         a[imax][k]=a[j][k];            for (kk=1; kk<=cptcovage;kk++) {
         a[j][k]=dum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       *d = -(*d);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       vv[imax]=vv[j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     indx[j]=imax;            oldm=newm;
     if (a[j][j] == 0.0) a[j][j]=TINY;          } /* end mult */
     if (j != n) {        
       dum=1.0/(a[j][j]);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          /* 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 
   free_vector(vv,1,n);  /* Doesn't work */           * 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
 }           * (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
 void lubksb(double **a, int n, int *indx, double b[])           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 {           * -stepm/2 to stepm/2 .
   int i,ii=0,ip,j;           * For stepm=1 the results are the same as for previous versions of Imach.
   double sum;           * For stepm > 1 the results are less biased than in previous versions. 
             */
   for (i=1;i<=n;i++) {          s1=s[mw[mi][i]][i];
     ip=indx[i];          s2=s[mw[mi+1][i]][i];
     sum=b[ip];          bbh=(double)bh[mi][i]/(double)stepm; 
     b[ip]=b[i];          /* bias is positive if real duration
     if (ii)           * is higher than the multiple of stepm and negative otherwise.
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           */
     else if (sum) ii=i;          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     b[i]=sum;          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 */
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (i=n;i>=1;i--) {          /*if(lli ==000.0)*/
     sum=b[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); */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          ipmx +=1;
     b[i]=sum/a[i][i];          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }        } /* end of wave */
       } /* end of individual */
 /************ Frequencies ********************/    }else{  /* ml=4 no inter-extrapolation */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {  /* Some frequencies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***freq; /* Frequencies */            for (j=1;j<=nlstate+ndeath;j++){
   double *pp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2, dateintsum=0,k2cpt=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   FILE *ficresp;            }
   char fileresp[FILENAMELENGTH];          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   pp=vector(1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (kk=1; kk<=cptcovage;kk++) {
   strcpy(fileresp,"p");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   strcat(fileresp,fileres);            }
   if((ficresp=fopen(fileresp,"w"))==NULL) {          
     printf("Problem with prevalence resultfile: %s\n", fileresp);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     exit(0);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            oldm=newm;
   j1=0;          } /* end mult */
         
   j=cptcoveff;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          ipmx +=1;
           sw += weight[i];
   for(k1=1; k1<=j;k1++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    for(i1=1; i1<=ncodemax[k1];i1++){        } /* end of wave */
        j1++;      } /* end of individual */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    } /* End of if */
          scanf("%d", i);*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         for (i=-1; i<=nlstate+ndeath; i++)      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            for(m=agemin; m <= agemax+3; m++)    return -l;
              freq[i][jk][m]=0;  }
   
         dateintsum=0;  
         k2cpt=0;  /*********** Maximum Likelihood Estimation ***************/
        for (i=1; i<=imx; i++) {  
          bool=1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
          if  (cptcovn>0) {  {
            for (z1=1; z1<=cptcoveff; z1++)    int i,j, iter;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double **xi;
                bool=0;    double fret;
          }    char filerespow[FILENAMELENGTH];
          if (bool==1) {    xi=matrix(1,npar,1,npar);
            for(m=firstpass; m<=lastpass; m++){    for (i=1;i<=npar;i++)
              k2=anint[m][i]+(mint[m][i]/12.);      for (j=1;j<=npar;j++)
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        xi[i][j]=(i==j ? 1.0 : 0.0);
                if(agev[m][i]==0) agev[m][i]=agemax+1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
                if(agev[m][i]==1) agev[m][i]=agemax+2;    strcpy(filerespow,"pow"); 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    strcat(filerespow,fileres);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      printf("Problem with resultfile: %s\n", filerespow);
                  dateintsum=dateintsum+k2;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                  k2cpt++;    }
                }    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");
        }    powell(p,xi,npar,ftol,&iter,&fret,func);
          
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         if  (cptcovn>0) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
          fprintf(ficresp, "\n#********** Variable ");    fprintf(ficres,"#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(ficresp, "**********\n#");  }
         }  
        for(i=1; i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        fprintf(ficresp, "\n");  {
            double  **a,**y,*x,pd;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    double **hess;
     if(i==(int)agemax+3)    int i, j,jk;
       printf("Total");    int *indx;
     else  
       printf("Age %d", i);    double hessii(double p[], double delta, int theta, double delti[]);
     for(jk=1; jk <=nlstate ; jk++){    double hessij(double p[], double delti[], int i, int j);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
         pp[jk] += freq[jk][m][i];    void ludcmp(double **a, int npar, int *indx, double *d) ;
     }  
     for(jk=1; jk <=nlstate ; jk++){    hess=matrix(1,npar,1,npar);
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];    printf("\nCalculation of the hessian matrix. Wait...\n");
       if(pp[jk]>=1.e-10)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for (i=1;i<=npar;i++){
       else      printf("%d",i);fflush(stdout);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      fprintf(ficlog,"%d",i);fflush(ficlog);
     }      hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
      for(jk=1; jk <=nlstate ; jk++){      /*printf(" %lf ",hess[i][i]);*/
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    }
         pp[jk] += freq[jk][m][i];    
      }    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
     for(jk=1,pos=0; jk <=nlstate ; jk++)        if (j>i) { 
       pos += pp[jk];          printf(".%d%d",i,j);fflush(stdout);
     for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       if(pos>=1.e-5)          hess[i][j]=hessij(p,delti,i,j);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          hess[j][i]=hess[i][j];    
       else          /*printf(" %lf ",hess[i][j]);*/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        }
       if( i <= (int) agemax){      }
         if(pos>=1.e-5){    }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    printf("\n");
           probs[i][jk][j1]= pp[jk]/pos;    fprintf(ficlog,"\n");
           /*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("\nInverting the hessian to get the covariance matrix. Wait...\n");
       else    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    
       }    a=matrix(1,npar,1,npar);
     }    y=matrix(1,npar,1,npar);
     for(jk=-1; jk <=nlstate+ndeath; jk++)    x=vector(1,npar);
       for(m=-1; m <=nlstate+ndeath; m++)    indx=ivector(1,npar);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    for (i=1;i<=npar;i++)
     if(i <= (int) agemax)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       fprintf(ficresp,"\n");    ludcmp(a,npar,indx,&pd);
     printf("\n");  
     }    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
  }      x[j]=1;
   dateintmean=dateintsum/k2cpt;      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   fclose(ficresp);        matcov[i][j]=x[i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);    }
   
   /* End of Freq */    printf("\n#Hessian matrix#\n");
 }    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
 /************ Prevalence ********************/      for (j=1;j<=npar;j++) { 
 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)        printf("%.3e ",hess[i][j]);
 {  /* Some frequencies */        fprintf(ficlog,"%.3e ",hess[i][j]);
        }
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      printf("\n");
   double ***freq; /* Frequencies */      fprintf(ficlog,"\n");
   double *pp;    }
   double pos, k2;  
     /* Recompute Inverse */
   pp=vector(1,nlstate);    for (i=1;i<=npar;i++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ludcmp(a,npar,indx,&pd);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    /*  printf("\n#Hessian matrix recomputed#\n");
    
   j=cptcoveff;    for (j=1;j<=npar;j++) {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
  for(k1=1; k1<=j;k1++){      lubksb(a,npar,indx,x);
     for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1;i<=npar;i++){ 
       j1++;        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
       for (i=-1; i<=nlstate+ndeath; i++)          fprintf(ficlog,"%.3e ",y[i][j]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)        }
           for(m=agemin; m <= agemax+3; m++)      printf("\n");
             freq[i][jk][m]=0;      fprintf(ficlog,"\n");
          }
       for (i=1; i<=imx; i++) {    */
         bool=1;  
         if  (cptcovn>0) {    free_matrix(a,1,npar,1,npar);
           for (z1=1; z1<=cptcoveff; z1++)    free_matrix(y,1,npar,1,npar);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    free_vector(x,1,npar);
               bool=0;    free_ivector(indx,1,npar);
         }    free_matrix(hess,1,npar,1,npar);
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  /*************** hessian matrix ****************/
               if(agev[m][i]==1) agev[m][i]=agemax+2;  double hessii( double x[], double delta, int theta, double delti[])
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  {
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    int i;
             }    int l=1, lmax=20;
           }    double k1,k2;
         }    double p2[NPARMAX+1];
       }    double res;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           for(jk=1; jk <=nlstate ; jk++){    double fx;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int k=0,kmax=10;
               pp[jk] += freq[jk][m][i];    double l1;
           }  
           for(jk=1; jk <=nlstate ; jk++){    fx=func(x);
             for(m=-1, pos=0; m <=0 ; m++)    for (i=1;i<=npar;i++) p2[i]=x[i];
             pos += freq[jk][m][i];    for(l=0 ; l <=lmax; l++){
         }      l1=pow(10,l);
              delts=delt;
          for(jk=1; jk <=nlstate ; jk++){      for(k=1 ; k <kmax; k=k+1){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        delt = delta*(l1*k);
              pp[jk] += freq[jk][m][i];        p2[theta]=x[theta] +delt;
          }        k1=func(p2)-fx;
                  p2[theta]=x[theta]-delt;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
          for(jk=1; jk <=nlstate ; jk++){                  res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
            if( i <= (int) agemax){        
              if(pos>=1.e-5){  #ifdef DEBUG
                probs[i][jk][j1]= pp[jk]/pos;        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. */
            k=kmax; l=lmax*10.;
          }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   free_vector(pp,1,nlstate);          delts=delt;
          }
 }  /* End of Freq */      }
     }
 /************* Waves Concatenation ***************/    delti[theta]=delts;
     return res; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    
 {  }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).  double hessij( double x[], double delti[], int thetai,int thetaj)
      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]    int i;
      and mw[mi+1][i]. dh depends on stepm.    int l=1, l1, lmax=20;
      */    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
   int i, mi, m;    int k;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/    fx=func(x);
     for (k=1; k<=2; k++) {
   int j, k=0,jk, ju, jl;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double sum=0.;      p2[thetai]=x[thetai]+delti[thetai]/k;
   jmin=1e+5;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   jmax=-1;      k1=func(p2)-fx;
   jmean=0.;    
   for(i=1; i<=imx; i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
     mi=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     m=firstpass;      k2=func(p2)-fx;
     while(s[m][i] <= nlstate){    
       if(s[m][i]>=1)      p2[thetai]=x[thetai]-delti[thetai]/k;
         mw[++mi][i]=m;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       if(m >=lastpass)      k3=func(p2)-fx;
         break;    
       else      p2[thetai]=x[thetai]-delti[thetai]/k;
         m++;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     }/* end while */      k4=func(p2)-fx;
     if (s[m][i] > nlstate){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       mi++;     /* Death is another wave */  #ifdef DEBUG
       /* if(mi==0)  never been interviewed correctly before death */      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);
          /* Only death is a correct wave */      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);
       mw[mi][i]=m;  #endif
     }    }
     return res;
     wav[i]=mi;  }
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /************** Inverse of matrix **************/
   }  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
   for(i=1; i<=imx; i++){    int i,imax,j,k; 
     for(mi=1; mi<wav[i];mi++){    double big,dum,sum,temp; 
       if (stepm <=0)    double *vv; 
         dh[mi][i]=1;   
       else{    vv=vector(1,n); 
         if (s[mw[mi+1][i]][i] > nlstate) {    *d=1.0; 
           if (agedc[i] < 2*AGESUP) {    for (i=1;i<=n;i++) { 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      big=0.0; 
           if(j==0) j=1;  /* Survives at least one month after exam */      for (j=1;j<=n;j++) 
           k=k+1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           if (j >= jmax) jmax=j;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           if (j <= jmin) jmin=j;      vv[i]=1.0/big; 
           sum=sum+j;    } 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    for (j=1;j<=n;j++) { 
           }      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
         else{        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        a[i][j]=sum; 
           k=k+1;      } 
           if (j >= jmax) jmax=j;      big=0.0; 
           else if (j <= jmin)jmin=j;      for (i=j;i<=n;i++) { 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        sum=a[i][j]; 
           sum=sum+j;        for (k=1;k<j;k++) 
         }          sum -= a[i][k]*a[k][j]; 
         jk= j/stepm;        a[i][j]=sum; 
         jl= j -jk*stepm;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         ju= j -(jk+1)*stepm;          big=dum; 
         if(jl <= -ju)          imax=i; 
           dh[mi][i]=jk;        } 
         else      } 
           dh[mi][i]=jk+1;      if (j != imax) { 
         if(dh[mi][i]==0)        for (k=1;k<=n;k++) { 
           dh[mi][i]=1; /* At least one step */          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
     }          a[j][k]=dum; 
   }        } 
   jmean=sum/k;        *d = -(*d); 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        vv[imax]=vv[j]; 
  }      } 
 /*********** Tricode ****************************/      indx[j]=imax; 
 void tricode(int *Tvar, int **nbcode, int imx)      if (a[j][j] == 0.0) a[j][j]=TINY; 
 {      if (j != n) { 
   int Ndum[20],ij=1, k, j, i;        dum=1.0/(a[j][j]); 
   int cptcode=0;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   cptcoveff=0;      } 
      } 
   for (k=0; k<19; k++) Ndum[k]=0;    free_vector(vv,1,n);  /* Doesn't work */
   for (k=1; k<=7; k++) ncodemax[k]=0;  ;
   } 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  void lubksb(double **a, int n, int *indx, double b[]) 
       ij=(int)(covar[Tvar[j]][i]);  { 
       Ndum[ij]++;    int i,ii=0,ip,j; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    double sum; 
       if (ij > cptcode) cptcode=ij;   
     }    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     for (i=0; i<=cptcode; i++) {      sum=b[ip]; 
       if(Ndum[i]!=0) ncodemax[j]++;      b[ip]=b[i]; 
     }      if (ii) 
     ij=1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
       b[i]=sum; 
     for (i=1; i<=ncodemax[j]; i++) {    } 
       for (k=0; k<=19; k++) {    for (i=n;i>=1;i--) { 
         if (Ndum[k] != 0) {      sum=b[i]; 
           nbcode[Tvar[j]][ij]=k;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           ij++;      b[i]=sum/a[i][i]; 
         }    } 
         if (ij > ncodemax[j]) break;  } 
       }    
     }  /************ Frequencies ********************/
   }    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 (k=0; k<19; k++) Ndum[k]=0;    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
  for (i=1; i<=ncovmodel-2; i++) {    int first;
       ij=Tvar[i];    double ***freq; /* Frequencies */
       Ndum[ij]++;    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
  ij=1;    char fileresp[FILENAMELENGTH];
  for (i=1; i<=10; i++) {    
    if((Ndum[i]!=0) && (i<=ncov)){    pp=vector(1,nlstate);
      Tvaraff[ij]=i;    prop=matrix(1,nlstate,iagemin,iagemax+3);
      ij++;    strcpy(fileresp,"p");
    }    strcat(fileresp,fileres);
  }    if((ficresp=fopen(fileresp,"w"))==NULL) {
        printf("Problem with prevalence resultfile: %s\n", fileresp);
     cptcoveff=ij-1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 }      exit(0);
     }
 /*********** Health Expectancies ****************/    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    
 {    j=cptcoveff;
   /* Health expectancies */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;    first=1;
   double ***p3mat;  
      for(k1=1; k1<=j;k1++){
   fprintf(ficreseij,"# Health expectancies\n");      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficreseij,"# Age");        j1++;
   for(i=1; i<=nlstate;i++)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for(j=1; j<=nlstate;j++)          scanf("%d", i);*/
       fprintf(ficreseij," %1d-%1d",i,j);        for (i=-1; i<=nlstate+ndeath; i++)  
   fprintf(ficreseij,"\n");          for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
   hstepm=1*YEARM; /*  Every j years of age (in month) */              freq[i][jk][m]=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
       for (i=1; i<=nlstate; i++)  
   agelim=AGESUP;        for(m=iagemin; m <= iagemax+3; m++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          prop[i][m]=0;
     /* nhstepm age range expressed in number of stepm */        
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        dateintsum=0;
     /* Typically if 20 years = 20*12/6=40 stepm */        k2cpt=0;
     /*if (stepm >= YEARM) hstepm=1;*/        for (i=1; i<=imx; i++) {
 hstepm=1;          bool=1;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          if  (cptcovn>0) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (z1=1; z1<=cptcoveff; z1++) 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                bool=0;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
 hf=stepm/YEARM;          if (bool==1){
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/            for(m=firstpass; m<=lastpass; m++){
     for(i=1; i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
       for(j=1; j<=nlstate;j++)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    if (m<lastpass) {
     /* hf=1;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
        if (stepm >= YEARM) hf=stepm/YEARM;*/                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 hf=stepm/YEARM;                }
                  
     fprintf(ficreseij,"%3.0f",age );                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for(i=1; i<=nlstate;i++)                  dateintsum=dateintsum+k2;
       for(j=1; j<=nlstate;j++){                  k2cpt++;
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);                }
       }              }
     fprintf(ficreseij,"\n");            }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   }        }
 }         
         fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 /************ 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)        if  (cptcovn>0) {
 {          fprintf(ficresp, "\n#********** Variable "); 
   /* Variance of health expectancies */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          fprintf(ficresp, "**********\n#");
   double **newm;        }
   double **dnewm,**doldm;        for(i=1; i<=nlstate;i++) 
   int i, j, nhstepm, hstepm, h;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int k, cptcode;        fprintf(ficresp, "\n");
   double *xp;        
   double **gp, **gm;        for(i=iagemin; i <= iagemax+3; i++){
   double ***gradg, ***trgradg;          if(i==iagemax+3){
   double ***p3mat;            fprintf(ficlog,"Total");
   double age,agelim;          }else{
   int theta;            if(first==1){
               first=0;
    fprintf(ficresvij,"# Covariances of life expectancies\n");              printf("See log file for details...\n");
   fprintf(ficresvij,"# Age");            }
   for(i=1; i<=nlstate;i++)            fprintf(ficlog,"Age %d", i);
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresvij,"\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   doldm=matrix(1,nlstate,1,nlstate);            for(m=-1, pos=0; m <=0 ; m++)
                pos += freq[jk][m][i];
   hstepm=1*YEARM; /* Every year of age */            if(pp[jk]>=1.e-10){
   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]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     if (stepm >= YEARM) hstepm=1;            }else{
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              if(first==1)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     gp=matrix(0,nhstepm,1,nlstate);            }
     gm=matrix(0,nhstepm,1,nlstate);          }
   
     for(theta=1; theta <=npar; theta++){          for(jk=1; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++){ /* Computes gradient */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              pp[jk] += freq[jk][m][i];
       }          }       
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            pos += pp[jk];
             posprop += prop[jk][i];
       if (popbased==1) {          }
         for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
           prlim[i][i]=probs[(int)age][i][ij];            if(pos>=1.e-5){
       }              if(first==1)
                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(j=1; j<= nlstate; j++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(h=0; h<=nhstepm; h++){            }else{
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              if(first==1)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
                if( i <= iagemax){
       for(i=1; i<=npar; i++) /* Computes gradient */              if(pos>=1.e-5){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  probs[i][jk][j1]= pp[jk]/pos;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
       if (popbased==1) {              else
         for(i=1; i<=nlstate;i++)                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          }
           
       for(j=1; j<= nlstate; j++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
         for(h=0; h<=nhstepm; h++){            for(m=-1; m <=nlstate+ndeath; m++)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              if(freq[jk][m][i] !=0 ) {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              if(first==1)
         }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
       for(j=1; j<= nlstate; j++)          if(i <= iagemax)
         for(h=0; h<=nhstepm; h++){            fprintf(ficresp,"\n");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          if(first==1)
         }            printf("Others in log...\n");
     } /* End theta */          fprintf(ficlog,"\n");
         }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      }
     }
     for(h=0; h<=nhstepm; h++)    dateintmean=dateintsum/k2cpt; 
       for(j=1; j<=nlstate;j++)   
         for(theta=1; theta <=npar; theta++)    fclose(ficresp);
           trgradg[h][j][theta]=gradg[h][theta][j];    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       for(j=1;j<=nlstate;j++)    /* End of Freq */
         vareij[i][j][(int)age] =0.;  }
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){  /************ Prevalence ********************/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  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)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  {  
         for(i=1;i<=nlstate;i++)    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
           for(j=1;j<=nlstate;j++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
             vareij[i][j][(int)age] += doldm[i][j];       We still use firstpass and lastpass as another selection.
       }    */
     }   
     h=1;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     if (stepm >= YEARM) h=stepm/YEARM;    double ***freq; /* Frequencies */
     fprintf(ficresvij,"%.0f ",age );    double *pp, **prop;
     for(i=1; i<=nlstate;i++)    double pos,posprop; 
       for(j=1; j<=nlstate;j++){    double  y2; /* in fractional years */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    int iagemin, iagemax;
       }  
     fprintf(ficresvij,"\n");    iagemin= (int) agemin;
     free_matrix(gp,0,nhstepm,1,nlstate);    iagemax= (int) agemax;
     free_matrix(gm,0,nhstepm,1,nlstate);    /*pp=vector(1,nlstate);*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    j1=0;
   } /* End age */    
      j=cptcoveff;
   free_vector(xp,1,npar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   free_matrix(doldm,1,nlstate,1,npar);    
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
         
 /************ Variance of prevlim ******************/        for (i=1; i<=nlstate; i++)  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          for(m=iagemin; m <= iagemax+3; m++)
 {            prop[i][m]=0.0;
   /* Variance of prevalence limit */       
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (i=1; i<=imx; i++) { /* Each individual */
   double **newm;          bool=1;
   double **dnewm,**doldm;          if  (cptcovn>0) {
   int i, j, nhstepm, hstepm;            for (z1=1; z1<=cptcoveff; z1++) 
   int k, cptcode;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double *xp;                bool=0;
   double *gp, *gm;          } 
   double **gradg, **trgradg;          if (bool==1) { 
   double age,agelim;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   int theta;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresvpl,"# Age");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   for(i=1; i<=nlstate;i++)                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); 
       fprintf(ficresvpl," %1d-%1d",i,i);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficresvpl,"\n");                  /*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]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   xp=vector(1,npar);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   dnewm=matrix(1,nlstate,1,npar);                } 
   doldm=matrix(1,nlstate,1,nlstate);              }
              } /* end selection of waves */
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        }
   agelim = AGESUP;        for(i=iagemin; i <= iagemax+3; i++){  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     if (stepm >= YEARM) hstepm=1;            posprop += prop[jk][i]; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          } 
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);          for(jk=1; jk <=nlstate ; jk++){     
     gm=vector(1,nlstate);            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
     for(theta=1; theta <=npar; theta++){                probs[i][jk][j1]= prop[jk][i]/posprop;
       for(i=1; i<=npar; i++){ /* Computes gradient */              } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            } 
       }          }/* end jk */ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }/* end i */ 
       for(i=1;i<=nlstate;i++)      } /* end i1 */
         gp[i] = prlim[i][i];    } /* end k1 */
        
       for(i=1; i<=npar; i++) /* Computes gradient */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*free_vector(pp,1,nlstate);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       for(i=1;i<=nlstate;i++)  }  /* End of prevalence */
         gm[i] = prlim[i][i];  
   /************* Waves Concatenation ***************/
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  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)
     } /* End theta */  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     trgradg =matrix(1,nlstate,1,npar);       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     for(j=1; j<=nlstate;j++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(theta=1; theta <=npar; theta++)       and mw[mi+1][i]. dh depends on stepm.
         trgradg[j][theta]=gradg[theta][j];       */
   
     for(i=1;i<=nlstate;i++)    int i, mi, m;
       varpl[i][(int)age] =0.;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       double sum=0., jmean=0.;*/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    int first;
     for(i=1;i<=nlstate;i++)    int j, k=0,jk, ju, jl;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double sum=0.;
     first=0;
     fprintf(ficresvpl,"%.0f ",age );    jmin=1e+5;
     for(i=1; i<=nlstate;i++)    jmax=-1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    jmean=0.;
     fprintf(ficresvpl,"\n");    for(i=1; i<=imx; i++){
     free_vector(gp,1,nlstate);      mi=0;
     free_vector(gm,1,nlstate);      m=firstpass;
     free_matrix(gradg,1,npar,1,nlstate);      while(s[m][i] <= nlstate){
     free_matrix(trgradg,1,nlstate,1,npar);        if(s[m][i]>=1)
   } /* End age */          mw[++mi][i]=m;
         if(m >=lastpass)
   free_vector(xp,1,npar);          break;
   free_matrix(doldm,1,nlstate,1,npar);        else
   free_matrix(dnewm,1,nlstate,1,nlstate);          m++;
       }/* end while */
 }      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
 /************ Variance of one-step probabilities  ******************/        /* if(mi==0)  never been interviewed correctly before death */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)           /* Only death is a correct wave */
 {        mw[mi][i]=m;
   int i, j;      }
   int k=0, cptcode;  
   double **dnewm,**doldm;      wav[i]=mi;
   double *xp;      if(mi==0){
   double *gp, *gm;        if(first==0){
   double **gradg, **trgradg;          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
   double age,agelim, cov[NCOVMAX];          first=1;
   int theta;        }
   char fileresprob[FILENAMELENGTH];        if(first==1){
           fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   strcpy(fileresprob,"prob");        }
   strcat(fileresprob,fileres);      } /* end mi==0 */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    } /* End individuals */
     printf("Problem with resultfile: %s\n", fileresprob);  
   }    for(i=1; i<=imx; i++){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
           dh[mi][i]=1;
   xp=vector(1,npar);        else{
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            if (agedc[i] < 2*AGESUP) {
              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   cov[1]=1;            if(j==0) j=1;  /* Survives at least one month after exam */
   for (age=bage; age<=fage; age ++){            k=k+1;
     cov[2]=age;            if (j >= jmax) jmax=j;
     gradg=matrix(1,npar,1,9);            if (j <= jmin) jmin=j;
     trgradg=matrix(1,9,1,npar);            sum=sum+j;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                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]);
     for(theta=1; theta <=npar; theta++){            }
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          else{
                  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                k=k+1;
       k=0;            if (j >= jmax) jmax=j;
       for(i=1; i<= (nlstate+ndeath); i++){            else if (j <= jmin)jmin=j;
         for(j=1; j<=(nlstate+ndeath);j++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
            k=k+1;            /*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]);*/
           gp[k]=pmmij[i][j];            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]);
         }            sum=sum+j;
       }          }
           jk= j/stepm;
       for(i=1; i<=npar; i++)          jl= j -jk*stepm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ju= j -(jk+1)*stepm;
              if(mle <=1){ 
             if(jl==0){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              dh[mi][i]=jk;
       k=0;              bh[mi][i]=0;
       for(i=1; i<=(nlstate+ndeath); i++){            }else{ /* We want a negative bias in order to only have interpolation ie
         for(j=1; j<=(nlstate+ndeath);j++){                    * at the price of an extra matrix product in likelihood */
           k=k+1;              dh[mi][i]=jk+1;
           gm[k]=pmmij[i][j];              bh[mi][i]=ju;
         }            }
       }          }else{
                  if(jl <= -ju){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              dh[mi][i]=jk;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                bh[mi][i]=jl;       /* bias is positive if real duration
     }                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            }
       for(theta=1; theta <=npar; theta++)            else{
       trgradg[j][theta]=gradg[theta][j];              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
      pmij(pmmij,cov,ncovmodel,x,nlstate);              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);*/
      k=0;            }
      for(i=1; i<=(nlstate+ndeath); i++){          }
        for(j=1; j<=(nlstate+ndeath);j++){        } /* end if mle */
          k=k+1;      } /* end wave */
          gm[k]=pmmij[i][j];    }
         }    jmean=sum/k;
      }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
          fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      /*printf("\n%d ",(int)age);   }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
          /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  {
      }*/    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficresprob,"\n%d ",(int)age);    int cptcode=0;
     cptcoveff=0; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){   
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    for (k=1; k<=7; k++) ncodemax[k]=0;
   }  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                                 modality*/ 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        Ndum[ij]++; /*store the modality */
 }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  free_vector(xp,1,npar);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 fclose(ficresprob);                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
 }      }
   
 /******************* Printing html file ***********/      for (i=0; i<=cptcode; 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[] ){        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 */
   int jj1, k1, i1, cpt;      }
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
   strcpy(optionfilehtm,optionfile);        for (k=0; k<= maxncov; k++) {
   strcat(optionfilehtm,".htm");          if (Ndum[k] != 0) {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            nbcode[Tvar[j]][ij]=k; 
     printf("Problem with %s \n",optionfilehtm), exit(0);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   }            
             ij++;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">          }
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          if (ij > ncodemax[j]) break; 
         }  
 Total number of observations=%d <br>      } 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    }  
 <hr  size=\"2\" color=\"#EC5E5E\">  
 <li>Outputs files<br><br>\n   for (k=0; k< maxncov; k++) Ndum[k]=0;
         - 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>   for (i=1; i<=ncovmodel-2; i++) { 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>     ij=Tvar[i];
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>     Ndum[ij]++;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>   }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>   ij=1;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>   for (i=1; i<= maxncov; i++) {
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>     if((Ndum[i]!=0) && (i<=ncovcol)){
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>       Tvaraff[ij]=i; /*For printing */
         <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);       ij++;
       }
 fprintf(fichtm," <li>Graphs</li><p>");   }
    
  m=cptcoveff;   cptcoveff=ij-1; /*Number of simple covariates*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  }
   
  jj1=0;  /*********** Health Expectancies ****************/
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  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 )
        jj1++;  
        if (cptcovn > 0) {  {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    /* Health expectancies */
          for (cpt=1; cpt<=cptcoveff;cpt++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double age, agelim, hf;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double ***p3mat,***varhe;
        }    double **dnewm,**doldm;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double *xp;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double **gp, **gm;
        for(cpt=1; cpt<nlstate;cpt++){    double ***gradg, ***trgradg;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    int theta;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     for(cpt=1; cpt<=nlstate;cpt++) {    xp=vector(1,npar);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    dnewm=matrix(1,nlstate*nlstate,1,npar);
 interval) in state (%d): v%s%d%d.gif <br>    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      
      }    fprintf(ficreseij,"# Health expectancies\n");
      for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficreseij,"# Age");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    for(i=1; i<=nlstate;i++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for(j=1; j<=nlstate;j++)
      }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    fprintf(ficreseij,"\n");
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    if(estepm < stepm){
 fprintf(fichtm,"\n</body>");      printf ("Problem %d lower than %d\n",estepm, stepm);
    }    }
    }    else  hstepm=estepm;   
 fclose(fichtm);    /* We compute the life expectancy from trapezoids spaced every estepm months
 }     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
 /******************* Gnuplot file **************/     * we are calculating an estimate of the Life Expectancy assuming a linear 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;     * 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 
   strcpy(optionfilegnuplot,optionfilefiname);     * hypothesis. A more precise result, taking into account a more precise
   strcat(optionfilegnuplot,".plt");     * curvature will be obtained if estepm is as small as stepm. */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
 #ifdef windows       nstepm is the number of stepm from age to agelin. 
     fprintf(ficgp,"cd \"%s\" \n",pathc);       Look at hpijx to understand the reason of that which relies in memory size
 #endif       and note for a fixed period like estepm months */
 m=pow(2,cptcoveff);    /* 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
  /* 1eme*/       means that if the survival funtion is printed only each two years of age and if
   for (cpt=1; cpt<= nlstate ; cpt ++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    for (k1=1; k1<= m ; k1 ++) {       results. So we changed our mind and took the option of the best precision.
     */
 #ifdef windows    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     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);  
 #endif    agelim=AGESUP;
 #ifdef unix    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      /* nhstepm age range expressed in number of stepm */
 #endif      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 for (i=1; i<= nlstate ; i ++) {      /* if (stepm >= YEARM) hstepm=1;*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      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\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
      for (i=1; i<= nlstate ; i ++) {   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      /* Computing Variances of health expectancies */
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");       for(theta=1; theta <=npar; theta++){
 #endif        for(i=1; i<=npar; i++){ 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    }        }
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /*2 eme*/    
         cptj=0;
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          for(i=1; i<=nlstate; i++){
                cptj=cptj+1;
     for (i=1; i<= nlstate+1 ; i ++) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       k=2*i;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            }
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");       
 }         
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(i=1; i<=npar; i++) 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (j=1; j<= nlstate+1 ; j ++) {        
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        cptj=0;
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate; j++){
 }            for(i=1;i<=nlstate;i++){
       fprintf(ficgp,"\" t\"\" w l 0,");            cptj=cptj+1;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        }
       else fprintf(ficgp,"\" t\"\" w l 0,");        for(j=1; j<= nlstate*nlstate; j++)
     }          for(h=0; h<=nhstepm-1; h++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
         } 
   /*3eme*/     
   /* End theta */
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       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(h=0; h<=nhstepm-1; h++)
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<=nlstate*nlstate;j++)
         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(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       
     }  
     }       for(i=1;i<=nlstate*nlstate;i++)
          for(j=1;j<=nlstate*nlstate;j++)
   /* CV preval stat */          varhe[i][j][(int)age] =0.;
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {       printf("%d|",(int)age);fflush(stdout);
       k=3;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
       for (i=1; i< nlstate ; i ++)          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         fprintf(ficgp,"+$%d",k+i+1);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          for(i=1;i<=nlstate*nlstate;i++)
                  for(j=1;j<=nlstate*nlstate;j++)
       l=3+(nlstate+ndeath)*cpt;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {      }
         l=3+(nlstate+ndeath)*cpt;      /* Computing expectancies */
         fprintf(ficgp,"+$%d",l+i+1);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     }            
   }    /* 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]);*/
    
   /* proba elementaires */          }
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficreseij,"%3.0f",age );
       if (k != i) {      cptj=0;
         for(j=1; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          cptj++;
           jk++;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           fprintf(ficgp,"\n");        }
         }      fprintf(ficreseij,"\n");
       }     
     }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     for(jk=1; jk <=m; jk++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    i=1;    }
    for(k2=1; k2<=nlstate; k2++) {    printf("\n");
      k3=i;    fprintf(ficlog,"\n");
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    free_vector(xp,1,npar);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 ij=1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         for(j=3; j <=ncovmodel; j++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  /************ Variance ******************/
           }  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)
           else  {
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Variance of health expectancies */
         }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           fprintf(ficgp,")/(1");    /* double **newm;*/
            double **dnewm,**doldm;
         for(k1=1; k1 <=nlstate; k1++){      double **dnewmp,**doldmp;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int i, j, nhstepm, hstepm, h, nstepm ;
 ij=1;    int k, cptcode;
           for(j=3; j <=ncovmodel; j++){    double *xp;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **gp, **gm;  /* for var eij */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double ***gradg, ***trgradg; /*for var eij */
             ij++;    double **gradgp, **trgradgp; /* for var p point j */
           }    double *gpp, *gmp; /* for var p point j */
           else    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double ***p3mat;
           }    double age,agelim, hf;
           fprintf(ficgp,")");    double ***mobaverage;
         }    int theta;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    char digit[4];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    char digitp[25];
         i=i+ncovmodel;  
        }    char fileresprobmorprev[FILENAMELENGTH];
      }  
    }    if(popbased==1){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      if(mobilav!=0)
    }        strcpy(digitp,"-populbased-mobilav-");
          else strcpy(digitp,"-populbased-nomobil-");
   fclose(ficgp);    }
 }  /* end gnuplot */    else 
       strcpy(digitp,"-stablbased-");
   
 /*************** Moving average **************/    if (mobilav!=0) {
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   int i, cpt, cptcod;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     for (agedeb=agemin; agedeb<=fage; agedeb++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       for (i=1; i<=nlstate;i++)      }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
        strcpy(fileresprobmorprev,"prmorprev"); 
     for (agedeb=agemin+4; 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[cptcoveff];cptcod++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           for (cpt=0;cpt<=4;cpt++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    strcat(fileresprobmorprev,fileres);
           }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       }    }
     }    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);
 }    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++){
 /************** Forecasting ******************/      fprintf(ficresprobmorprev," p.%-d SE",j);
 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){      for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }  
   int *popage;    fprintf(ficresprobmorprev,"\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double *popeffectif,*popcount;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double ***p3mat;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   char fileresf[FILENAMELENGTH];      exit(0);
     }
  agelim=AGESUP;    else{
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      fprintf(ficgp,"\n# Routine varevsij");
     }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   strcpy(fileresf,"f");      exit(0);
   strcat(fileresf,fileres);    }
   if((ficresf=fopen(fileresf,"w"))==NULL) {    else{
     printf("Problem with forecast resultfile: %s\n", fileresf);      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);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    }
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   if (mobilav==1) {    fprintf(ficresvij,"# Age");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(i=1; i<=nlstate;i++)
     movingaverage(agedeb, fage, agemin, mobaverage);      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
   agelim=AGESUP;    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   hstepm=1;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   anprojmean=yp;    gpp=vector(nlstate+1,nlstate+ndeath);
   yp2=modf((yp1*12),&yp);    gmp=vector(nlstate+1,nlstate+ndeath);
   mprojmean=yp;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   yp1=modf((yp2*30.5),&yp);    
   jprojmean=yp;    if(estepm < stepm){
   if(jprojmean==0) jprojmean=1;      printf ("Problem %d lower than %d\n",estepm, stepm);
   if(mprojmean==0) jprojmean=1;    }
      else  hstepm=estepm;   
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   for(cptcov=1;cptcov<=i2;cptcov++){       nhstepm is the number of hstepm from age to agelim 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       nstepm is the number of stepm from age to agelin. 
       k=k+1;       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficresf,"\n#******");       and note for a fixed period like k years */
       for(j=1;j<=cptcoveff;j++) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       survival function given by stepm (the optimization length). Unfortunately it
       }       means that if the survival funtion is printed every two years of age and if
       fprintf(ficresf,"******\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficresf,"# StartingAge FinalAge");       results. So we changed our mind and took the option of the best precision.
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    */
          hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          agelim = AGESUP;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         fprintf(ficresf,"\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      gp=matrix(0,nhstepm,1,nlstate);
           nhstepm = nhstepm/hstepm;      gm=matrix(0,nhstepm,1,nlstate);
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      for(theta=1; theta <=npar; theta++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }  
             for(j=1; j<=nlstate+ndeath;j++) {        if (popbased==1) {
               kk1=0.;kk2=0;          if(mobilav ==0){
               for(i=1; i<=nlstate;i++) {                          for(i=1; i<=nlstate;i++)
                 if (mobilav==1)              prlim[i][i]=probs[(int)age][i][ij];
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          }else{ /* mobilav */ 
                 else {            for(i=1; i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              prlim[i][i]=mobaverage[(int)age][i][ij];
                 }          }
                        }
               }    
               if (h==(int)(calagedate+12*cpt)){        for(j=1; j<= nlstate; j++){
                 fprintf(ficresf," %.3f", kk1);          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];
             }          }
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* 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++){
                  for(i=1,gpp[j]=0.; i<= nlstate; i++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   fclose(ficresf);        /* end probability of death */
 }  
 /************** Forecasting ******************/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 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){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   int *popage;   
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        if (popbased==1) {
   double *popeffectif,*popcount;          if(mobilav ==0){
   double ***p3mat,***tabpop,***tabpopprev;            for(i=1; i<=nlstate;i++)
   char filerespop[FILENAMELENGTH];              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1; i<=nlstate;i++)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              prlim[i][i]=mobaverage[(int)age][i][ij];
   agelim=AGESUP;          }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        }
    
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   strcpy(filerespop,"pop");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcat(filerespop,fileres);          }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", filerespop);        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
   printf("Computing forecasting: result on file '%s' \n", filerespop);           as a weighted average of prlim.
         */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
   if (mobilav==1) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }    
     movingaverage(agedeb, fage, agemin, mobaverage);        /* end probability of death */
   }  
         for(j=1; j<= nlstate; j++) /* vareij */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(h=0; h<=nhstepm; h++){
   if (stepm<=12) stepsize=1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   agelim=AGESUP;  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   hstepm=1;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   hstepm=hstepm/stepm;        }
    
   if (popforecast==1) {      } /* End theta */
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     }  
     popage=ivector(0,AGESUP);      for(h=0; h<=nhstepm; h++) /* veij */
     popeffectif=vector(0,AGESUP);        for(j=1; j<=nlstate;j++)
     popcount=vector(0,AGESUP);          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
            for(theta=1; theta <=npar; theta++)
     imx=i;          trgradgp[j][theta]=gradgp[theta][j];
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    
   }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   for(cptcov=1;cptcov<=i2;cptcov++){      for(i=1;i<=nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(j=1;j<=nlstate;j++)
       k=k+1;          vareij[i][j][(int)age] =0.;
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      for(h=0;h<=nhstepm;h++){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(k=0;k<=nhstepm;k++){
       }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficrespop,"******\n");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficrespop,"# Age");          for(i=1;i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            for(j=1;j<=nlstate;j++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
              }
       for (cpt=0; cpt<=0;cpt++) {      }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      
              /* pptj */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           nhstepm = nhstepm/hstepm;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                  for(i=nlstate+1;i<=nlstate+ndeath;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          varppt[j][i]=doldmp[j][i];
           oldm=oldms;savm=savms;      /* end ppptj */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /*  x centered again */
              hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           for (h=0; h<=nhstepm; h++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             if (h==(int) (calagedate+YEARM*cpt)) {   
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      if (popbased==1) {
             }        if(mobilav ==0){
             for(j=1; j<=nlstate+ndeath;j++) {          for(i=1; i<=nlstate;i++)
               kk1=0.;kk2=0;            prlim[i][i]=probs[(int)age][i][ij];
               for(i=1; i<=nlstate;i++) {                      }else{ /* mobilav */ 
                 if (mobilav==1)          for(i=1; i<=nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            prlim[i][i]=mobaverage[(int)age][i][ij];
                 else {        }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      }
                 }               
               }      /* This for computing probability of death (h=1 means
               if (h==(int)(calagedate+12*cpt)){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;         as a weighted average of prlim.
                   /*fprintf(ficrespop," %.3f", kk1);      */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for(j=nlstate+1;j<=nlstate+ndeath;j++){
               }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
             }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
             for(i=1; i<=nlstate;i++){      }    
               kk1=0.;      /* end probability of death */
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                 }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
             }        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      } 
           }      fprintf(ficresprobmorprev,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      fprintf(ficresvij,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   /******/          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      fprintf(ficresvij,"\n");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        free_matrix(gp,0,nhstepm,1,nlstate);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      free_matrix(gm,0,nhstepm,1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           nhstepm = nhstepm/hstepm;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* End age */
           oldm=oldms;savm=savms;    free_vector(gpp,nlstate+1,nlstate+ndeath);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_vector(gmp,nlstate+1,nlstate+ndeath);
           for (h=0; h<=nhstepm; h++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             if (h==(int) (calagedate+YEARM*cpt)) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
             }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
               kk1=0.;kk2=0;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
               for(i=1; i<=nlstate;i++) {                /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*   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);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
             }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
           }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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);
       }  */
    }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   }  
      free_vector(xp,1,npar);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
   if (popforecast==1) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_ivector(popage,0,AGESUP);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_vector(popeffectif,0,AGESUP);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_vector(popcount,0,AGESUP);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    fclose(ficresprobmorprev);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fclose(ficgp);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fclose(fichtm);
   fclose(ficrespop);  }  
 }  
   /************ Variance of prevlim ******************/
 /***********************************************/  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)
 /**************** Main Program *****************/  {
 /***********************************************/    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 int main(int argc, char *argv[])    double **newm;
 {    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int k, cptcode;
   double agedeb, agefin,hf;    double *xp;
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double *gp, *gm;
     double **gradg, **trgradg;
   double fret;    double age,agelim;
   double **xi,tmp,delta;    int theta;
      
   double dum; /* Dummy variable */    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   double ***p3mat;    fprintf(ficresvpl,"# Age");
   int *indx;    for(i=1; i<=nlstate;i++)
   char line[MAXLINE], linepar[MAXLINE];        fprintf(ficresvpl," %1d-%1d",i,i);
   char title[MAXLINE];    fprintf(ficresvpl,"\n");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    doldm=matrix(1,nlstate,1,nlstate);
     
   char filerest[FILENAMELENGTH];    hstepm=1*YEARM; /* Every year of age */
   char fileregp[FILENAMELENGTH];    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   char popfile[FILENAMELENGTH];    agelim = AGESUP;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   int firstobs=1, lastobs=10;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   int sdeb, sfin; /* Status at beginning and end */      if (stepm >= YEARM) hstepm=1;
   int c,  h , cpt,l;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   int ju,jl, mi;      gradg=matrix(1,npar,1,nlstate);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      gp=vector(1,nlstate);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      gm=vector(1,nlstate);
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;      for(theta=1; theta <=npar; theta++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;        for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double **prlim;        for(i=1;i<=nlstate;i++)
   double *severity;          gp[i] = prlim[i][i];
   double ***param; /* Matrix of parameters */      
   double  *p;        for(i=1; i<=npar; i++) /* Computes gradient */
   double **matcov; /* Matrix of covariance */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double ***delti3; /* Scale */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double *delti; /* Scale */        for(i=1;i<=nlstate;i++)
   double ***eij, ***vareij;          gm[i] = prlim[i][i];
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;        for(i=1;i<=nlstate;i++)
   double kk1, kk2;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      } /* End theta */
    
       trgradg =matrix(1,nlstate,1,npar);
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   char z[1]="c", occ;  
 #include <sys/time.h>      for(i=1;i<=nlstate;i++)
 #include <time.h>        varpl[i][(int)age] =0.;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /* long total_usecs;      for(i=1;i<=nlstate;i++)
   struct timeval start_time, end_time;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   printf("\n%s",version);      fprintf(ficresvpl,"\n");
   if(argc <=1){      free_vector(gp,1,nlstate);
     printf("\nEnter the parameter file name: ");      free_vector(gm,1,nlstate);
     scanf("%s",pathtot);      free_matrix(gradg,1,npar,1,nlstate);
   }      free_matrix(trgradg,1,nlstate,1,npar);
   else{    } /* End age */
     strcpy(pathtot,argv[1]);  
   }    free_vector(xp,1,npar);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    free_matrix(doldm,1,nlstate,1,npar);
   /*cygwin_split_path(pathtot,path,optionfile);    free_matrix(dnewm,1,nlstate,1,nlstate);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/  }
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  /************ Variance of one-step probabilities  ******************/
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   chdir(path);  {
   replace(pathc,path);    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
 /*-------- arguments in the command line --------*/    int k=0,l, cptcode;
     int first=1, first1;
   strcpy(fileres,"r");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   strcat(fileres, optionfilefiname);    double **dnewm,**doldm;
   strcat(fileres,".txt");    /* Other files have txt extension */    double *xp;
     double *gp, *gm;
   /*---------arguments file --------*/    double **gradg, **trgradg;
     double **mu;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double age,agelim, cov[NCOVMAX];
     printf("Problem with optionfile %s\n",optionfile);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     goto end;    int theta;
   }    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   strcpy(filereso,"o");    char fileresprobcor[FILENAMELENGTH];
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    double ***varpij;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   /* Reads comments: lines beginning with '#' */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", fileresprob);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    strcpy(fileresprobcov,"probcov"); 
     fputs(line,ficparo);    strcat(fileresprobcov,fileres);
   }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   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);    }
   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);    strcpy(fileresprobcor,"probcor"); 
   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);    strcat(fileresprobcor,fileres);
 while((c=getc(ficpar))=='#' && c!= EOF){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprobcor);
     fgets(line, MAXLINE, ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     puts(line);    }
     fputs(line,ficparo);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    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);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   cptcovn=0;    
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
   ncovmodel=2+cptcovn;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficresprobcov,"# Age");
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   /* Read guess parameters */    fprintf(ficresprobcov,"# Age");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     fputs(line,ficparo);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   ungetc(c,ficpar);      }  
     /* fprintf(ficresprob,"\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresprobcov,"\n");
     for(i=1; i <=nlstate; i++)    fprintf(ficresprobcor,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){   */
       fscanf(ficpar,"%1d%1d",&i1,&j1);   xp=vector(1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       printf("%1d%1d",i,j);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       for(k=1; k<=ncovmodel;k++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         fscanf(ficpar," %lf",&param[i][j][k]);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         printf(" %lf",param[i][j][k]);    first=1;
         fprintf(ficparo," %lf",param[i][j][k]);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fscanf(ficpar,"\n");      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       printf("\n");      exit(0);
       fprintf(ficparo,"\n");    }
     }    else{
        fprintf(ficgp,"\n# Routine varprob");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   p=param[1][1];      printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   /* Reads comments: lines beginning with '#' */      exit(0);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    else{
     fgets(line, MAXLINE, ficpar);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     puts(line);      fprintf(fichtm,"\n");
     fputs(line,ficparo);  
   }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   ungetc(c,ficpar);      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   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++){    cov[1]=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    tj=cptcoveff;
       printf("%1d%1d",i,j);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       fprintf(ficparo,"%1d%1d",i1,j1);    j1=0;
       for(k=1; k<=ncovmodel;k++){    for(t=1; t<=tj;t++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for(i1=1; i1<=ncodemax[t];i1++){ 
         printf(" %le",delti3[i][j][k]);        j1++;
         fprintf(ficparo," %le",delti3[i][j][k]);        if  (cptcovn>0) {
       }          fprintf(ficresprob, "\n#********** Variable "); 
       fscanf(ficpar,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("\n");          fprintf(ficresprob, "**********\n#\n");
       fprintf(ficparo,"\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcov, "**********\n#\n");
   delti=delti3[1][1];          
            fprintf(ficgp, "\n#********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp, "**********\n#\n");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          
     puts(line);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     fputs(line,ficparo);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   ungetc(c,ficpar);          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   matcov=matrix(1,npar,1,npar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(i=1; i <=npar; i++){          fprintf(ficresprobcor, "**********\n#");    
     fscanf(ficpar,"%s",&str);        }
     printf("%s",str);        
     fprintf(ficparo,"%s",str);        for (age=bage; age<=fage; age ++){ 
     for(j=1; j <=i; j++){          cov[2]=age;
       fscanf(ficpar," %le",&matcov[i][j]);          for (k=1; k<=cptcovn;k++) {
       printf(" %.5le",matcov[i][j]);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       fprintf(ficparo," %.5le",matcov[i][j]);          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     fscanf(ficpar,"\n");          for (k=1; k<=cptcovprod;k++)
     printf("\n");            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     fprintf(ficparo,"\n");          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   for(i=1; i <=npar; i++)          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     for(j=i+1;j<=npar;j++)          gp=vector(1,(nlstate)*(nlstate+ndeath));
       matcov[i][j]=matcov[j][i];          gm=vector(1,(nlstate)*(nlstate+ndeath));
          
   printf("\n");          for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     /*-------- Rewriting paramater file ----------*/            
      strcpy(rfileres,"r");    /* "Rparameterfile */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            
      strcat(rfileres,".");    /* */            k=0;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            for(i=1; i<= (nlstate); i++){
     if((ficres =fopen(rfileres,"w"))==NULL) {              for(j=1; j<=(nlstate+ndeath);j++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                k=k+1;
     }                gp[k]=pmmij[i][j];
     fprintf(ficres,"#%s\n",version);              }
                }
     /*-------- data file ----------*/            
     if((fic=fopen(datafile,"r"))==NULL)    {            for(i=1; i<=npar; i++)
       printf("Problem with datafile: %s\n", datafile);goto end;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     }      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
     n= lastobs;            k=0;
     severity = vector(1,maxwav);            for(i=1; i<=(nlstate); i++){
     outcome=imatrix(1,maxwav+1,1,n);              for(j=1; j<=(nlstate+ndeath);j++){
     num=ivector(1,n);                k=k+1;
     moisnais=vector(1,n);                gm[k]=pmmij[i][j];
     annais=vector(1,n);              }
     moisdc=vector(1,n);            }
     andc=vector(1,n);       
     agedc=vector(1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     cod=ivector(1,n);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     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);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     anint=matrix(1,maxwav,1,n);            for(theta=1; theta <=npar; theta++)
     s=imatrix(1,maxwav+1,1,n);              trgradg[j][theta]=gradg[theta][j];
     adl=imatrix(1,maxwav+1,1,n);              
     tab=ivector(1,NCOVMAX);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     ncodemax=ivector(1,8);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     i=1;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     while (fgets(line, MAXLINE, fic) != NULL)    {          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       if ((i >= firstobs) && (i <=lastobs)) {          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          
         for (j=maxwav;j>=1;j--){          pmij(pmmij,cov,ncovmodel,x,nlstate);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          
           strcpy(line,stra);          k=0;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1; i<=(nlstate); i++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(j=1; j<=(nlstate+ndeath);j++){
         }              k=k+1;
                      mu[k][(int) age]=pmmij[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);          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              varpij[i][j][(int)age] = doldm[i][j];
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          /*printf("\n%d ",(int)age);
         for (j=ncov;j>=1;j--){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           cutv(stra, strb,line,' '); covar[j][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]));
         }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         num[i]=atol(stra);            }*/
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          fprintf(ficresprob,"\n%d ",(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;}*/          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
         i=i+1;  
       }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     /* printf("ii=%d", ij);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        scanf("%d",i);*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   imx=i-1; /* Number of individuals */            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   /* for (i=1; i<=imx; i++){          i=0;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          for (k=1; k<=(nlstate);k++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            for (l=1; l<=(nlstate+ndeath);l++){ 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              i=i++;
     }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     for (i=1; i<=imx; i++)              for (j=1; j<=i;j++){
     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]));*/                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   /* Calculation of the number of parameter from char model*/              }
   Tvar=ivector(1,15);            }
   Tprod=ivector(1,15);          }/* end of loop for state */
   Tvaraff=ivector(1,15);        } /* end of loop for age */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);              /* Confidence intervalle of pij  */
            /*
   if (strlen(model) >1){          fprintf(ficgp,"\nset noparametric;unset label");
     j=0, j1=0, k1=1, k2=1;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     j=nbocc(model,'+');          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     j1=nbocc(model,'*');          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);
     cptcovn=j+1;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     cptcovprod=j1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
              fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
            */
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       printf("Error. Non available option model=%s ",model);        first1=1;
       goto end;        for (k2=1; k2<=(nlstate);k2++){
     }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                if(l2==k2) continue;
     for(i=(j+1); i>=1;i--){            j=(k2-1)*(nlstate+ndeath)+l2;
       cutv(stra,strb,modelsav,'+');            for (k1=1; k1<=(nlstate);k1++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                if(l1==k1) continue;
       /*scanf("%d",i);*/                i=(k1-1)*(nlstate+ndeath)+l1;
       if (strchr(strb,'*')) {                if(i<=j) continue;
         cutv(strd,strc,strb,'*');                for (age=bage; age<=fage; age ++){ 
         if (strcmp(strc,"age")==0) {                  if ((int)age %5==0){
           cptcovprod--;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(strb,stre,strd,'V');                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           Tvar[i]=atoi(stre);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cptcovage++;                    mu1=mu[i][(int) age]/stepm*YEARM ;
             Tage[cptcovage]=i;                    mu2=mu[j][(int) age]/stepm*YEARM;
             /*printf("stre=%s ", stre);*/                    c12=cv12/sqrt(v1*v2);
         }                    /* Computing eigen value of matrix of covariance */
         else if (strcmp(strd,"age")==0) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           cptcovprod--;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           cutv(strb,stre,strc,'V');                    /* Eigen vectors */
           Tvar[i]=atoi(stre);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           cptcovage++;                    /*v21=sqrt(1.-v11*v11); *//* error */
           Tage[cptcovage]=i;                    v21=(lc1-v1)/cv12*v11;
         }                    v12=-v21;
         else {                    v22=v11;
           cutv(strb,stre,strc,'V');                    tnalp=v21/v11;
           Tvar[i]=ncov+k1;                    if(first1==1){
           cutv(strb,strc,strd,'V');                      first1=0;
           Tprod[k1]=i;                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           Tvard[k1][1]=atoi(strc);                    }
           Tvard[k1][2]=atoi(stre);                    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[cptcovn+k2]=Tvard[k1][1];                    /*printf(fignu*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           for (k=1; k<=lastobs;k++)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    if(first==1){
           k1++;                      first=0;
           k2=k2+2;                      fprintf(ficgp,"\nset parametric;unset label");
         }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
       }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       else {                      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);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
        /*  scanf("%d",i);*/                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       cutv(strd,strc,strb,'V');                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       Tvar[i]=atoi(strc);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       strcpy(modelsav,stra);                        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",\
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         scanf("%d",i);*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     }                    }else{
 }                      first=0;
                        fprintf(fichtm," %d (%.3f),",(int) age, c12);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   printf("cptcovprod=%d ", cptcovprod);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   scanf("%d ",i);*/                      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",\
     fclose(fic);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     /*  if(mle==1){*/                    }/* if first */
     if (weightopt != 1) { /* Maximisation without weights*/                  } /* age mod 5 */
       for(i=1;i<=n;i++) weight[i]=1.0;                } /* end loop age */
     }                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
     /*-calculation of age at interview from date of interview and age at death -*/                first=1;
     agev=matrix(1,maxwav,1,imx);              } /*l12 */
             } /* k12 */
    for (i=1; i<=imx; i++)          } /*l1 */
      for(m=2; (m<= maxwav); m++)        }/* k1 */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      } /* loop covariates */
          anint[m][i]=9999;    }
          s[m][i]=-1;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
        }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        free_vector(xp,1,npar);
     for (i=1; i<=imx; i++)  {    fclose(ficresprob);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fclose(ficresprobcov);
       for(m=1; (m<= maxwav); m++){    fclose(ficresprobcor);
         if(s[m][i] >0){    fclose(ficgp);
           if (s[m][i] == nlstate+1) {    fclose(fichtm);
             if(agedc[i]>0)  }
               if(moisdc[i]!=99 && andc[i]!=9999)  
               agev[m][i]=agedc[i];  
             else {  /******************* Printing html file ***********/
               if (andc[i]!=9999){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                    int lastpass, int stepm, int weightopt, char model[],\
               agev[m][i]=-1;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
               }                    int popforecast, int estepm ,\
             }                    double jprev1, double mprev1,double anprev1, \
           }                    double jprev2, double mprev2,double anprev2){
           else if(s[m][i] !=9){ /* Should no more exist */    int jj1, k1, i1, cpt;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /*char optionfilehtm[FILENAMELENGTH];*/
             if(mint[m][i]==99 || anint[m][i]==9999)    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
               agev[m][i]=1;      printf("Problem with %s \n",optionfilehtm), exit(0);
             else if(agev[m][i] <agemin){      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
               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);*/  
             }     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
             else if(agev[m][i] >agemax){   - 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
               agemax=agev[m][i];   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
             }   - Life expectancies by age and initial health status (estepm=%2d months): 
             /*agev[m][i]=anint[m][i]-annais[i];*/     <a href=\"e%s\">e%s</a> <br>\n</li>", \
             /*   agev[m][i] = age[i]+2*m;*/    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
           }  
           else { /* =9 */  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
             agev[m][i]=1;  
             s[m][i]=-1;   m=cptcoveff;
           }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         }  
         else /*= 0 Unknown */   jj1=0;
           agev[m][i]=1;   for(k1=1; k1<=m;k1++){
       }     for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
     }       if (cptcovn > 0) {
     for (i=1; i<=imx; i++)  {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       for(m=1; (m<= maxwav); m++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
         if (s[m][i] > (nlstate+ndeath)) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           printf("Error: Wrong value in nlstate or ndeath\n");           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           goto end;       }
         }       /* Pij */
       }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
     }  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       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); 
     free_vector(severity,1,maxwav);         /* Stable prevalence in each health state */
     free_imatrix(outcome,1,maxwav+1,1,n);         for(cpt=1; cpt<nlstate;cpt++){
     free_vector(moisnais,1,n);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
     free_vector(annais,1,n);  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     /* free_matrix(mint,1,maxwav,1,n);         }
        free_matrix(anint,1,maxwav,1,n);*/       for(cpt=1; cpt<=nlstate;cpt++) {
     free_vector(moisdc,1,n);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     free_vector(andc,1,n);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
           fprintf(fichtm,"\n<br>- Total life expectancy by age and
     wav=ivector(1,imx);  health expectancies in states (1) and (2): e%s%d.png<br>
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);     } /* end i1 */
       }/* End k1 */
     /* Concatenates waves */   fprintf(fichtm,"</ul>");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
       Tcode=ivector(1,100);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
       ncodemax[1]=1;   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   - 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 
    codtab=imatrix(1,100,1,10);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    h=0;   - 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);
    m=pow(2,cptcoveff);  
    /*  if(popforecast==1) fprintf(fichtm,"\n */
    for(k=1;k<=cptcoveff; k++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      for(i=1; i <=(m/pow(2,k));i++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
        for(j=1; j <= ncodemax[k]; j++){  /*      <br>",fileres,fileres,fileres,fileres); */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /*  else  */
            h++;  /*    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); */
            if (h>m) h=1;codtab[h][k]=j;  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
          }  
        }   m=cptcoveff;
      }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    }  
    jj1=0;
    for(k1=1; k1<=m;k1++){
    /*for(i=1; i <=m ;i++){     for(i1=1; i1<=ncodemax[k1];i1++){
      for(k=1; k <=cptcovn; k++){       jj1++;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);       if (cptcovn > 0) {
      }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
      printf("\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
    }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
    scanf("%d",i);*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           }
    /* Calculates basic frequencies. Computes observed prevalence at single age       for(cpt=1; cpt<=nlstate;cpt++) {
        and prints on file fileres'p'. */         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
      <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     } /* end i1 */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   }/* End k1 */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   fprintf(fichtm,"</ul>");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  fclose(fichtm);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  }
        
     /* For Powell, parameters are in a vector p[] starting at p[1]  /******************* Gnuplot file **************/
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     if(mle==1){    int ng;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     }      printf("Problem with file %s",optionfilegnuplot);
          fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     /*--------- results files --------------*/    }
     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);  
      /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
    jk=1;      /*#endif */
    fprintf(ficres,"# Parameters\n");  m=pow(2,cptcoveff);
    printf("# Parameters\n");    
    for(i=1,jk=1; i <=nlstate; i++){   /* 1eme*/
      for(k=1; k <=(nlstate+ndeath); k++){    for (cpt=1; cpt<= nlstate ; cpt ++) {
        if (k != i)     for (k1=1; k1<= m ; k1 ++) {
          {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
            printf("%d%d ",i,k);       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
            fprintf(ficres,"%1d%1d ",i,k);  
            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\"Stable prevalence\" w l 0,\"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\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
  if(mle==1){       for (i=1; i<= nlstate ; i ++) {
     /* Computing hessian and covariance matrix */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     ftolhess=ftol; /* Usually correct */         else fprintf(ficgp," \%%*lf (\%%*lf)");
     hesscov(matcov, p, npar, delti, ftolhess, func);       }  
  }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     fprintf(ficres,"# Scales\n");     }
     printf("# Scales\n");    }
      for(i=1,jk=1; i <=nlstate; i++){    /*2 eme*/
       for(j=1; j <=nlstate+ndeath; j++){    
         if (j!=i) {    for (k1=1; k1<= m ; k1 ++) { 
           fprintf(ficres,"%1d%1d",i,j);      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
           printf("%1d%1d",i,j);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           for(k=1; k<=ncovmodel;k++){      
             printf(" %.5e",delti[jk]);      for (i=1; i<= nlstate+1 ; i ++) {
             fprintf(ficres," %.5e",delti[jk]);        k=2*i;
             jk++;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
           }        for (j=1; j<= nlstate+1 ; j ++) {
           printf("\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           fprintf(ficres,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }        }   
       }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
      }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
            fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
     k=1;        for (j=1; j<= nlstate+1 ; j ++) {
     fprintf(ficres,"# Covariance\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     printf("# Covariance\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(i=1;i<=npar;i++){        }   
       /*  if (k>nlstate) k=1;        fprintf(ficgp,"\" t\"\" w l 0,");
       i1=(i-1)/(ncovmodel*nlstate)+1;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for (j=1; j<= nlstate+1 ; j ++) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficres,"%3d",i);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("%3d",i);        }   
       for(j=1; j<=i;j++){        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         fprintf(ficres," %.5e",matcov[i][j]);        else fprintf(ficgp,"\" t\"\" w l 0,");
         printf(" %.5e",matcov[i][j]);      }
       }    }
       fprintf(ficres,"\n");    
       printf("\n");    /*3eme*/
       k++;    
     }    for (k1=1; k1<= m ; k1 ++) { 
          for (cpt=1; cpt<= nlstate ; cpt ++) {
     while((c=getc(ficpar))=='#' && c!= EOF){        k=2+nlstate*(2*cpt-2);
       ungetc(c,ficpar);        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
       puts(line);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fputs(line,ficparo);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     ungetc(c,ficpar);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              
     if (fage <= 2) {        */
       bage = agemin;        for (i=1; i< nlstate ; i ++) {
       fage = agemaxpar;          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
     }          
            } 
     fprintf(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\n",agemin,agemaxpar,bage,fage);    }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    
      /* CV preval stable (period) */
     while((c=getc(ficpar))=='#' && c!= EOF){    for (k1=1; k1<= m ; k1 ++) { 
     ungetc(c,ficpar);      for (cpt=1; cpt<=nlstate ; cpt ++) {
     fgets(line, MAXLINE, ficpar);        k=3;
     puts(line);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     fputs(line,ficparo);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   }        
   ungetc(c,ficpar);        for (i=1; i<= nlstate ; i ++)
            fprintf(ficgp,"+$%d",k+i+1);
   fscanf(ficpar,"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",cpt,cpt+1);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        l=3+(nlstate+ndeath)*cpt;
              fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i< nlstate ; i ++) {
     ungetc(c,ficpar);          l=3+(nlstate+ndeath)*cpt;
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"+$%d",l+i+1);
     puts(line);        }
     fputs(line,ficparo);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   }      } 
   ungetc(c,ficpar);    }  
      
     /* proba elementaires */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    for(i=1,jk=1; i <=nlstate; i++){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);          for(j=1; j <=ncovmodel; j++){
   fprintf(ficparo,"pop_based=%d\n",popbased);              fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   fprintf(ficres,"pop_based=%d\n",popbased);              jk++; 
              fprintf(ficgp,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      }
     puts(line);     }
     fputs(line,ficparo);  
   }     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++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);         if (ng==2)
 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);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
 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);         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 while((c=getc(ficpar))=='#' && c!= EOF){         i=1;
     ungetc(c,ficpar);         for(k2=1; k2<=nlstate; k2++) {
     fgets(line, MAXLINE, ficpar);           k3=i;
     puts(line);           for(k=1; k<=(nlstate+ndeath); k++) {
     fputs(line,ficparo);             if (k != k2){
   }               if(ng==2)
   ungetc(c,ficpar);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
   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(ficgp," exp(p%d+p%d*x",i,i+1);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);               ij=1;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);               for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
 /*------------ gnuplot -------------*/                 }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);                 else
                     fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 /*------------ free_vector  -------------*/               }
  chdir(path);               fprintf(ficgp,")/(1");
                 
  free_ivector(wav,1,imx);               for(k1=1; k1 <=nlstate; k1++){   
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                   ij=1;
  free_ivector(num,1,n);                 for(j=3; j <=ncovmodel; j++){
  free_vector(agedc,1,n);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  fclose(ficparo);                     ij++;
  fclose(ficres);                   }
                    else
 /*--------- index.htm --------*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                 fprintf(ficgp,")");
                }
                 fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   /*--------------- Prevalence limit --------------*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                 i=i+ncovmodel;
   strcpy(filerespl,"pl");             }
   strcat(filerespl,fileres);           } /* end k */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {         } /* end k2 */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       } /* end jk */
   }     } /* end ng */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);     fclose(ficgp); 
   fprintf(ficrespl,"#Prevalence limit\n");  }  /* end gnuplot */
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  /*************** Moving average **************/
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i, cpt, cptcod;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int modcovmax =1;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int mobilavrange, mob;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double age;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   agebase=agemin;                             a covariate has 2 modalities */
   agelim=agemaxpar;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   ftolpl=1.e-10;  
   i1=cptcoveff;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   if (cptcovn < 1){i1=1;}      if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
   for(cptcov=1;cptcov<=i1;cptcov++){      for (age=bage; age<=fage; age++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for (i=1; i<=nlstate;i++)
         k=k+1;          for (cptcod=1;cptcod<=modcovmax;cptcod++)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
         fprintf(ficrespl,"\n#******");      /* We keep the original values on the extreme ages bage, fage and for 
         for(j=1;j<=cptcoveff;j++)         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         we use a 5 terms etc. until the borders are no more concerned. 
         fprintf(ficrespl,"******\n");      */ 
              for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=agebase; age<=agelim; age++){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for (i=1; i<=nlstate;i++){
           fprintf(ficrespl,"%.0f",age );            for (cptcod=1;cptcod<=modcovmax;cptcod++){
           for(i=1; i<=nlstate;i++)              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
           fprintf(ficrespl," %.5f", prlim[i][i]);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
           fprintf(ficrespl,"\n");                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
         }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
       }                }
     }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   fclose(ficrespl);            }
           }
   /*------------- h Pij x at various ages ------------*/        }/* end age */
        }/* end mob */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    }else return -1;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    return 0;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  }/* End movingaverage */
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);  
    /************** Forecasting ******************/
   stepsize=(int) (stepm+YEARM-1)/YEARM;  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){
   /*if (stepm<=24) stepsize=2;*/    /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
   agelim=AGESUP;       dateprev1 dateprev2 range of dates during which prevalence is computed
   hstepm=stepsize*YEARM; /* Every year of age */       anproj2 year of en of projection (same day and month as proj1).
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    */
      int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   k=0;    int *popage;
   for(cptcov=1;cptcov<=i1;cptcov++){    double agec; /* generic age */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       k=k+1;    double *popeffectif,*popcount;
         fprintf(ficrespij,"\n#****** ");    double ***p3mat;
         for(j=1;j<=cptcoveff;j++)    double ***mobaverage;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char fileresf[FILENAMELENGTH];
         fprintf(ficrespij,"******\n");  
            agelim=AGESUP;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    strcpy(fileresf,"f"); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresf,fileres);
           oldm=oldms;savm=savms;    if((ficresf=fopen(fileresf,"w"))==NULL) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf("Problem with forecast resultfile: %s\n", fileresf);
           fprintf(ficrespij,"# Age");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           for(i=1; i<=nlstate;i++)    }
             for(j=1; j<=nlstate+ndeath;j++)    printf("Computing forecasting: result on file '%s' \n", fileresf);
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)    if (mobilav!=0) {
               for(j=1; j<=nlstate+ndeath;j++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             fprintf(ficrespij,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           fprintf(ficrespij,"\n");    }
         }  
     }    stepsize=(int) (stepm+YEARM-1)/YEARM;
   }    if (stepm<=12) stepsize=1;
     if(estepm < stepm){
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   fclose(ficrespij);    else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
   /*---------- Forecasting ------------------*/    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   if((stepm == 1) && (model==".")){                                 fractional in yp1 */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    anprojmean=yp;
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    yp2=modf((yp1*12),&yp);
     free_matrix(mint,1,maxwav,1,n);    mprojmean=yp;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    yp1=modf((yp2*30.5),&yp);
     free_vector(weight,1,n);}    jprojmean=yp;
   else{    if(jprojmean==0) jprojmean=1;
     erreur=108;    if(mprojmean==0) jprojmean=1;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);  
   }    i1=cptcoveff;
      if (cptcovn < 1){i1=1;}
     
   /*---------- Health expectancies and variances ------------*/    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
   strcpy(filerest,"t");    fprintf(ficresf,"#****** Routine prevforecast **\n");
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {  /*            if (h==(int)(YEARM*yearp)){ */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
   strcpy(filerese,"e");          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]]);
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {        fprintf(ficresf,"******\n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   }        for(j=1; j<=nlstate+ndeath;j++){ 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
  strcpy(fileresv,"v");          fprintf(ficresf," p.%d",j);
   strcat(fileresv,fileres);        }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          fprintf(ficresf,"\n");
   }          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
   k=0;            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   for(cptcov=1;cptcov<=i1;cptcov++){            nhstepm = nhstepm/hstepm; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=k+1;            oldm=oldms;savm=savms;
       fprintf(ficrest,"\n#****** ");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       for(j=1;j<=cptcoveff;j++)          
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (h=0; h<=nhstepm; h++){
       fprintf(ficrest,"******\n");              if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
       fprintf(ficreseij,"\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(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       fprintf(ficreseij,"******\n");              } 
               for(j=1; j<=nlstate+ndeath;j++) {
       fprintf(ficresvij,"\n#****** ");                ppij=0.;
       for(j=1;j<=cptcoveff;j++)                for(i=1; i<=nlstate;i++) {
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                  if (mobilav==1) 
       fprintf(ficresvij,"******\n");                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       oldm=oldms;savm=savms;                  }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                    if (h*hstepm/YEARM*stepm== yearp) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       oldm=oldms;savm=savms;                  }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                } /* end i */
                    if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                  }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              }/* end j */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            } /* end h */
       fprintf(ficrest,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
       hf=1;        } /* end yearp */
       if (stepm >= YEARM) hf=stepm/YEARM;      } /* end cptcod */
       epj=vector(1,nlstate+1);    } /* end  cptcov */
       for(age=bage; age <=fage ;age++){         
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    fclose(ficresf);
             prlim[i][i]=probs[(int)age][i][k];  }
         }  
          /************** Forecasting *****not tested NB*************/
         fprintf(ficrest," %.0f",age);  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    int *popage;
           }    double calagedatem, agelim, kk1, kk2;
           epj[nlstate+1] +=epj[j];    double *popeffectif,*popcount;
         }    double ***p3mat,***tabpop,***tabpopprev;
         for(i=1, vepp=0.;i <=nlstate;i++)    double ***mobaverage;
           for(j=1;j <=nlstate;j++)    char filerespop[FILENAMELENGTH];
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1;j <=nlstate;j++){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    agelim=AGESUP;
         }    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
         fprintf(ficrest,"\n");    
       }    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     }    
   }    
     strcpy(filerespop,"pop"); 
   fclose(ficreseij);    strcat(filerespop,fileres);
   fclose(ficresvij);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   fclose(ficrest);      printf("Problem with forecast resultfile: %s\n", filerespop);
   fclose(ficpar);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   free_vector(epj,1,nlstate+1);    }
      printf("Computing forecasting: result on file '%s' \n", filerespop);
   /*------- Variance limit prevalence------*/      fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
   strcpy(fileresvpl,"vpl");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    if (mobilav!=0) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     exit(0);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   k=0;    }
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    stepsize=(int) (stepm+YEARM-1)/YEARM;
       k=k+1;    if (stepm<=12) stepsize=1;
       fprintf(ficresvpl,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    agelim=AGESUP;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvpl,"******\n");    hstepm=1;
          hstepm=hstepm/stepm; 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    
       oldm=oldms;savm=savms;    if (popforecast==1) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      if((ficpop=fopen(popfile,"r"))==NULL) {
     }        printf("Problem with population file : %s\n",popfile);exit(0);
  }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
   fclose(ficresvpl);      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
   /*---------- End : free ----------------*/      popcount=vector(0,AGESUP);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      
        i=1;   
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);     
        imx=i;
        for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   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);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
          k=k+1;
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficrespop,"\n#******");
   free_vector(delti,1,npar);        for(j=1;j<=cptcoveff;j++) {
   free_matrix(agev,1,maxwav,1,imx);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        }
         fprintf(ficrespop,"******\n");
   if(erreur >0)        fprintf(ficrespop,"# Age");
     printf("End of Imach with error %d\n",erreur);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   else   printf("End of Imach\n");        if (popforecast==1)  fprintf(ficrespop," [Population]");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        
          for (cpt=0; cpt<=0;cpt++) { 
   /* 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);*/          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   /*printf("Total time was %d uSec.\n", total_usecs);*/          
   /*------ End -----------*/          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
  end:            
 #ifdef windows            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* chdir(pathcd);*/            oldm=oldms;savm=savms;
 #endif            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
  /*system("wgnuplot graph.plt");*/          
  /*system("../gp37mgw/wgnuplot graph.plt");*/            for (h=0; h<=nhstepm; h++){
  /*system("cd ../gp37mgw");*/              if (h==(int) (calagedatem+YEARM*cpt)) {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
  strcpy(plotcmd,GNUPLOTPROGRAM);              } 
  strcat(plotcmd," ");              for(j=1; j<=nlstate+ndeath;j++) {
  strcat(plotcmd,optionfilegnuplot);                kk1=0.;kk2=0;
  system(plotcmd);                for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
 #ifdef windows                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
   while (z[0] != 'q') {                  else {
     chdir(path);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                  }
     scanf("%s",z);                }
     if (z[0] == 'c') system("./imach");                if (h==(int)(calagedatem+12*cpt)){
     else if (z[0] == 'e') {                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
       chdir(path);                    /*fprintf(ficrespop," %.3f", kk1);
       system(optionfilehtm);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     }                }
     else if (z[0] == 'q') exit(0);              }
   }              for(i=1; i<=nlstate;i++){
 #endif                kk1=0.;
 }                  for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               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",version);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*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.1.30  
changed lines
  Added in v.1.80


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