Diff for /imach/src/imach.c between versions 1.29 and 1.82

version 1.29, 2002/03/06 19:02:50 version 1.82, 2003/06/05 15:57:20
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  */
   first survey ("cross") where individuals from different ages are  /*
   interviewed on their health status or degree of disability (in the     Interpolated Markov Chain
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Short summary of the programme:
   (if any) in individual health status.  Health expectancies are    
   computed from the time spent in each health state according to a    This program computes Healthy Life Expectancies from
   model. More health states you consider, more time is necessary to reach the    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Maximum Likelihood of the parameters involved in the model.  The    first survey ("cross") where individuals from different ages are
   simplest model is the multinomial logistic model where pij is the    interviewed on their health status or degree of disability (in the
   probabibility to be observed in state j at the second wave    case of a health survey which is our main interest) -2- at least a
   conditional to be observed in state i at the first wave. Therefore    second wave of interviews ("longitudinal") which measure each change
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (if any) in individual health status.  Health expectancies are
   'age' is age and 'sex' is a covariate. If you want to have a more    computed from the time spent in each health state according to a
   complex model than "constant and age", you should modify the program    model. More health states you consider, more time is necessary to reach the
   where the markup *Covariates have to be included here again* invites    Maximum Likelihood of the parameters involved in the model.  The
   you to do it.  More covariates you add, slower the    simplest model is the multinomial logistic model where pij is the
   convergence.    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
   The advantage of this computer programme, compared to a simple    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   multinomial logistic model, is clear when the delay between waves is not    'age' is age and 'sex' is a covariate. If you want to have a more
   identical for each individual. Also, if a individual missed an    complex model than "constant and age", you should modify the program
   intermediate interview, the information is lost, but taken into    where the markup *Covariates have to be included here again* invites
   account using an interpolation or extrapolation.      you to do it.  More covariates you add, slower the
     convergence.
   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    The advantage of this computer programme, compared to a simple
   split into an exact number (nh*stepm) of unobserved intermediate    multinomial logistic model, is clear when the delay between waves is not
   states. This elementary transition (by month or quarter trimester,    identical for each individual. Also, if a individual missed an
   semester or year) is model as a multinomial logistic.  The hPx    intermediate interview, the information is lost, but taken into
   matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply  
   hPijx.    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
   Also this programme outputs the covariance matrix of the parameters but also    split into an exact number (nh*stepm) of unobserved intermediate
   of the life expectancies. It also computes the prevalence limits.    states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    matrix is simply the matrix product of nh*stepm elementary matrices
            Institut national d'études démographiques, Paris.    and the contribution of each individual to the likelihood is simply
   This software have been partly granted by Euro-REVES, a concerted action    hPijx.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Also this programme outputs the covariance matrix of the parameters but also
   software can be distributed freely for non commercial use. Latest version    of the life expectancies. It also computes the stable prevalence. 
   can be accessed at http://euroreves.ined.fr/imach .    
   **********************************************************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
 #include <math.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdio.h>    from the European Union.
 #include <stdlib.h>    It is copyrighted identically to a GNU software product, ie programme and
 #include <unistd.h>    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define FILENAMELENGTH 80    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 /*#define DEBUG*/    
 #define windows    **********************************************************************/
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  /*
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    main
     read parameterfile
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    read datafile
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    concatwav
     if (mle >= 1)
 #define NINTERVMAX 8      mlikeli
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    print results files
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    if mle==1 
 #define NCOVMAX 8 /* Maximum number of covariates */       computes hessian
 #define MAXN 20000    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define YEARM 12. /* Number of months per year */        begin-prev-date,...
 #define AGESUP 130    open gnuplot file
 #define AGEBASE 40    open html file
     stable prevalence
      for age prevalim()
 int erreur; /* Error number */    h Pij x
 int nvar;    variance of p varprob
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    forecasting if prevfcast==1 prevforecast call prevalence()
 int npar=NPARMAX;    health expectancies
 int nlstate=2; /* Number of live states */    Variance-covariance of DFLE
 int ndeath=1; /* Number of dead states */    prevalence()
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */     movingaverage()
 int popbased=0;    varevsij() 
     if popbased==1 varevsij(,popbased)
 int *wav; /* Number of waves for this individuual 0 is possible */    total life expectancies
 int maxwav; /* Maxim number of waves */    Variance of stable prevalence
 int jmin, jmax; /* min, max spacing between 2 waves */   end
 int mle, weightopt;  */
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */   
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #include <math.h>
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #include <stdio.h>
 FILE *ficgp,*ficresprob,*ficpop;  #include <stdlib.h>
 FILE *ficreseij;  #include <unistd.h>
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;  #define MAXLINE 256
   char fileresv[FILENAMELENGTH];  #define GNUPLOTPROGRAM "gnuplot"
  FILE  *ficresvpl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   char fileresvpl[FILENAMELENGTH];  #define FILENAMELENGTH 80
   /*#define DEBUG*/
 #define NR_END 1  #define windows
 #define FREE_ARG char*  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define FTOL 1.0e-10  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define NRANSI  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define ITMAX 200  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define TOL 2.0e-4  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define CGOLD 0.3819660  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define ZEPS 1.0e-10  #define NCOVMAX 8 /* Maximum number of covariates */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 #define GOLD 1.618034  #define AGESUP 130
 #define GLIMIT 100.0  #define AGEBASE 40
 #define TINY 1.0e-20  #ifdef windows
   #define DIRSEPARATOR '\\'
 static double maxarg1,maxarg2;  #define ODIRSEPARATOR '/'
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #else
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define DIRSEPARATOR '/'
    #define ODIRSEPARATOR '\\'
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #endif
 #define rint(a) floor(a+0.5)  
   /* $Id$ */
 static double sqrarg;  /* $State$ */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 int imx;  int erreur; /* Error number */
 int stepm;  int nvar;
 /* Stepm, step in month: minimum step interpolation*/  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 int m,nb;  int nlstate=2; /* Number of live states */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int ndeath=1; /* Number of dead states */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double **pmmij, ***probs, ***mobaverage;  int popbased=0;
 double dateintmean=0;  
   int *wav; /* Number of waves for this individuual 0 is possible */
 double *weight;  int maxwav; /* Maxim number of waves */
 int **s; /* Status */  int jmin, jmax; /* min, max spacing between 2 waves */
 double *agedc, **covar, idx;  int mle, weightopt;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double ftolhess; /* Tolerance for computing hessian */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 /**************** split *************************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    char *s;                             /* pointer */  FILE *ficlog, *ficrespow;
    int  l1, l2;                         /* length counters */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
    l1 = strlen( path );                 /* length of path */  FILE *fichtm; /* Html File */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  FILE *ficreseij;
 #ifdef windows  char filerese[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  FILE  *ficresvij;
 #else  char fileresv[FILENAMELENGTH];
    s = strrchr( path, '/' );            /* find last / */  FILE  *ficresvpl;
 #endif  char fileresvpl[FILENAMELENGTH];
    if ( s == NULL ) {                   /* no directory, so use current */  char title[MAXLINE];
 #if     defined(__bsd__)                /* get current working directory */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       extern char       *getwd( );  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
       if ( getwd( dirc ) == NULL ) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #else  char filelog[FILENAMELENGTH]; /* Log file */
       extern char       *getcwd( );  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  char popfile[FILENAMELENGTH];
 #endif  
          return( GLOCK_ERROR_GETCWD );  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
       }  
       strcpy( name, path );             /* we've got it */  #define NR_END 1
    } else {                             /* strip direcotry from path */  #define FREE_ARG char*
       s++;                              /* after this, the filename */  #define FTOL 1.0e-10
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NRANSI 
       strcpy( name, s );                /* save file name */  #define ITMAX 200 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  #define TOL 2.0e-4 
    }  
    l1 = strlen( dirc );                 /* length of directory */  #define CGOLD 0.3819660 
 #ifdef windows  #define ZEPS 1.0e-10 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define GOLD 1.618034 
 #endif  #define GLIMIT 100.0 
    s = strrchr( name, '.' );            /* find last / */  #define TINY 1.0e-20 
    s++;  
    strcpy(ext,s);                       /* save extension */  static double maxarg1,maxarg2;
    l1= strlen( name);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    l2= strlen( s)+1;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    strncpy( finame, name, l1-l2);    
    finame[l1-l2]= 0;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    return( 0 );                         /* we're done */  #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 stepm;
   int i;  /* Stepm, step in month: minimum step interpolation*/
   int lg=20;  
   i=0;  int estepm;
   lg=strlen(t);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  int m,nb;
     if (t[i]== '\\') s[i]='/';  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double dateintmean=0;
 int nbocc(char *s, char occ)  
 {  double *weight;
   int i,j=0;  int **s; /* Status */
   int lg=20;  double *agedc, **covar, idx;
   i=0;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if  (s[i] == occ ) j++;  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   l1, l2;                         /* length counters */
   int i,lg,j,p=0;  
   i=0;    l1 = strlen(path );                   /* length of path */
   for(j=0; j<=strlen(t)-1; j++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   lg=strlen(t);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for(j=0; j<p; j++) {      /* get current working directory */
     (u[j] = t[j]);      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
      u[p]='\0';        return( GLOCK_ERROR_GETCWD );
       }
    for(j=0; j<= lg; j++) {      strcpy( name, path );               /* we've got it */
     if (j>=(p+1))(v[j-p-1] = t[j]);    } else {                              /* strip direcotry from path */
   }      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /********************** nrerror ********************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void nrerror(char error_text[])      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   fprintf(stderr,"ERREUR ...\n");    l1 = strlen( dirc );                  /* length of directory */
   fprintf(stderr,"%s\n",error_text);  #ifdef windows
   exit(1);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 }  #else
 /*********************** vector *******************/    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 double *vector(int nl, int nh)  #endif
 {    ss = strrchr( name, '.' );            /* find last / */
   double *v;    ss++;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    strcpy(ext,ss);                       /* save extension */
   if (!v) nrerror("allocation failure in vector");    l1= strlen( name);
   return v-nl+NR_END;    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /************************ free vector ******************/    return( 0 );                          /* we're done */
 void free_vector(double*v, int nl, int nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  
 }  /******************************************/
   
 /************************ivector *******************************/  void replace(char *s, char*t)
 int *ivector(long nl,long nh)  {
 {    int i;
   int *v;    int lg=20;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    i=0;
   if (!v) nrerror("allocation failure in ivector");    lg=strlen(t);
   return v-nl+NR_END;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /******************free ivector **************************/    }
 void free_ivector(int *v, long nl, long nh)  }
 {  
   free((FREE_ARG)(v+nl-NR_END));  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /******************* imatrix *******************************/    int lg=20;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    i=0;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if  (s[i] == occ ) j++;
   int **m;    }
      return j;
   /* allocate pointers to rows */  }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  void cutv(char *u,char *v, char*t, char occ)
   m += NR_END;  {
   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)
         gives u="abcedf" and v="ghi2j" */
   /* allocate rows and set pointers to them */    int i,lg,j,p=0;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    i=0;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(j=0; j<=strlen(t)-1; j++) {
   m[nrl] += NR_END;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m[nrl] -= ncl;    }
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    lg=strlen(t);
      for(j=0; j<p; j++) {
   /* return pointer to array of pointers to rows */      (u[j] = t[j]);
   return m;    }
 }       u[p]='\0';
   
 /****************** free_imatrix *************************/     for(j=0; j<= lg; j++) {
 void free_imatrix(m,nrl,nrh,ncl,nch)      if (j>=(p+1))(v[j-p-1] = t[j]);
       int **m;    }
       long nch,ncl,nrh,nrl;  }
      /* free an int matrix allocated by imatrix() */  
 {  /********************** nrerror ********************/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  void nrerror(char error_text[])
 }  {
     fprintf(stderr,"ERREUR ...\n");
 /******************* matrix *******************************/    fprintf(stderr,"%s\n",error_text);
 double **matrix(long nrl, long nrh, long ncl, long nch)    exit(EXIT_FAILURE);
 {  }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /*********************** vector *******************/
   double **m;  double *vector(int nl, int nh)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    double *v;
   if (!m) nrerror("allocation failure 1 in matrix()");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m += NR_END;    if (!v) nrerror("allocation failure in vector");
   m -= nrl;    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()");  /************************ free vector ******************/
   m[nrl] += NR_END;  void free_vector(double*v, int nl, int nh)
   m[nrl] -= ncl;  {
     free((FREE_ARG)(v+nl-NR_END));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  /************************ivector *******************************/
   char *cvector(long nl,long nh)
 /*************************free matrix ************************/  {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    char *v;
 {    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!v) nrerror("allocation failure in cvector");
   free((FREE_ARG)(m+nrl-NR_END));    return v-nl+NR_END;
 }  }
   
 /******************* ma3x *******************************/  /******************free ivector **************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  void free_cvector(char *v, long nl, long nh)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    free((FREE_ARG)(v+nl-NR_END));
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /************************ivector *******************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  int *ivector(long nl,long nh)
   m += NR_END;  {
   m -= nrl;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!v) nrerror("allocation failure in ivector");
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    return v-nl+NR_END;
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   /******************free ivector **************************/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  void free_ivector(int *v, long nl, long nh)
   {
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    free((FREE_ARG)(v+nl-NR_END));
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  }
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /******************* imatrix *******************************/
   for (j=ncl+1; j<=nch; j++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     m[nrl][j]=m[nrl][j-1]+nlay;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
   for (i=nrl+1; i<=nrh; i++) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    int **m; 
     for (j=ncl+1; j<=nch; j++)    
       m[i][j]=m[i][j-1]+nlay;    /* allocate pointers to rows */ 
   }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   return m;    if (!m) nrerror("allocation failure 1 in matrix()"); 
 }    m += NR_END; 
     m -= nrl; 
 /*************************free ma3x ************************/    
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    
 {    /* allocate rows and set pointers to them */ 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl] += NR_END; 
 }    m[nrl] -= ncl; 
     
 /***************** f1dim *************************/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 extern int ncom;    
 extern double *pcom,*xicom;    /* return pointer to array of pointers to rows */ 
 extern double (*nrfunc)(double []);    return m; 
    } 
 double f1dim(double x)  
 {  /****************** free_imatrix *************************/
   int j;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double f;        int **m;
   double *xt;        long nch,ncl,nrh,nrl; 
         /* free an int matrix allocated by imatrix() */ 
   xt=vector(1,ncom);  { 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   f=(*nrfunc)(xt);    free((FREE_ARG) (m+nrl-NR_END)); 
   free_vector(xt,1,ncom);  } 
   return f;  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /*****************brent *************************/  {
 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;
 {    double **m;
   int iter;  
   double a,b,d,etemp;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double fu,fv,fw,fx;    if (!m) nrerror("allocation failure 1 in matrix()");
   double ftemp;    m += NR_END;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m -= nrl;
   double e=0.0;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   a=(ax < cx ? ax : cx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   b=(ax > cx ? ax : cx);    m[nrl] += NR_END;
   x=w=v=bx;    m[nrl] -= ncl;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     xm=0.5*(a+b);    return m;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/     */
     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);  /*************************free matrix ************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 #endif  {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       *xmin=x;    free((FREE_ARG)(m+nrl-NR_END));
       return fx;  }
     }  
     ftemp=fu;  /******************* ma3x *******************************/
     if (fabs(e) > tol1) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       p=(x-v)*q-(x-w)*r;    double ***m;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       q=fabs(q);    if (!m) nrerror("allocation failure 1 in matrix()");
       etemp=e;    m += NR_END;
       e=d;    m -= nrl;
       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));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       else {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         d=p/q;    m[nrl] += NR_END;
         u=x+d;    m[nrl] -= ncl;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
     } else {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl][ncl] -= nll;
     fu=(*f)(u);    for (j=ncl+1; j<=nch; j++) 
     if (fu <= fx) {      m[nrl][j]=m[nrl][j-1]+nlay;
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    for (i=nrl+1; i<=nrh; i++) {
         SHFT(fv,fw,fx,fu)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         } else {      for (j=ncl+1; j<=nch; j++) 
           if (u < x) a=u; else b=u;        m[i][j]=m[i][j-1]+nlay;
           if (fu <= fw || w == x) {    }
             v=w;    return m; 
             w=u;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             fv=fw;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
             fw=fu;    */
           } 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)
         }  {
   }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   nrerror("Too many iterations in brent");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   *xmin=x;    free((FREE_ARG)(m+nrl-NR_END));
   return fx;  }
 }  
   /***************** f1dim *************************/
 /****************** mnbrak ***********************/  extern int ncom; 
   extern double *pcom,*xicom;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  extern double (*nrfunc)(double []); 
             double (*func)(double))   
 {  double f1dim(double x) 
   double ulim,u,r,q, dum;  { 
   double fu;    int j; 
      double f;
   *fa=(*func)(*ax);    double *xt; 
   *fb=(*func)(*bx);   
   if (*fb > *fa) {    xt=vector(1,ncom); 
     SHFT(dum,*ax,*bx,dum)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       SHFT(dum,*fb,*fa,dum)    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
   *cx=(*bx)+GOLD*(*bx-*ax);    return f; 
   *fc=(*func)(*cx);  } 
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /*****************brent *************************/
     q=(*bx-*cx)*(*fb-*fa);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  { 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    int iter; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double a,b,d,etemp;
     if ((*bx-u)*(u-*cx) > 0.0) {    double fu,fv,fw,fx;
       fu=(*func)(u);    double ftemp;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       fu=(*func)(u);    double e=0.0; 
       if (fu < *fc) {   
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    a=(ax < cx ? ax : cx); 
           SHFT(*fb,*fc,fu,(*func)(u))    b=(ax > cx ? ax : cx); 
           }    x=w=v=bx; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    fw=fv=fx=(*f)(x); 
       u=ulim;    for (iter=1;iter<=ITMAX;iter++) { 
       fu=(*func)(u);      xm=0.5*(a+b); 
     } else {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       u=(*cx)+GOLD*(*cx-*bx);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       fu=(*func)(u);      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
     SHFT(*ax,*bx,*cx,u)  #ifdef DEBUG
       SHFT(*fa,*fb,*fc,fu)      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)))) { */
   #endif
 /*************** linmin ************************/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
 int ncom;        return fx; 
 double *pcom,*xicom;      } 
 double (*nrfunc)(double []);      ftemp=fu;
        if (fabs(e) > tol1) { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        r=(x-w)*(fx-fv); 
 {        q=(x-v)*(fx-fw); 
   double brent(double ax, double bx, double cx,        p=(x-v)*q-(x-w)*r; 
                double (*f)(double), double tol, double *xmin);        q=2.0*(q-r); 
   double f1dim(double x);        if (q > 0.0) p = -p; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        q=fabs(q); 
               double *fc, double (*func)(double));        etemp=e; 
   int j;        e=d; 
   double xx,xmin,bx,ax;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double fx,fb,fa;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          else { 
   ncom=n;          d=p/q; 
   pcom=vector(1,n);          u=x+d; 
   xicom=vector(1,n);          if (u-a < tol2 || b-u < tol2) 
   nrfunc=func;            d=SIGN(tol1,xm-x); 
   for (j=1;j<=n;j++) {        } 
     pcom[j]=p[j];      } else { 
     xicom[j]=xi[j];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   }      } 
   ax=0.0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   xx=1.0;      fu=(*f)(u); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      if (fu <= fx) { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        if (u >= x) a=x; else b=x; 
 #ifdef DEBUG        SHFT(v,w,x,u) 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);          SHFT(fv,fw,fx,fu) 
 #endif          } else { 
   for (j=1;j<=n;j++) {            if (u < x) a=u; else b=u; 
     xi[j] *= xmin;            if (fu <= fw || w == x) { 
     p[j] += xi[j];              v=w; 
   }              w=u; 
   free_vector(xicom,1,n);              fv=fw; 
   free_vector(pcom,1,n);              fw=fu; 
 }            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 /*************** powell ************************/              fv=fu; 
 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,    nrerror("Too many iterations in brent"); 
               double (*func)(double []));    *xmin=x; 
   int i,ibig,j;    return fx; 
   double del,t,*pt,*ptt,*xit;  } 
   double fp,fptt;  
   double *xits;  /****************** mnbrak ***********************/
   pt=vector(1,n);  
   ptt=vector(1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   xit=vector(1,n);              double (*func)(double)) 
   xits=vector(1,n);  { 
   *fret=(*func)(p);    double ulim,u,r,q, dum;
   for (j=1;j<=n;j++) pt[j]=p[j];    double fu; 
   for (*iter=1;;++(*iter)) {   
     fp=(*fret);    *fa=(*func)(*ax); 
     ibig=0;    *fb=(*func)(*bx); 
     del=0.0;    if (*fb > *fa) { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      SHFT(dum,*ax,*bx,dum) 
     for (i=1;i<=n;i++)        SHFT(dum,*fb,*fa,dum) 
       printf(" %d %.12f",i, p[i]);        } 
     printf("\n");    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (i=1;i<=n;i++) {    *fc=(*func)(*cx); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    while (*fb > *fc) { 
       fptt=(*fret);      r=(*bx-*ax)*(*fb-*fc); 
 #ifdef DEBUG      q=(*bx-*cx)*(*fb-*fa); 
       printf("fret=%lf \n",*fret);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 #endif        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       printf("%d",i);fflush(stdout);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       linmin(p,xit,n,fret,func);      if ((*bx-u)*(u-*cx) > 0.0) { 
       if (fabs(fptt-(*fret)) > del) {        fu=(*func)(u); 
         del=fabs(fptt-(*fret));      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         ibig=i;        fu=(*func)(u); 
       }        if (fu < *fc) { 
 #ifdef DEBUG          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       printf("%d %.12e",i,(*fret));            SHFT(*fb,*fc,fu,(*func)(u)) 
       for (j=1;j<=n;j++) {            } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         printf(" x(%d)=%.12e",j,xit[j]);        u=ulim; 
       }        fu=(*func)(u); 
       for(j=1;j<=n;j++)      } else { 
         printf(" p=%.12e",p[j]);        u=(*cx)+GOLD*(*cx-*bx); 
       printf("\n");        fu=(*func)(u); 
 #endif      } 
     }      SHFT(*ax,*bx,*cx,u) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        SHFT(*fa,*fb,*fc,fu) 
 #ifdef DEBUG        } 
       int k[2],l;  } 
       k[0]=1;  
       k[1]=-1;  /*************** linmin ************************/
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  int ncom; 
         printf(" %.12e",p[j]);  double *pcom,*xicom;
       printf("\n");  double (*nrfunc)(double []); 
       for(l=0;l<=1;l++) {   
         for (j=1;j<=n;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  { 
           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, 
         }                 double (*f)(double), double tol, double *xmin); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double f1dim(double x); 
       }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 #endif                double *fc, double (*func)(double)); 
     int j; 
     double xx,xmin,bx,ax; 
       free_vector(xit,1,n);    double fx,fb,fa;
       free_vector(xits,1,n);   
       free_vector(ptt,1,n);    ncom=n; 
       free_vector(pt,1,n);    pcom=vector(1,n); 
       return;    xicom=vector(1,n); 
     }    nrfunc=func; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (j=1;j<=n;j++) { 
     for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
       ptt[j]=2.0*p[j]-pt[j];      xicom[j]=xi[j]; 
       xit[j]=p[j]-pt[j];    } 
       pt[j]=p[j];    ax=0.0; 
     }    xx=1.0; 
     fptt=(*func)(ptt);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     if (fptt < fp) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #ifdef DEBUG
       if (t < 0.0) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         linmin(p,xit,n,fret,func);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (j=1;j<=n;j++) {  #endif
           xi[j][ibig]=xi[j][n];    for (j=1;j<=n;j++) { 
           xi[j][n]=xit[j];      xi[j] *= xmin; 
         }      p[j] += xi[j]; 
 #ifdef DEBUG    } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    free_vector(xicom,1,n); 
         for(j=1;j<=n;j++)    free_vector(pcom,1,n); 
           printf(" %.12e",xit[j]);  } 
         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, 
                 double (*func)(double [])); 
 /**** Prevalence limit ****************/    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double fp,fptt;
 {    double *xits;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    pt=vector(1,n); 
      matrix by transitions matrix until convergence is reached */    ptt=vector(1,n); 
     xit=vector(1,n); 
   int i, ii,j,k;    xits=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    *fret=(*func)(p); 
   double **matprod2();    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **out, cov[NCOVMAX], **pmij();    for (*iter=1;;++(*iter)) { 
   double **newm;      fp=(*fret); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      ibig=0; 
       del=0.0; 
   for (ii=1;ii<=nlstate+ndeath;ii++)      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fprintf(ficrespow,"%d %.12f",*iter,*fret);
     }      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
    cov[1]=1.;        fprintf(ficlog," %d %.12lf",i, p[i]);
          fprintf(ficrespow," %.12lf", p[i]);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      printf("\n");
     newm=savm;      fprintf(ficlog,"\n");
     /* Covariates have to be included here again */      fprintf(ficrespow,"\n");
      cov[2]=agefin;      for (i=1;i<=n;i++) { 
          for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for (k=1; k<=cptcovn;k++) {        fptt=(*fret); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #ifdef DEBUG
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
       for (k=1; k<=cptcovage;k++)  #endif
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        printf("%d",i);fflush(stdout);
       for (k=1; k<=cptcovprod;k++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/          del=fabs(fptt-(*fret)); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          ibig=i; 
         } 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
     savm=oldm;        fprintf(ficlog,"%d %.12e",i,(*fret));
     oldm=newm;        for (j=1;j<=n;j++) {
     maxmax=0.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for(j=1;j<=nlstate;j++){          printf(" x(%d)=%.12e",j,xit[j]);
       min=1.;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       max=0.;        }
       for(i=1; i<=nlstate; i++) {        for(j=1;j<=n;j++) {
         sumnew=0;          printf(" p=%.12e",p[j]);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          fprintf(ficlog," p=%.12e",p[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);        }
         max=FMAX(max,prlim[i][j]);        printf("\n");
         min=FMIN(min,prlim[i][j]);        fprintf(ficlog,"\n");
       }  #endif
       maxmin=max-min;      } 
       maxmax=FMAX(maxmax,maxmin);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
     if(maxmax < ftolpl){        int k[2],l;
       return prlim;        k[0]=1;
     }        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
 }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
 /*************** transition probabilities ***************/          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        }
 {        printf("\n");
   double s1, s2;        fprintf(ficlog,"\n");
   /*double t34;*/        for(l=0;l<=1;l++) {
   int i,j,j1, nc, ii, jj;          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for(i=1; i<= nlstate; i++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(j=1; j<i;j++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          }
         /*s2 += param[i][j][nc]*cov[nc];*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          fprintf(ficlog,"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);*/        }
       }  #endif
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }        free_vector(xit,1,n); 
     for(j=i+1; j<=nlstate+ndeath;j++){        free_vector(xits,1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        free_vector(ptt,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        free_vector(pt,1,n); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        return; 
       }      } 
       ps[i][j]=s2;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
   }        ptt[j]=2.0*p[j]-pt[j]; 
     /*ps[3][2]=1;*/        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   for(i=1; i<= nlstate; i++){      } 
      s1=0;      fptt=(*func)(ptt); 
     for(j=1; j<i; j++)      if (fptt < fp) { 
       s1+=exp(ps[i][j]);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(j=i+1; j<=nlstate+ndeath; j++)        if (t < 0.0) { 
       s1+=exp(ps[i][j]);          linmin(p,xit,n,fret,func); 
     ps[i][i]=1./(s1+1.);          for (j=1;j<=n;j++) { 
     for(j=1; j<i; j++)            xi[j][ibig]=xi[j][n]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];            xi[j][n]=xit[j]; 
     for(j=i+1; j<=nlstate+ndeath; j++)          }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #ifdef DEBUG
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   } /* end i */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){            printf(" %.12e",xit[j]);
     for(jj=1; jj<= nlstate+ndeath; jj++){            fprintf(ficlog," %.12e",xit[j]);
       ps[ii][jj]=0;          }
       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]);  
    }  /**** Prevalence limit (stable prevalence)  ****************/
     printf("\n ");  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(i=1; i<= npar; i++) printf("%f ",x[i]);       matrix by transitions matrix until convergence is reached */
   goto end;*/  
     return ps;    int i, ii,j,k;
 }    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 /**************** Product of 2 matrices ******************/    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    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    for (ii=1;ii<=nlstate+ndeath;ii++)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      for (j=1;j<=nlstate+ndeath;j++){
   /* in, b, out are matrice of pointers which should have been initialized        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      before: only the contents of out is modified. The function returns      }
      a pointer to pointers identical to out */  
   long i, j, k;     cov[1]=1.;
   for(i=nrl; i<= nrh; i++)   
     for(k=ncolol; k<=ncoloh; k++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         out[i][k] +=in[i][j]*b[j][k];      newm=savm;
       /* Covariates have to be included here again */
   return out;       cov[2]=agefin;
 }    
         for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 /************* Higher Matrix Product ***************/          /*      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];
 {        for (k=1; k<=cptcovprod;k++)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      (typically every 2 years instead of every month which is too big).        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      Model is determined by parameters x and covariates have to be      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      included manually here.  
       savm=oldm;
      */      oldm=newm;
       maxmax=0.;
   int i, j, d, h, k;      for(j=1;j<=nlstate;j++){
   double **out, cov[NCOVMAX];        min=1.;
   double **newm;        max=0.;
         for(i=1; i<=nlstate; i++) {
   /* Hstepm could be zero and should return the unit matrix */          sumnew=0;
   for (i=1;i<=nlstate+ndeath;i++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for (j=1;j<=nlstate+ndeath;j++){          prlim[i][j]= newm[i][j]/(1-sumnew);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          max=FMAX(max,prlim[i][j]);
       po[i][j][0]=(i==j ? 1.0 : 0.0);          min=FMIN(min,prlim[i][j]);
     }        }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        maxmin=max-min;
   for(h=1; h <=nhstepm; h++){        maxmax=FMAX(maxmax,maxmin);
     for(d=1; d <=hstepm; d++){      }
       newm=savm;      if(maxmax < ftolpl){
       /* Covariates have to be included here again */        return prlim;
       cov[1]=1.;      }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*************** transition probabilities ***************/ 
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
     double s1, s2;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    /*double t34;*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    int i,j,j1, nc, ii, jj;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      for(i=1; i<= nlstate; i++){
       savm=oldm;      for(j=1; j<i;j++){
       oldm=newm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }          /*s2 += param[i][j][nc]*cov[nc];*/
     for(i=1; i<=nlstate+ndeath; i++)          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for(j=1;j<=nlstate+ndeath;j++) {          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         po[i][j][h]=newm[i][j];        }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        ps[i][j]=s2;
          */        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }      }
   } /* end h */      for(j=i+1; j<=nlstate+ndeath;j++){
   return po;        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 *************/        ps[i][j]=s2;
 double func( double *x)      }
 {    }
   int i, ii, j, k, mi, d, kk;      /*ps[3][2]=1;*/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    for(i=1; i<= nlstate; i++){
   double sw; /* Sum of weights */       s1=0;
   double lli; /* Individual log likelihood */      for(j=1; j<i; j++)
   long ipmx;        s1+=exp(ps[i][j]);
   /*extern weight */      for(j=i+1; j<=nlstate+ndeath; j++)
   /* We are differentiating ll according to initial status */        s1+=exp(ps[i][j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      ps[i][i]=1./(s1+1.);
   /*for(i=1;i<imx;i++)      for(j=1; j<i; j++)
     printf(" %d\n",s[4][i]);        ps[i][j]= exp(ps[i][j])*ps[i][i];
   */      for(j=i+1; j<=nlstate+ndeath; j++)
   cov[1]=1.;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    } /* end i */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for(mi=1; mi<= wav[i]-1; mi++){      for(jj=1; jj<= nlstate+ndeath; jj++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        ps[ii][jj]=0;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        ps[ii][ii]=1;
       for(d=0; d<dh[mi][i]; d++){      }
         newm=savm;    }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  
           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++){
               printf("%lf ",ps[ii][jj]);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,     }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      printf("\n ");
         savm=oldm;      }
         oldm=newm;      printf("\n ");printf("%lf ",cov[2]);*/
          /*
            for(i=1; i<= npar; i++) printf("%f ",x[i]);
       } /* end mult */    goto end;*/
            return ps;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  /**************** Product of 2 matrices ******************/
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     } /* end of wave */  {
   } /* end of individual */    /* 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(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* in, b, out are matrice of pointers which should have been initialized 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */       before: only the contents of out is modified. The function returns
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */       a pointer to pointers identical to out */
   return -l;    long i, j, k;
 }    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
 /*********** Maximum Likelihood Estimation ***************/          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;  /************* Higher Matrix Product ***************/
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    /* Computes the transition matrix starting at age 'age' over 
   printf("Powell\n");       'nhstepm*hstepm*stepm' months (i.e. until
   powell(p,xi,npar,ftol,&iter,&fret,func);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
    printf("\n#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 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       (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 
        included manually here. 
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))       */
 {  
   double  **a,**y,*x,pd;    int i, j, d, h, k;
   double **hess;    double **out, cov[NCOVMAX];
   int i, j,jk;    double **newm;
   int *indx;  
     /* Hstepm could be zero and should return the unit matrix */
   double hessii(double p[], double delta, int theta, double delti[]);    for (i=1;i<=nlstate+ndeath;i++)
   double hessij(double p[], double delti[], int i, int j);      for (j=1;j<=nlstate+ndeath;j++){
   void lubksb(double **a, int npar, int *indx, double b[]) ;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   void ludcmp(double **a, int npar, int *indx, double *d) ;        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 */
     for(h=1; h <=nhstepm; h++){
   printf("\nCalculation of the hessian matrix. Wait...\n");      for(d=1; d <=hstepm; d++){
   for (i=1;i<=npar;i++){        newm=savm;
     printf("%d",i);fflush(stdout);        /* Covariates have to be included here again */
     hess[i][i]=hessii(p,ftolhess,i,delti);        cov[1]=1.;
     /*printf(" %f ",p[i]);*/        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     /*printf(" %lf ",hess[i][i]);*/        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 (i=1;i<=npar;i++) {        for (k=1; k<=cptcovprod;k++)
     for (j=1;j<=npar;j++)  {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         hess[j][i]=hess[i][j];            /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         /*printf(" %lf ",hess[i][j]);*/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
   }        oldm=newm;
   printf("\n");      }
       for(i=1; i<=nlstate+ndeath; i++)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   a=matrix(1,npar,1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   y=matrix(1,npar,1,npar);           */
   x=vector(1,npar);        }
   indx=ivector(1,npar);    } /* end h */
   for (i=1;i<=npar;i++)    return po;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   
   for (j=1;j<=npar;j++) {  /*************** log-likelihood *************/
     for (i=1;i<=npar;i++) x[i]=0;  double func( double *x)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    int i, ii, j, k, mi, d, kk;
     for (i=1;i<=npar;i++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       matcov[i][j]=x[i];    double **out;
     }    double sw; /* Sum of weights */
   }    double lli; /* Individual log likelihood */
     int s1, s2;
   printf("\n#Hessian matrix#\n");    double bbh, survp;
   for (i=1;i<=npar;i++) {    long ipmx;
     for (j=1;j<=npar;j++) {    /*extern weight */
       printf("%.3e ",hess[i][j]);    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     printf("\n");    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
     */
   /* Recompute Inverse */    cov[1]=1.;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ludcmp(a,npar,indx,&pd);  
     if(mle==1){
   /*  printf("\n#Hessian matrix recomputed#\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1;j<=npar;j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<=npar;i++) x[i]=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
     x[j]=1;            for (j=1;j<=nlstate+ndeath;j++){
     lubksb(a,npar,indx,x);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       y[i][j]=x[i];            }
       printf("%.3e ",y[i][j]);          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
     printf("\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   free_matrix(a,1,npar,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_matrix(y,1,npar,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(x,1,npar);            savm=oldm;
   free_ivector(indx,1,npar);            oldm=newm;
   free_matrix(hess,1,npar,1,npar);          } /* 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.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
 /*************** hessian matrix ****************/           * (in months) between two waves is not a multiple of stepm, we rounded to 
 double hessii( double x[], double delta, int theta, double delti[])           * 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
   int i;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   int l=1, lmax=20;           * probability in order to take into account the bias as a fraction of the way
   double k1,k2;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double p2[NPARMAX+1];           * -stepm/2 to stepm/2 .
   double res;           * For stepm=1 the results are the same as for previous versions of Imach.
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;           * For stepm > 1 the results are less biased than in previous versions. 
   double fx;           */
   int k=0,kmax=10;          s1=s[mw[mi][i]][i];
   double l1;          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   fx=func(x);          /* bias is positive if real duration
   for (i=1;i<=npar;i++) p2[i]=x[i];           * is higher than the multiple of stepm and negative otherwise.
   for(l=0 ; l <=lmax; l++){           */
     l1=pow(10,l);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     delts=delt;          if( s2 > nlstate){ 
     for(k=1 ; k <kmax; k=k+1){            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       delt = delta*(l1*k);               to the likelihood is the probability to die between last step unit time and current 
       p2[theta]=x[theta] +delt;               step unit time, which is also the differences between probability to die before dh 
       k1=func(p2)-fx;               and probability to die before dh-stepm . 
       p2[theta]=x[theta]-delt;               In version up to 0.92 likelihood was computed
       k2=func(p2)-fx;          as if date of death was unknown. Death was treated as any other
       /*res= (k1-2.0*fx+k2)/delt/delt; */          health state: the date of the interview describes the actual state
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          and not the date of a change in health state. The former idea was
                to consider that at each interview the state was recorded
 #ifdef DEBUG          (healthy, disable or death) and IMaCh was corrected; but when we
       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);          introduced the exact date of death then we should have modified
 #endif          the contribution of an exact death to the likelihood. This new
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          contribution is smaller and very dependent of the step unit
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          stepm. It is no more the probability to die between last interview
         k=kmax;          and month of death but the probability to survive from last
       }          interview up to one month before death multiplied by the
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          probability to die within a month. Thanks to Chris
         k=kmax; l=lmax*10.;          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          which slows down the processing. The difference can be up to 10%
         delts=delt;          lower mortality.
       }            */
     }            lli=log(out[s1][s2] - savm[s1][s2]);
   }          }else{
   delti[theta]=delts;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   return res;            /*  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]);*/
           /*if(lli ==000.0)*/
 double hessij( double x[], double delti[], int thetai,int thetaj)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 {          ipmx +=1;
   int i;          sw += weight[i];
   int l=1, l1, lmax=20;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double k1,k2,k3,k4,res,fx;        } /* end of wave */
   double p2[NPARMAX+1];      } /* end of individual */
   int k;    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fx=func(x);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (k=1; k<=2; k++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<=npar;i++) p2[i]=x[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     p2[thetai]=x[thetai]+delti[thetai]/k;            for (j=1;j<=nlstate+ndeath;j++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     k1=func(p2)-fx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
     p2[thetai]=x[thetai]+delti[thetai]/k;          for(d=0; d<=dh[mi][i]; d++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            newm=savm;
     k2=func(p2)-fx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k3=func(p2)-fx;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetai]=x[thetai]-delti[thetai]/k;            savm=oldm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            oldm=newm;
     k4=func(p2)-fx;          } /* end mult */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        
 #ifdef DEBUG          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     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);          /* But now since version 0.9 we anticipate for bias and large stepm.
 #endif           * 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 
   return res;           * 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
 /************** Inverse of matrix **************/           * probability in order to take into account the bias as a fraction of the way
 void ludcmp(double **a, int n, int *indx, double *d)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 {           * -stepm/2 to stepm/2 .
   int i,imax,j,k;           * For stepm=1 the results are the same as for previous versions of Imach.
   double big,dum,sum,temp;           * For stepm > 1 the results are less biased than in previous versions. 
   double *vv;           */
            s1=s[mw[mi][i]][i];
   vv=vector(1,n);          s2=s[mw[mi+1][i]][i];
   *d=1.0;          bbh=(double)bh[mi][i]/(double)stepm; 
   for (i=1;i<=n;i++) {          /* bias is positive if real duration
     big=0.0;           * is higher than the multiple of stepm and negative otherwise.
     for (j=1;j<=n;j++)           */
       if ((temp=fabs(a[i][j])) > big) big=temp;          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 */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     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.-+bh)*out[s1][s2])); */ /* exponential interpolation */
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (j=1;j<=n;j++) {          /*if(lli ==000.0)*/
     for (i=1;i<j;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); */
       sum=a[i][j];          ipmx +=1;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          sw += weight[i];
       a[i][j]=sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     big=0.0;      } /* end of individual */
     for (i=j;i<=n;i++) {    }  else if(mle==3){  /* exponential inter-extrapolation */
       sum=a[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1;k<j;k++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         sum -= a[i][k]*a[k][j];        for(mi=1; mi<= wav[i]-1; mi++){
       a[i][j]=sum;          for (ii=1;ii<=nlstate+ndeath;ii++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {            for (j=1;j<=nlstate+ndeath;j++){
         big=dum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         imax=i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          for(d=0; d<dh[mi][i]; d++){
     if (j != imax) {            newm=savm;
       for (k=1;k<=n;k++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         dum=a[imax][k];            for (kk=1; kk<=cptcovage;kk++) {
         a[imax][k]=a[j][k];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         a[j][k]=dum;            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       *d = -(*d);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       vv[imax]=vv[j];            savm=oldm;
     }            oldm=newm;
     indx[j]=imax;          } /* end mult */
     if (a[j][j] == 0.0) a[j][j]=TINY;        
     if (j != n) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       dum=1.0/(a[j][j]);          /* But now since version 0.9 we anticipate for bias and large stepm.
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
   free_vector(vv,1,n);  /* Doesn't work */           * 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
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 void lubksb(double **a, int n, int *indx, double b[])           * -stepm/2 to stepm/2 .
 {           * For stepm=1 the results are the same as for previous versions of Imach.
   int i,ii=0,ip,j;           * For stepm > 1 the results are less biased than in previous versions. 
   double sum;           */
            s1=s[mw[mi][i]][i];
   for (i=1;i<=n;i++) {          s2=s[mw[mi+1][i]][i];
     ip=indx[i];          bbh=(double)bh[mi][i]/(double)stepm; 
     sum=b[ip];          /* bias is positive if real duration
     b[ip]=b[i];           * is higher than the multiple of stepm and negative otherwise.
     if (ii)           */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          /* 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 */
     else if (sum) ii=i;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     b[i]=sum;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   }          /*if(lli ==000.0)*/
   for (i=n;i>=1;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); */
     sum=b[i];          ipmx +=1;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          sw += weight[i];
     b[i]=sum/a[i][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
 }      } /* end of individual */
     }else{  /* ml=4 no inter-extrapolation */
 /************ Frequencies ********************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 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 (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {  /* Some frequencies */        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            for (j=1;j<=nlstate+ndeath;j++){
   double ***freq; /* Frequencies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2, dateintsum=0,k2cpt=0;            }
   FILE *ficresp;          for(d=0; d<dh[mi][i]; d++){
   char fileresp[FILENAMELENGTH];            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   pp=vector(1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   strcpy(fileresp,"p");            }
   strcat(fileresp,fileres);          
   if((ficresp=fopen(fileresp,"w"))==NULL) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("Problem with prevalence resultfile: %s\n", fileresp);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     exit(0);            savm=oldm;
   }            oldm=newm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } /* end mult */
   j1=0;        
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   j=cptcoveff;          ipmx +=1;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(k1=1; k1<=j;k1++){        } /* end of wave */
    for(i1=1; i1<=ncodemax[k1];i1++){      } /* end of individual */
        j1++;    } /* End of if */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          scanf("%d", i);*/    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for (i=-1; i<=nlstate+ndeath; i++)      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      return -l;
            for(m=agemin; m <= agemax+3; m++)  }
              freq[i][jk][m]=0;  
   
         dateintsum=0;  /*********** Maximum Likelihood Estimation ***************/
         k2cpt=0;  
        for (i=1; i<=imx; i++) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
          bool=1;  {
          if  (cptcovn>0) {    int i,j, iter;
            for (z1=1; z1<=cptcoveff; z1++)    double **xi;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double fret;
                bool=0;    char filerespow[FILENAMELENGTH];
          }    xi=matrix(1,npar,1,npar);
          if (bool==1) {    for (i=1;i<=npar;i++)
            for(m=firstpass; m<=lastpass; m++){      for (j=1;j<=npar;j++)
              k2=anint[m][i]+(mint[m][i]/12.);        xi[i][j]=(i==j ? 1.0 : 0.0);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
                if(agev[m][i]==0) agev[m][i]=agemax+1;    strcpy(filerespow,"pow"); 
                if(agev[m][i]==1) agev[m][i]=agemax+2;    strcat(filerespow,fileres);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      printf("Problem with resultfile: %s\n", filerespow);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                  dateintsum=dateintsum+k2;    }
                  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);
        }  
            fclose(ficrespow);
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         if  (cptcovn>0) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
        fprintf(ficresp, "**********\n#");  
         }  /**** Computes Hessian and covariance matrix ***/
        for(i=1; i<=nlstate;i++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
        fprintf(ficresp, "\n");    double  **a,**y,*x,pd;
            double **hess;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    int i, j,jk;
     if(i==(int)agemax+3)    int *indx;
       printf("Total");  
     else    double hessii(double p[], double delta, int theta, double delti[]);
       printf("Age %d", i);    double hessij(double p[], double delti[], int i, int j);
     for(jk=1; jk <=nlstate ; jk++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
         pp[jk] += freq[jk][m][i];  
     }    hess=matrix(1,npar,1,npar);
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)    printf("\nCalculation of the hessian matrix. Wait...\n");
         pos += freq[jk][m][i];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       if(pp[jk]>=1.e-10)    for (i=1;i<=npar;i++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      printf("%d",i);fflush(stdout);
       else      fprintf(ficlog,"%d",i);fflush(ficlog);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      hess[i][i]=hessii(p,ftolhess,i,delti);
     }      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
      for(jk=1; jk <=nlstate ; jk++){    }
       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++)  {
         if (j>i) { 
     for(jk=1,pos=0; jk <=nlstate ; jk++)          printf(".%d%d",i,j);fflush(stdout);
       pos += pp[jk];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     for(jk=1; jk <=nlstate ; jk++){          hess[i][j]=hessij(p,delti,i,j);
       if(pos>=1.e-5)          hess[j][i]=hess[i][j];    
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          /*printf(" %lf ",hess[i][j]);*/
       else        }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
       if( i <= (int) agemax){    }
         if(pos>=1.e-5){    printf("\n");
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    fprintf(ficlog,"\n");
           probs[i][jk][j1]= pp[jk]/pos;  
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       else    
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
     for(jk=-1; jk <=nlstate+ndeath; jk++)    indx=ivector(1,npar);
       for(m=-1; m <=nlstate+ndeath; m++)    for (i=1;i<=npar;i++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     if(i <= (int) agemax)    ludcmp(a,npar,indx,&pd);
       fprintf(ficresp,"\n");  
     printf("\n");    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
     }      x[j]=1;
  }      lubksb(a,npar,indx,x);
   dateintmean=dateintsum/k2cpt;      for (i=1;i<=npar;i++){ 
          matcov[i][j]=x[i];
   fclose(ficresp);      }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }
   free_vector(pp,1,nlstate);  
     printf("\n#Hessian matrix#\n");
   /* End of Freq */    fprintf(ficlog,"\n#Hessian matrix#\n");
 }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 /************ Prevalence ********************/        printf("%.3e ",hess[i][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)        fprintf(ficlog,"%.3e ",hess[i][j]);
 {  /* Some frequencies */      }
        printf("\n");
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      fprintf(ficlog,"\n");
   double ***freq; /* Frequencies */    }
   double *pp;  
   double pos, k2;    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
   pp=vector(1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    ludcmp(a,npar,indx,&pd);
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /*  printf("\n#Hessian matrix recomputed#\n");
   j1=0;  
      for (j=1;j<=npar;j++) {
   j=cptcoveff;      for (i=1;i<=npar;i++) x[i]=0;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      x[j]=1;
        lubksb(a,npar,indx,x);
  for(k1=1; k1<=j;k1++){      for (i=1;i<=npar;i++){ 
     for(i1=1; i1<=ncodemax[k1];i1++){        y[i][j]=x[i];
       j1++;        printf("%.3e ",y[i][j]);
          fprintf(ficlog,"%.3e ",y[i][j]);
       for (i=-1; i<=nlstate+ndeath; i++)        }
         for (jk=-1; jk<=nlstate+ndeath; jk++)        printf("\n");
           for(m=agemin; m <= agemax+3; m++)      fprintf(ficlog,"\n");
             freq[i][jk][m]=0;    }
          */
       for (i=1; i<=imx; i++) {  
         bool=1;    free_matrix(a,1,npar,1,npar);
         if  (cptcovn>0) {    free_matrix(y,1,npar,1,npar);
           for (z1=1; z1<=cptcoveff; z1++)    free_vector(x,1,npar);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    free_ivector(indx,1,npar);
               bool=0;    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)) {  /*************** hessian matrix ****************/
               if(agev[m][i]==0) agev[m][i]=agemax+1;  double hessii( double x[], double delta, int theta, double delti[])
               if(agev[m][i]==1) agev[m][i]=agemax+2;  {
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    int i;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    int l=1, lmax=20;
             }    double k1,k2;
           }    double p2[NPARMAX+1];
         }    double res;
       }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         for(i=(int)agemin; i <= (int)agemax+3; i++){    double fx;
           for(jk=1; jk <=nlstate ; jk++){    int k=0,kmax=10;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double l1;
               pp[jk] += freq[jk][m][i];  
           }    fx=func(x);
           for(jk=1; jk <=nlstate ; jk++){    for (i=1;i<=npar;i++) p2[i]=x[i];
             for(m=-1, pos=0; m <=0 ; m++)    for(l=0 ; l <=lmax; l++){
             pos += freq[jk][m][i];      l1=pow(10,l);
         }      delts=delt;
              for(k=1 ; k <kmax; k=k+1){
          for(jk=1; jk <=nlstate ; jk++){        delt = delta*(l1*k);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        p2[theta]=x[theta] +delt;
              pp[jk] += freq[jk][m][i];        k1=func(p2)-fx;
          }        p2[theta]=x[theta]-delt;
                  k2=func(p2)-fx;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          for(jk=1; jk <=nlstate ; jk++){                  
            if( i <= (int) agemax){  #ifdef DEBUG
              if(pos>=1.e-5){        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);
                probs[i][jk][j1]= pp[jk]/pos;        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.;
          }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          delts=delt;
   free_vector(pp,1,nlstate);        }
        }
 }  /* End of Freq */    }
     delti[theta]=delts;
 /************* Waves Concatenation ***************/    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.  double hessij( double x[], double delti[], int thetai,int thetaj)
      Death is a valid wave (if date is known).  {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    int i;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int l=1, l1, lmax=20;
      and mw[mi+1][i]. dh depends on stepm.    double k1,k2,k3,k4,res,fx;
      */    double p2[NPARMAX+1];
     int k;
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    fx=func(x);
      double sum=0., jmean=0.;*/    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   int j, k=0,jk, ju, jl;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double sum=0.;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   jmin=1e+5;      k1=func(p2)-fx;
   jmax=-1;    
   jmean=0.;      p2[thetai]=x[thetai]+delti[thetai]/k;
   for(i=1; i<=imx; i++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     mi=0;      k2=func(p2)-fx;
     m=firstpass;    
     while(s[m][i] <= nlstate){      p2[thetai]=x[thetai]-delti[thetai]/k;
       if(s[m][i]>=1)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         mw[++mi][i]=m;      k3=func(p2)-fx;
       if(m >=lastpass)    
         break;      p2[thetai]=x[thetai]-delti[thetai]/k;
       else      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         m++;      k4=func(p2)-fx;
     }/* end while */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     if (s[m][i] > nlstate){  #ifdef DEBUG
       mi++;     /* Death is another wave */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       /* if(mi==0)  never been interviewed correctly before death */      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);
          /* Only death is a correct wave */  #endif
       mw[mi][i]=m;    }
     }    return res;
   }
     wav[i]=mi;  
     if(mi==0)  /************** Inverse of matrix **************/
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
     int i,imax,j,k; 
   for(i=1; i<=imx; i++){    double big,dum,sum,temp; 
     for(mi=1; mi<wav[i];mi++){    double *vv; 
       if (stepm <=0)   
         dh[mi][i]=1;    vv=vector(1,n); 
       else{    *d=1.0; 
         if (s[mw[mi+1][i]][i] > nlstate) {    for (i=1;i<=n;i++) { 
           if (agedc[i] < 2*AGESUP) {      big=0.0; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for (j=1;j<=n;j++) 
           if(j==0) j=1;  /* Survives at least one month after exam */        if ((temp=fabs(a[i][j])) > big) big=temp; 
           k=k+1;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           if (j >= jmax) jmax=j;      vv[i]=1.0/big; 
           if (j <= jmin) jmin=j;    } 
           sum=sum+j;    for (j=1;j<=n;j++) { 
           /* if (j<10) printf("j=%d num=%d ",j,i); */      for (i=1;i<j;i++) { 
           }        sum=a[i][j]; 
         }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         else{        a[i][j]=sum; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      } 
           k=k+1;      big=0.0; 
           if (j >= jmax) jmax=j;      for (i=j;i<=n;i++) { 
           else if (j <= jmin)jmin=j;        sum=a[i][j]; 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        for (k=1;k<j;k++) 
           sum=sum+j;          sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
         jk= j/stepm;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         jl= j -jk*stepm;          big=dum; 
         ju= j -(jk+1)*stepm;          imax=i; 
         if(jl <= -ju)        } 
           dh[mi][i]=jk;      } 
         else      if (j != imax) { 
           dh[mi][i]=jk+1;        for (k=1;k<=n;k++) { 
         if(dh[mi][i]==0)          dum=a[imax][k]; 
           dh[mi][i]=1; /* At least one step */          a[imax][k]=a[j][k]; 
       }          a[j][k]=dum; 
     }        } 
   }        *d = -(*d); 
   jmean=sum/k;        vv[imax]=vv[j]; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      } 
  }      indx[j]=imax; 
 /*********** Tricode ****************************/      if (a[j][j] == 0.0) a[j][j]=TINY; 
 void tricode(int *Tvar, int **nbcode, int imx)      if (j != n) { 
 {        dum=1.0/(a[j][j]); 
   int Ndum[20],ij=1, k, j, i;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   int cptcode=0;      } 
   cptcoveff=0;    } 
      free_vector(vv,1,n);  /* Doesn't work */
   for (k=0; k<19; k++) Ndum[k]=0;  ;
   for (k=1; k<=7; k++) ncodemax[k]=0;  } 
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  void lubksb(double **a, int n, int *indx, double b[]) 
     for (i=1; i<=imx; i++) {  { 
       ij=(int)(covar[Tvar[j]][i]);    int i,ii=0,ip,j; 
       Ndum[ij]++;    double sum; 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/   
       if (ij > cptcode) cptcode=ij;    for (i=1;i<=n;i++) { 
     }      ip=indx[i]; 
       sum=b[ip]; 
     for (i=0; i<=cptcode; i++) {      b[ip]=b[i]; 
       if(Ndum[i]!=0) ncodemax[j]++;      if (ii) 
     }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     ij=1;      else if (sum) ii=i; 
       b[i]=sum; 
     } 
     for (i=1; i<=ncodemax[j]; i++) {    for (i=n;i>=1;i--) { 
       for (k=0; k<=19; k++) {      sum=b[i]; 
         if (Ndum[k] != 0) {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           nbcode[Tvar[j]][ij]=k;      b[i]=sum/a[i][i]; 
           ij++;    } 
         }  } 
         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;
     int first;
  for (i=1; i<=ncovmodel-2; i++) {    double ***freq; /* Frequencies */
       ij=Tvar[i];    double *pp, **prop;
       Ndum[ij]++;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     }    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
  ij=1;    
  for (i=1; i<=10; i++) {    pp=vector(1,nlstate);
    if((Ndum[i]!=0) && (i<=ncov)){    prop=matrix(1,nlstate,iagemin,iagemax+3);
      Tvaraff[ij]=i;    strcpy(fileresp,"p");
      ij++;    strcat(fileresp,fileres);
    }    if((ficresp=fopen(fileresp,"w"))==NULL) {
  }      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     cptcoveff=ij-1;      exit(0);
 }    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
 /*********** Health Expectancies ****************/    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;
 {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;    first=1;
   double age, agelim,hf;  
   double ***p3mat;    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficreseij,"# Health expectancies\n");        j1++;
   fprintf(ficreseij,"# Age");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   for(i=1; i<=nlstate;i++)          scanf("%d", i);*/
     for(j=1; j<=nlstate;j++)        for (i=-1; i<=nlstate+ndeath; i++)  
       fprintf(ficreseij," %1d-%1d",i,j);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   fprintf(ficreseij,"\n");            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
   agelim=AGESUP;          prop[i][m]=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     /* nhstepm age range expressed in number of stepm */        dateintsum=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        k2cpt=0;
     /* Typically if 20 years = 20*12/6=40 stepm */        for (i=1; i<=imx; i++) {
     if (stepm >= YEARM) 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);            }
           if (bool==1){
             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] +=(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];
                 }
     for(i=1; i<=nlstate;i++)                
       for(j=1; j<=nlstate;j++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         if (j==i) eij[i][j][(int)age]= (eij[i][j][(int)age]-0.5*stepm/12./hf);                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
                 }
     fprintf(ficreseij,"%3.0f",age );              }
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          }
         fprintf(ficreseij," %9.4f", hf*eij[i][j][(int)age]);        }
       }         
     fprintf(ficreseij,"\n");        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }        if  (cptcovn>0) {
 }          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 /************ Variance ******************/          fprintf(ficresp, "**********\n#");
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        }
 {        for(i=1; i<=nlstate;i++) 
   /* Variance of health expectancies */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /*  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=iagemin; i <= iagemax+3; i++){
   int i, j, nhstepm, hstepm, h;          if(i==iagemax+3){
   int k, cptcode;            fprintf(ficlog,"Total");
   double *xp;          }else{
   double **gp, **gm;            if(first==1){
   double ***gradg, ***trgradg;              first=0;
   double ***p3mat;              printf("See log file for details...\n");
   double age,agelim;            }
   int theta;            fprintf(ficlog,"Age %d", i);
           }
    fprintf(ficresvij,"# Covariances of life expectancies\n");          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresvij,"# Age");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for(i=1; i<=nlstate;i++)              pp[jk] += freq[jk][m][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, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   xp=vector(1,npar);            if(pp[jk]>=1.e-10){
   dnewm=matrix(1,nlstate,1,npar);              if(first==1){
   doldm=matrix(1,nlstate,1,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }
   hstepm=1*YEARM; /* Every year of age */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }else{
   agelim = AGESUP;              if(first==1)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
     gp=matrix(0,nhstepm,1,nlstate);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     gm=matrix(0,nhstepm,1,nlstate);              pp[jk] += freq[jk][m][i];
           }       
     for(theta=1; theta <=npar; theta++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       for(i=1; i<=npar; i++){ /* Computes gradient */            pos += pp[jk];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            posprop += prop[jk][i];
       }          }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(jk=1; jk <=nlstate ; jk++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            if(pos>=1.e-5){
               if(first==1)
       if (popbased==1) {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           prlim[i][i]=probs[(int)age][i][ij];            }else{
       }              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<= nlstate; j++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            if( i <= iagemax){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              if(pos>=1.e-5){
         }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       }                probs[i][jk][j1]= pp[jk]/pos;
                    /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for(i=1; i<=npar; i++) /* Computes gradient */              }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              else
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
            }
       if (popbased==1) {          
         for(i=1; i<=nlstate;i++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
           prlim[i][i]=probs[(int)age][i][ij];            for(m=-1; m <=nlstate+ndeath; m++)
       }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
       for(j=1; j<= nlstate; j++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(h=0; h<=nhstepm; h++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          if(i <= iagemax)
         }            fprintf(ficresp,"\n");
       }          if(first==1)
             printf("Others in log...\n");
       for(j=1; j<= nlstate; j++)          fprintf(ficlog,"\n");
         for(h=0; h<=nhstepm; h++){        }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      }
         }    }
     } /* End theta */    dateintmean=dateintsum/k2cpt; 
    
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     for(h=0; h<=nhstepm; h++)    free_vector(pp,1,nlstate);
       for(j=1; j<=nlstate;j++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         for(theta=1; theta <=npar; theta++)    /* End of Freq */
           trgradg[h][j][theta]=gradg[h][theta][j];  }
   
     for(i=1;i<=nlstate;i++)  /************ Prevalence ********************/
       for(j=1;j<=nlstate;j++)  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)
         vareij[i][j][(int)age] =0.;  {  
     for(h=0;h<=nhstepm;h++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       for(k=0;k<=nhstepm;k++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);       We still use firstpass and lastpass as another selection.
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    */
         for(i=1;i<=nlstate;i++)   
           for(j=1;j<=nlstate;j++)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
             vareij[i][j][(int)age] += doldm[i][j];    double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop; 
     h=1;    double  y2; /* in fractional years */
     if (stepm >= YEARM) h=stepm/YEARM;    int iagemin, iagemax;
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    iagemin= (int) agemin;
       for(j=1; j<=nlstate;j++){    iagemax= (int) agemax;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    /*pp=vector(1,nlstate);*/
       }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     fprintf(ficresvij,"\n");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     free_matrix(gp,0,nhstepm,1,nlstate);    j1=0;
     free_matrix(gm,0,nhstepm,1,nlstate);    
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    j=cptcoveff;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
   } /* End age */    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   free_vector(xp,1,npar);        j1++;
   free_matrix(doldm,1,nlstate,1,npar);        
   free_matrix(dnewm,1,nlstate,1,nlstate);        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
 }            prop[i][m]=0.0;
        
 /************ Variance of prevlim ******************/        for (i=1; i<=imx; i++) { /* Each individual */
 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)          bool=1;
 {          if  (cptcovn>0) {
   /* Variance of prevalence limit */            for (z1=1; z1<=cptcoveff; z1++) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double **newm;                bool=0;
   double **dnewm,**doldm;          } 
   int i, j, nhstepm, hstepm;          if (bool==1) { 
   int k, cptcode;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   double *xp;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   double *gp, *gm;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   double **gradg, **trgradg;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double age,agelim;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   int theta;                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); 
                    if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\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]]);*/
   fprintf(ficresvpl,"# Age");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   for(i=1; i<=nlstate;i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficresvpl," %1d-%1d",i,i);                } 
   fprintf(ficresvpl,"\n");              }
             } /* end selection of waves */
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);        for(i=iagemin; i <= iagemax+3; i++){  
            
   hstepm=1*YEARM; /* Every year of age */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            posprop += prop[jk][i]; 
   agelim = AGESUP;          } 
   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; jk <=nlstate ; jk++){     
     if (stepm >= YEARM) hstepm=1;            if( i <=  iagemax){ 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              if(posprop>=1.e-5){ 
     gradg=matrix(1,npar,1,nlstate);                probs[i][jk][j1]= prop[jk][i]/posprop;
     gp=vector(1,nlstate);              } 
     gm=vector(1,nlstate);            } 
           }/* end jk */ 
     for(theta=1; theta <=npar; theta++){        }/* end i */ 
       for(i=1; i<=npar; i++){ /* Computes gradient */      } /* end i1 */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } /* end k1 */
       }    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       for(i=1;i<=nlstate;i++)    /*free_vector(pp,1,nlstate);*/
         gp[i] = prlim[i][i];    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      }  /* End of prevalence */
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /************* Waves Concatenation ***************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  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)
         gm[i] = prlim[i][i];  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for(i=1;i<=nlstate;i++)       Death is a valid wave (if date is known).
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     } /* End theta */       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     trgradg =matrix(1,nlstate,1,npar);       */
   
     for(j=1; j<=nlstate;j++)    int i, mi, m;
       for(theta=1; theta <=npar; theta++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         trgradg[j][theta]=gradg[theta][j];       double sum=0., jmean=0.;*/
     int first;
     for(i=1;i<=nlstate;i++)    int j, k=0,jk, ju, jl;
       varpl[i][(int)age] =0.;    double sum=0.;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    first=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    jmin=1e+5;
     for(i=1;i<=nlstate;i++)    jmax=-1;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    jmean=0.;
     for(i=1; i<=imx; i++){
     fprintf(ficresvpl,"%.0f ",age );      mi=0;
     for(i=1; i<=nlstate;i++)      m=firstpass;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      while(s[m][i] <= nlstate){
     fprintf(ficresvpl,"\n");        if(s[m][i]>=1)
     free_vector(gp,1,nlstate);          mw[++mi][i]=m;
     free_vector(gm,1,nlstate);        if(m >=lastpass)
     free_matrix(gradg,1,npar,1,nlstate);          break;
     free_matrix(trgradg,1,nlstate,1,npar);        else
   } /* End age */          m++;
       }/* end while */
   free_vector(xp,1,npar);      if (s[m][i] > nlstate){
   free_matrix(doldm,1,nlstate,1,npar);        mi++;     /* Death is another wave */
   free_matrix(dnewm,1,nlstate,1,nlstate);        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
 }        mw[mi][i]=m;
       }
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      wav[i]=mi;
 {      if(mi==0){
   int i, j;        if(first==0){
   int k=0, cptcode;          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
   double **dnewm,**doldm;          first=1;
   double *xp;        }
   double *gp, *gm;        if(first==1){
   double **gradg, **trgradg;          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   double age,agelim, cov[NCOVMAX];        }
   int theta;      } /* end mi==0 */
   char fileresprob[FILENAMELENGTH];    } /* End individuals */
   
   strcpy(fileresprob,"prob");    for(i=1; i<=imx; i++){
   strcat(fileresprob,fileres);      for(mi=1; mi<wav[i];mi++){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        if (stepm <=0)
     printf("Problem with resultfile: %s\n", fileresprob);          dh[mi][i]=1;
   }        else{
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   xp=vector(1,npar);            if(j==0) j=1;  /* Survives at least one month after exam */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            k=k+1;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            if (j >= jmax) jmax=j;
              if (j <= jmin) jmin=j;
   cov[1]=1;            sum=sum+j;
   for (age=bage; age<=fage; age ++){            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     cov[2]=age;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     gradg=matrix(1,npar,1,9);            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]);
     trgradg=matrix(1,9,1,npar);            }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          else{
                j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for(theta=1; theta <=npar; theta++){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for(i=1; i<=npar; i++)            k=k+1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (j >= jmax) jmax=j;
                  else if (j <= jmin)jmin=j;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                /*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]);*/
       k=0;            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]);
       for(i=1; i<= (nlstate+ndeath); i++){            sum=sum+j;
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;          jk= j/stepm;
           gp[k]=pmmij[i][j];          jl= j -jk*stepm;
         }          ju= j -(jk+1)*stepm;
       }          if(mle <=1){ 
             if(jl==0){
       for(i=1; i<=npar; i++)              dh[mi][i]=jk;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              bh[mi][i]=0;
                }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              dh[mi][i]=jk+1;
       k=0;              bh[mi][i]=ju;
       for(i=1; i<=(nlstate+ndeath); i++){            }
         for(j=1; j<=(nlstate+ndeath);j++){          }else{
           k=k+1;            if(jl <= -ju){
           gm[k]=pmmij[i][j];              dh[mi][i]=jk;
         }              bh[mi][i]=jl;       /* bias is positive if real duration
       }                                   * is higher than the multiple of stepm and negative otherwise.
                                         */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              else{
     }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            }
       for(theta=1; theta <=npar; theta++)            if(dh[mi][i]==0){
       trgradg[j][theta]=gradg[theta][j];              dh[mi][i]=1; /* At least one step */
                bh[mi][i]=ju; /* At least one step */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            }
           }
      pmij(pmmij,cov,ncovmodel,x,nlstate);        } /* end if mle */
       } /* end wave */
      k=0;    }
      for(i=1; i<=(nlstate+ndeath); i++){    jmean=sum/k;
        for(j=1; j<=(nlstate+ndeath);j++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
          k=k+1;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
          gm[k]=pmmij[i][j];   }
         }  
      }  /*********** Tricode ****************************/
        void tricode(int *Tvar, int **nbcode, int imx)
      /*printf("\n%d ",(int)age);  {
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    
            int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    cptcoveff=0; 
      }*/   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   fprintf(ficresprob,"\n%d ",(int)age);    for (k=1; k<=7; k++) ncodemax[k]=0;
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                                 modality*/ 
   }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                                         Tvar[j]. If V=sex and male is 0 and 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                                         female is 1, then  cptcode=1.*/
 }      }
  free_vector(xp,1,npar);  
 fclose(ficresprob);      for (i=0; i<=cptcode; i++) {
         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 */
 }      }
   
 /******************* Printing html file ***********/      ij=1; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){      for (i=1; i<=ncodemax[j]; i++) {
   int jj1, k1, i1, cpt;        for (k=0; k<= maxncov; k++) {
   FILE *fichtm;          if (Ndum[k] != 0) {
   /*char optionfilehtm[FILENAMELENGTH];*/            nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   strcpy(optionfilehtm,optionfile);            
   strcat(optionfilehtm,".htm");            ij++;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          }
     printf("Problem with %s \n",optionfilehtm), exit(0);          if (ij > ncodemax[j]) break; 
   }        }  
       } 
  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>  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>   for (i=1; i<=ncovmodel-2; i++) { 
 <hr  size=\"2\" color=\"#EC5E5E\">     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 <li>Outputs files<br><br>\n     ij=Tvar[i];
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n     Ndum[ij]++;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>   }
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>   ij=1;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>   for (i=1; i<= maxncov; i++) {
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>     if((Ndum[i]!=0) && (i<=ncovcol)){
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>       Tvaraff[ij]=i; /*For printing */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>       ij++;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>     }
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>   }
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>   
         <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);   cptcoveff=ij-1; /*Number of simple covariates*/
    }
 fprintf(fichtm," <li>Graphs</li><p>");  
   /*********** Health Expectancies ****************/
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  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=0;  {
  for(k1=1; k1<=m;k1++){    /* Health expectancies */
    for(i1=1; i1<=ncodemax[k1];i1++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        jj1++;    double age, agelim, hf;
        if (cptcovn > 0) {    double ***p3mat,***varhe;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double **dnewm,**doldm;
          for (cpt=1; cpt<=cptcoveff;cpt++)    double *xp;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double **gp, **gm;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double ***gradg, ***trgradg;
        }    int theta;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),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>- Prevalence of disability : p%s%d%d.gif<br>    dnewm=matrix(1,nlstate*nlstate,1,npar);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        }    
     for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficreseij,"# Health expectancies\n");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    fprintf(ficreseij,"# Age");
 interval) in state (%d): v%s%d%d.gif <br>    for(i=1; i<=nlstate;i++)
 <img src=\"v%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);
      for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficreseij,"\n");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if(estepm < stepm){
      }      printf ("Problem %d lower than %d\n",estepm, stepm);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    }
 health expectancies in states (1) and (2): e%s%d.gif<br>    else  hstepm=estepm;   
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /* We compute the life expectancy from trapezoids spaced every estepm months
 fprintf(fichtm,"\n</body>");     * This is mainly to measure the difference between two models: for example
    }     * if stepm=24 months pijx are given only every 2 years and by summing them
    }     * we are calculating an estimate of the Life Expectancy assuming a linear 
 fclose(fichtm);     * progression in between and thus overestimating or underestimating according
 }     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
 /******************* Gnuplot file **************/     * to compare the new estimate of Life expectancy with the same linear 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
     /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(optionfilegnuplot,optionfilefiname);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(optionfilegnuplot,".plt");       nhstepm is the number of hstepm from age to agelim 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with file %s",optionfilegnuplot);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 #ifdef windows       survival function given by stepm (the optimization length). Unfortunately it
     fprintf(ficgp,"cd \"%s\" \n",pathc);       means that if the survival funtion is printed only each two years of age and if
 #endif       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 m=pow(2,cptcoveff);       results. So we changed our mind and took the option of the best precision.
      */
  /* 1eme*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #ifdef windows      /* nhstepm age range expressed in number of stepm */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 #endif      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 #ifdef unix      /* if (stepm >= YEARM) hstepm=1;*/
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 #endif      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 for (i=1; i<= nlstate ; i ++) {      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     for (i=1; i<= nlstate ; i ++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {      /* Computing Variances of health expectancies */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");       for(theta=1; theta <=npar; theta++){
 }          for(i=1; i<=npar; i++){ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #ifdef unix        }
 fprintf(ficgp,"\nset ter gif small size 400,300");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #endif    
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        cptj=0;
    }        for(j=1; j<= nlstate; j++){
   }          for(i=1; i<=nlstate; i++){
   /*2 eme*/            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   for (k1=1; k1<= m ; k1 ++) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            }
              }
     for (i=1; i<= nlstate+1 ; i ++) {        }
       k=2*i;       
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1; i<=npar; i++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 }          
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        cptj=0;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(i=1;i<=nlstate;i++){
       for (j=1; j<= nlstate+1 ; j ++) {            cptj=cptj+1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       fprintf(ficgp,"\" t\"\" w l 0,");            }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<= nlstate*nlstate; j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(h=0; h<=nhstepm-1; h++){
 }              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          }
       else fprintf(ficgp,"\" t\"\" w l 0,");       } 
     }     
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  /* End theta */
   }  
         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   /*3eme*/  
        for(h=0; h<=nhstepm-1; h++)
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<=nlstate*nlstate;j++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(theta=1; theta <=npar; theta++)
       k=2+nlstate*(cpt-1);            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);       
       for (i=1; i< nlstate ; i ++) {  
         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(i=1;i<=nlstate*nlstate;i++)
       }        for(j=1;j<=nlstate*nlstate;j++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          varhe[i][j][(int)age] =0.;
     }  
     }       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   /* CV preval stat */       for(h=0;h<=nhstepm-1;h++){
     for (k1=1; k1<= m ; k1 ++) {        for(k=0;k<=nhstepm-1;k++){
     for (cpt=1; cpt<nlstate ; cpt ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       k=3;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
       for (i=1; i< nlstate ; i ++)              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         fprintf(ficgp,"+$%d",k+i+1);        }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      }
            /* Computing expectancies */
       l=3+(nlstate+ndeath)*cpt;      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=1; j<=nlstate;j++)
       for (i=1; i< nlstate ; i ++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         l=3+(nlstate+ndeath)*cpt;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         fprintf(ficgp,"+$%d",l+i+1);            
       }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }  
   }        fprintf(ficreseij,"%3.0f",age );
        cptj=0;
   /* proba elementaires */      for(i=1; i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j<=nlstate;j++){
     for(k=1; k <=(nlstate+ndeath); k++){          cptj++;
       if (k != i) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         for(j=1; j <=ncovmodel; j++){        }
              fprintf(ficreseij,"\n");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);     
           jk++;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficgp,"\n");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    }
     printf("\n");
     for(jk=1; jk <=m; jk++) {    fprintf(ficlog,"\n");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);  
    i=1;    free_vector(xp,1,npar);
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      k3=i;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      for(k=1; k<=(nlstate+ndeath); k++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
        if (k != k2){  }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;  /************ Variance ******************/
         for(j=3; j <=ncovmodel; j++) {  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
           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]]]);    /* Variance of health expectancies */
             ij++;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           }    /* double **newm;*/
           else    double **dnewm,**doldm;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
           fprintf(ficgp,")/(1");    int k, cptcode;
            double *xp;
         for(k1=1; k1 <=nlstate; k1++){      double **gp, **gm;  /* for var eij */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double ***gradg, ***trgradg; /*for var eij */
 ij=1;    double **gradgp, **trgradgp; /* for var p point j */
           for(j=3; j <=ncovmodel; j++){    double *gpp, *gmp; /* for var p point j */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double ***p3mat;
             ij++;    double age,agelim, hf;
           }    double ***mobaverage;
           else    int theta;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    char digit[4];
           }    char digitp[25];
           fprintf(ficgp,")");  
         }    char fileresprobmorprev[FILENAMELENGTH];
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    if(popbased==1){
         i=i+ncovmodel;      if(mobilav!=0)
        }        strcpy(digitp,"-populbased-mobilav-");
      }      else strcpy(digitp,"-populbased-nomobil-");
    }    }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    else 
    }      strcpy(digitp,"-stablbased-");
      
   fclose(ficgp);    if (mobilav!=0) {
 }  /* end gnuplot */      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);
 /*************** Moving average **************/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){      }
     }
   int i, cpt, cptcod;  
     for (agedeb=agemin; agedeb<=fage; agedeb++)    strcpy(fileresprobmorprev,"prmorprev"); 
       for (i=1; i<=nlstate;i++)    sprintf(digit,"%-d",ij);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           mobaverage[(int)agedeb][i][cptcod]=0.;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
        strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    strcat(fileresprobmorprev,fileres);
       for (i=1; i<=nlstate;i++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           for (cpt=0;cpt<=4;cpt++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    }
           }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    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++){
          fprintf(ficresprobmorprev," p.%-d SE",j);
 }      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
 /************** Forecasting ******************/    fprintf(ficresprobmorprev,"\n");
 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){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   int *popage;      exit(0);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    }
   double *popeffectif,*popcount;    else{
   double ***p3mat;      fprintf(ficgp,"\n# Routine varevsij");
   char fileresf[FILENAMELENGTH];    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
  agelim=AGESUP;      printf("Problem with html file: %s\n", optionfilehtm);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
       exit(0);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }
      else{
        fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   strcpy(fileresf,"f");      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   strcat(fileresf,fileres);    }
   if((ficresf=fopen(fileresf,"w"))==NULL) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("Problem with forecast resultfile: %s\n", fileresf);  
   }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   if (mobilav==1) {    fprintf(ficresvij,"\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, agemin, mobaverage);    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   if (stepm<=12) stepsize=1;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
   agelim=AGESUP;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
   hstepm=1;    gmp=vector(nlstate+1,nlstate+ndeath);
   hstepm=hstepm/stepm;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   yp1=modf(dateintmean,&yp);    
   anprojmean=yp;    if(estepm < stepm){
   yp2=modf((yp1*12),&yp);      printf ("Problem %d lower than %d\n",estepm, stepm);
   mprojmean=yp;    }
   yp1=modf((yp2*30.5),&yp);    else  hstepm=estepm;   
   jprojmean=yp;    /* For example we decided to compute the life expectancy with the smallest unit */
   if(jprojmean==0) jprojmean=1;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if(mprojmean==0) jprojmean=1;       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like k years */
   for(cptcov=1;cptcov<=i2;cptcov++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       survival function given by stepm (the optimization length). Unfortunately it
       k=k+1;       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 
       for(j=1;j<=cptcoveff;j++) {       results. So we changed our mind and took the option of the best precision.
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficresf,"******\n");    agelim = AGESUP;
       fprintf(ficresf,"# StartingAge FinalAge");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
            nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         fprintf(ficresf,"\n");      gp=matrix(0,nhstepm,1,nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        gm=matrix(0,nhstepm,1,nlstate);
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(theta=1; theta <=npar; theta++){
           nhstepm = nhstepm/hstepm;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                    xp[i] = x[i] + (i==theta ?delti[theta]:0);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          
           for (h=0; h<=nhstepm; h++){        if (popbased==1) {
             if (h==(int) (calagedate+YEARM*cpt)) {          if(mobilav ==0){
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            for(i=1; i<=nlstate;i++)
             }              prlim[i][i]=probs[(int)age][i][ij];
             for(j=1; j<=nlstate+ndeath;j++) {          }else{ /* mobilav */ 
               kk1=0.;kk2=0;            for(i=1; i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                            prlim[i][i]=mobaverage[(int)age][i][ij];
                 if (mobilav==1)          }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        }
                 else {    
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        for(j=1; j<= nlstate; j++){
                 }          for(h=0; h<=nhstepm; h++){
                            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
               if (h==(int)(calagedate+12*cpt)){          }
                 fprintf(ficresf," %.3f", kk1);        }
                                /* This for computing probability of death (h=1 means
               }           computed over hstepm matrices product = hstepm*stepm months) 
             }           as a weighted average of prlim.
           }        */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
   }        /* end probability of death */
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fclose(ficresf);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 /************** Forecasting ******************/   
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        if (popbased==1) {
            if(mobilav ==0){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            for(i=1; i<=nlstate;i++)
   int *popage;              prlim[i][i]=probs[(int)age][i][ij];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }else{ /* mobilav */ 
   double *popeffectif,*popcount;            for(i=1; i<=nlstate;i++)
   double ***p3mat,***tabpop,***tabpopprev;              prlim[i][i]=mobaverage[(int)age][i][ij];
   char filerespop[FILENAMELENGTH];          }
         }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<= nlstate; j++){
   agelim=AGESUP;          for(h=0; h<=nhstepm; h++){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          }
          }
          /* This for computing probability of death (h=1 means
   strcpy(filerespop,"pop");           computed over hstepm matrices product = hstepm*stepm months) 
   strcat(filerespop,fileres);           as a weighted average of prlim.
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        */
     printf("Problem with forecast resultfile: %s\n", filerespop);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        /* end probability of death */
   
   if (mobilav==1) {        for(j=1; j<= nlstate; j++) /* vareij */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(h=0; h<=nhstepm; h++){
     movingaverage(agedeb, fage, agemin, mobaverage);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   if (stepm<=12) stepsize=1;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   agelim=AGESUP;  
        } /* End theta */
   hstepm=1;  
   hstepm=hstepm/stepm;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   if (popforecast==1) {      for(h=0; h<=nhstepm; h++) /* veij */
     if((ficpop=fopen(popfile,"r"))==NULL) {        for(j=1; j<=nlstate;j++)
       printf("Problem with population file : %s\n",popfile);exit(0);          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     popcount=vector(0,AGESUP);        for(theta=1; theta <=npar; theta++)
              trgradgp[j][theta]=gradgp[theta][j];
     i=1;      
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     imx=i;      for(i=1;i<=nlstate;i++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(j=1;j<=nlstate;j++)
   }          vareij[i][j][(int)age] =0.;
   
   for(cptcov=1;cptcov<=i2;cptcov++){      for(h=0;h<=nhstepm;h++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(k=0;k<=nhstepm;k++){
       k=k+1;          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]);
       for(j=1;j<=cptcoveff;j++) {          for(i=1;i<=nlstate;i++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(j=1;j<=nlstate;j++)
       }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficrespop,"******\n");        }
       fprintf(ficrespop,"# Age");      }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    
       if (popforecast==1)  fprintf(ficrespop," [Population]");      /* pptj */
            matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       for (cpt=0; cpt<=0;cpt++) {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for(j=nlstate+1;j<=nlstate+ndeath;j++)
                for(i=nlstate+1;i<=nlstate+ndeath;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          varppt[j][i]=doldmp[j][i];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /* end ppptj */
           nhstepm = nhstepm/hstepm;      /*  x centered again */
                hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           oldm=oldms;savm=savms;   
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        if (popbased==1) {
                if(mobilav ==0){
           for (h=0; h<=nhstepm; h++){          for(i=1; i<=nlstate;i++)
             if (h==(int) (calagedate+YEARM*cpt)) {            prlim[i][i]=probs[(int)age][i][ij];
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        }else{ /* mobilav */ 
             }          for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                    }
                 if (mobilav==1)               
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      /* This for computing probability of death (h=1 means
                 else {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];         as a weighted average of prlim.
                 }      */
               }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
               if (h==(int)(calagedate+12*cpt)){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   /*fprintf(ficrespop," %.3f", kk1);      }    
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      /* end probability of death */
               }  
             }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             for(i=1; i<=nlstate;i++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
               kk1=0.;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                 for(j=1; j<=nlstate;j++){        for(i=1; i<=nlstate;i++){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      } 
             }      fprintf(ficresprobmorprev,"\n");
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      fprintf(ficresvij,"%.0f ",age );
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }        }
       }      fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
   /******/      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    } /* End age */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_vector(gpp,nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm;    free_vector(gmp,nlstate+1,nlstate+ndeath);
              free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           oldm=oldms;savm=savms;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
             if (h==(int) (calagedate+YEARM*cpt)) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
             }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
             for(j=1; j<=nlstate+ndeath;j++) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
               kk1=0.;kk2=0;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
               for(i=1; i<=nlstate;i++) {                  fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
               }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    /*  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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    free_vector(xp,1,npar);
       }    free_matrix(doldm,1,nlstate,1,nlstate);
    }    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if (popforecast==1) {    fclose(ficresprobmorprev);
     free_ivector(popage,0,AGESUP);    fclose(ficgp);
     free_vector(popeffectif,0,AGESUP);    fclose(fichtm);
     free_vector(popcount,0,AGESUP);  }  
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************ Variance of prevlim ******************/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   fclose(ficrespop);  {
 }    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 /***********************************************/    double **newm;
 /**************** Main Program *****************/    double **dnewm,**doldm;
 /***********************************************/    int i, j, nhstepm, hstepm;
     int k, cptcode;
 int main(int argc, char *argv[])    double *xp;
 {    double *gp, *gm;
     double **gradg, **trgradg;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    double age,agelim;
   double agedeb, agefin,hf;    int theta;
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   double fret;    fprintf(ficresvpl,"# Age");
   double **xi,tmp,delta;    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
   double dum; /* Dummy variable */    fprintf(ficresvpl,"\n");
   double ***p3mat;  
   int *indx;    xp=vector(1,npar);
   char line[MAXLINE], linepar[MAXLINE];    dnewm=matrix(1,nlstate,1,npar);
   char title[MAXLINE];    doldm=matrix(1,nlstate,1,nlstate);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    hstepm=1*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char filerest[FILENAMELENGTH];      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   char fileregp[FILENAMELENGTH];      if (stepm >= YEARM) hstepm=1;
   char popfile[FILENAMELENGTH];      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      gradg=matrix(1,npar,1,nlstate);
   int firstobs=1, lastobs=10;      gp=vector(1,nlstate);
   int sdeb, sfin; /* Status at beginning and end */      gm=vector(1,nlstate);
   int c,  h , cpt,l;  
   int ju,jl, mi;      for(theta=1; theta <=npar; theta++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        for(i=1; i<=npar; i++){ /* Computes gradient */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int mobilav=0,popforecast=0;        }
   int hstepm, nhstepm;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
   double bage, fage, age, agelim, agebase;      
   double ftolpl=FTOL;        for(i=1; i<=npar; i++) /* Computes gradient */
   double **prlim;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double *severity;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double ***param; /* Matrix of parameters */        for(i=1;i<=nlstate;i++)
   double  *p;          gm[i] = prlim[i][i];
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */        for(i=1;i<=nlstate;i++)
   double *delti; /* Scale */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   double ***eij, ***vareij;      } /* End theta */
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;      trgradg =matrix(1,nlstate,1,npar);
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   char z[1]="c", occ;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 #include <sys/time.h>      for(i=1;i<=nlstate;i++)
 #include <time.h>        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
        fprintf(ficresvpl,"%.0f ",age );
   /* long total_usecs;      for(i=1; i<=nlstate;i++)
   struct timeval start_time, end_time;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
   printf("\n%s",version);      free_matrix(trgradg,1,nlstate,1,npar);
   if(argc <=1){    } /* End age */
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,npar);
   else{    free_matrix(dnewm,1,nlstate,1,nlstate);
     strcpy(pathtot,argv[1]);  
   }  }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);  /************ Variance of one-step probabilities  ******************/
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   /* cutv(path,optionfile,pathtot,'\\');*/  {
     int i, j=0,  i1, k1, l1, t, tj;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    int k2, l2, j1,  z1;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    int k=0,l, cptcode;
   chdir(path);    int first=1, first1;
   replace(pathc,path);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
 /*-------- arguments in the command line --------*/    double *xp;
     double *gp, *gm;
   strcpy(fileres,"r");    double **gradg, **trgradg;
   strcat(fileres, optionfilefiname);    double **mu;
   strcat(fileres,".txt");    /* Other files have txt extension */    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   /*---------arguments file --------*/    int theta;
     char fileresprob[FILENAMELENGTH];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    char fileresprobcov[FILENAMELENGTH];
     printf("Problem with optionfile %s\n",optionfile);    char fileresprobcor[FILENAMELENGTH];
     goto end;  
   }    double ***varpij;
   
   strcpy(filereso,"o");    strcpy(fileresprob,"prob"); 
   strcat(filereso,fileres);    strcat(fileresprob,fileres);
   if((ficparo=fopen(filereso,"w"))==NULL) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      printf("Problem with resultfile: %s\n", fileresprob);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   /* Reads comments: lines beginning with '#' */    strcpy(fileresprobcov,"probcov"); 
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(fileresprobcov,fileres);
     ungetc(c,ficpar);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with resultfile: %s\n", fileresprobcov);
     puts(line);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     fputs(line,ficparo);    }
   }    strcpy(fileresprobcor,"probcor"); 
   ungetc(c,ficpar);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   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("Problem with resultfile: %s\n", fileresprobcor);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   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);    }
 while((c=getc(ficpar))=='#' && c!= EOF){    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     ungetc(c,ficpar);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fgets(line, MAXLINE, ficpar);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     puts(line);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fputs(line,ficparo);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   ungetc(c,ficpar);    
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
        fprintf(ficresprob,"# Age");
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   cptcovn=0;    fprintf(ficresprobcov,"# Age");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      for(i=1; i<=nlstate;i++)
   /* Read guess parameters */      for(j=1; j<=(nlstate+ndeath);j++){
   /* Reads comments: lines beginning with '#' */        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     ungetc(c,ficpar);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     fgets(line, MAXLINE, ficpar);      }  
     puts(line);   /* fprintf(ficresprob,"\n");
     fputs(line,ficparo);    fprintf(ficresprobcov,"\n");
   }    fprintf(ficresprobcor,"\n");
   ungetc(c,ficpar);   */
     xp=vector(1,npar);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     for(i=1; i <=nlstate; i++)    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     for(j=1; j <=nlstate+ndeath-1; j++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fprintf(ficparo,"%1d%1d",i1,j1);    first=1;
       printf("%1d%1d",i,j);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       for(k=1; k<=ncovmodel;k++){      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
         fscanf(ficpar," %lf",&param[i][j][k]);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
         printf(" %lf",param[i][j][k]);      exit(0);
         fprintf(ficparo," %lf",param[i][j][k]);    }
       }    else{
       fscanf(ficpar,"\n");      fprintf(ficgp,"\n# Routine varprob");
       printf("\n");    }
       fprintf(ficparo,"\n");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     }      printf("Problem with html file: %s\n", optionfilehtm);
        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      exit(0);
     }
   p=param[1][1];    else{
        fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   /* Reads comments: lines beginning with '#' */      fprintf(fichtm,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     fgets(line, MAXLINE, 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");
     puts(line);      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");
     fputs(line,ficparo);  
   }    }
   ungetc(c,ficpar);  
     cov[1]=1;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    tj=cptcoveff;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   for(i=1; i <=nlstate; i++){    j1=0;
     for(j=1; j <=nlstate+ndeath-1; j++){    for(t=1; t<=tj;t++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(i1=1; i1<=ncodemax[t];i1++){ 
       printf("%1d%1d",i,j);        j1++;
       fprintf(ficparo,"%1d%1d",i1,j1);        if  (cptcovn>0) {
       for(k=1; k<=ncovmodel;k++){          fprintf(ficresprob, "\n#********** Variable "); 
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         printf(" %le",delti3[i][j][k]);          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficparo," %le",delti3[i][j][k]);          fprintf(ficresprobcov, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fscanf(ficpar,"\n");          fprintf(ficresprobcov, "**********\n#\n");
       printf("\n");          
       fprintf(ficparo,"\n");          fprintf(ficgp, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficgp, "**********\n#\n");
   delti=delti3[1][1];          
            
   /* Reads comments: lines beginning with '#' */          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   while((c=getc(ficpar))=='#' && c!= EOF){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     ungetc(c,ficpar);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     fgets(line, MAXLINE, ficpar);          
     puts(line);          fprintf(ficresprobcor, "\n#********** Variable ");    
     fputs(line,ficparo);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcor, "**********\n#");    
   ungetc(c,ficpar);        }
          
   matcov=matrix(1,npar,1,npar);        for (age=bage; age<=fage; age ++){ 
   for(i=1; i <=npar; i++){          cov[2]=age;
     fscanf(ficpar,"%s",&str);          for (k=1; k<=cptcovn;k++) {
     printf("%s",str);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fprintf(ficparo,"%s",str);          }
     for(j=1; j <=i; j++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       fscanf(ficpar," %le",&matcov[i][j]);          for (k=1; k<=cptcovprod;k++)
       printf(" %.5le",matcov[i][j]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       fprintf(ficparo," %.5le",matcov[i][j]);          
     }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     fscanf(ficpar,"\n");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     printf("\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
     fprintf(ficparo,"\n");          gm=vector(1,(nlstate)*(nlstate+ndeath));
   }      
   for(i=1; i <=npar; i++)          for(theta=1; theta <=npar; theta++){
     for(j=i+1;j<=npar;j++)            for(i=1; i<=npar; i++)
       matcov[i][j]=matcov[j][i];              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                
   printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
     /*-------- Rewriting paramater file ----------*/            for(i=1; i<= (nlstate); i++){
      strcpy(rfileres,"r");    /* "Rparameterfile */              for(j=1; j<=(nlstate+ndeath);j++){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                k=k+1;
      strcat(rfileres,".");    /* */                gp[k]=pmmij[i][j];
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              }
     if((ficres =fopen(rfileres,"w"))==NULL) {            }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            
     }            for(i=1; i<=npar; i++)
     fprintf(ficres,"#%s\n",version);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
          
     /*-------- data file ----------*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     if((fic=fopen(datafile,"r"))==NULL)    {            k=0;
       printf("Problem with datafile: %s\n", datafile);goto end;            for(i=1; i<=(nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
     n= lastobs;                gm[k]=pmmij[i][j];
     severity = vector(1,maxwav);              }
     outcome=imatrix(1,maxwav+1,1,n);            }
     num=ivector(1,n);       
     moisnais=vector(1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     annais=vector(1,n);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     moisdc=vector(1,n);          }
     andc=vector(1,n);  
     agedc=vector(1,n);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     cod=ivector(1,n);            for(theta=1; theta <=npar; theta++)
     weight=vector(1,n);              trgradg[j][theta]=gradg[theta][j];
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          
     mint=matrix(1,maxwav,1,n);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     anint=matrix(1,maxwav,1,n);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     s=imatrix(1,maxwav+1,1,n);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     adl=imatrix(1,maxwav+1,1,n);              free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     tab=ivector(1,NCOVMAX);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     ncodemax=ivector(1,8);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
     i=1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
     while (fgets(line, MAXLINE, fic) != NULL)    {          
       if ((i >= firstobs) && (i <=lastobs)) {          k=0;
                  for(i=1; i<=(nlstate); i++){
         for (j=maxwav;j>=1;j--){            for(j=1; j<=(nlstate+ndeath);j++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              k=k+1;
           strcpy(line,stra);              mu[k][(int) age]=pmmij[i][j];
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                    for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              varpij[i][j][(int)age] = doldm[i][j];
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
           /*printf("\n%d ",(int)age);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         cutv(stra, strb,line,' '); moisnais[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]));
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            }*/
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresprob,"\n%d ",(int)age);
         }          fprintf(ficresprobcov,"\n%d ",(int)age);
         num[i]=atol(stra);          fprintf(ficresprobcor,"\n%d ",(int)age);
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           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(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         i=i+1;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     }          }
     /* printf("ii=%d", ij);          i=0;
        scanf("%d",i);*/          for (k=1; k<=(nlstate);k++){
   imx=i-1; /* Number of individuals */            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
   /* for (i=1; i<=imx; i++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              for (j=1; j<=i;j++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                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]));
               }
     for (i=1; i<=imx; i++)            }
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/          }/* end of loop for state */
         } /* end of loop for age */
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);        /* Confidence intervalle of pij  */
   Tprod=ivector(1,15);        /*
   Tvaraff=ivector(1,15);          fprintf(ficgp,"\nset noparametric;unset label");
   Tvard=imatrix(1,15,1,2);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   Tage=ivector(1,15);                fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              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);
   if (strlen(model) >1){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     j=0, j1=0, k1=1, k2=1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     j=nbocc(model,'+');          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     j1=nbocc(model,'*');        */
     cptcovn=j+1;  
     cptcovprod=j1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
            first1=1;
            for (k2=1; k2<=(nlstate);k2++){
     strcpy(modelsav,model);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            if(l2==k2) continue;
       printf("Error. Non available option model=%s ",model);            j=(k2-1)*(nlstate+ndeath)+l2;
       goto end;            for (k1=1; k1<=(nlstate);k1++){
     }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                    if(l1==k1) continue;
     for(i=(j+1); i>=1;i--){                i=(k1-1)*(nlstate+ndeath)+l1;
       cutv(stra,strb,modelsav,'+');                if(i<=j) continue;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                for (age=bage; age<=fage; age ++){ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                  if ((int)age %5==0){
       /*scanf("%d",i);*/                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       if (strchr(strb,'*')) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         cutv(strd,strc,strb,'*');                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         if (strcmp(strc,"age")==0) {                    mu1=mu[i][(int) age]/stepm*YEARM ;
           cptcovprod--;                    mu2=mu[j][(int) age]/stepm*YEARM;
           cutv(strb,stre,strd,'V');                    c12=cv12/sqrt(v1*v2);
           Tvar[i]=atoi(stre);                    /* Computing eigen value of matrix of covariance */
           cptcovage++;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             Tage[cptcovage]=i;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             /*printf("stre=%s ", stre);*/                    /* Eigen vectors */
         }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         else if (strcmp(strd,"age")==0) {                    /*v21=sqrt(1.-v11*v11); *//* error */
           cptcovprod--;                    v21=(lc1-v1)/cv12*v11;
           cutv(strb,stre,strc,'V');                    v12=-v21;
           Tvar[i]=atoi(stre);                    v22=v11;
           cptcovage++;                    tnalp=v21/v11;
           Tage[cptcovage]=i;                    if(first1==1){
         }                      first1=0;
         else {                      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);
           cutv(strb,stre,strc,'V');                    }
           Tvar[i]=ncov+k1;                    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);
           cutv(strb,strc,strd,'V');                    /*printf(fignu*/
           Tprod[k1]=i;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           Tvard[k1][1]=atoi(strc);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           Tvard[k1][2]=atoi(stre);                    if(first==1){
           Tvar[cptcovn+k2]=Tvard[k1][1];                      first=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                      fprintf(ficgp,"\nset parametric;unset label");
           for (k=1; k<=lastobs;k++)                      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);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           k1++;                      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);
           k2=k2+2;                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
         }                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       }                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
       else {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
        /*  scanf("%d",i);*/                      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",\
       cutv(strd,strc,strb,'V');                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       Tvar[i]=atoi(strc);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       }                    }else{
       strcpy(modelsav,stra);                        first=0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
         scanf("%d",i);*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 }                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   printf("cptcovprod=%d ", cptcovprod);                    }/* if first */
   scanf("%d ",i);*/                  } /* age mod 5 */
     fclose(fic);                } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
     /*  if(mle==1){*/                first=1;
     if (weightopt != 1) { /* Maximisation without weights*/              } /*l12 */
       for(i=1;i<=n;i++) weight[i]=1.0;            } /* k12 */
     }          } /*l1 */
     /*-calculation of age at interview from date of interview and age at death -*/        }/* k1 */
     agev=matrix(1,maxwav,1,imx);      } /* loop covariates */
     }
    for (i=1; i<=imx; i++)    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
      for(m=2; (m<= maxwav); m++)    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    free_vector(xp,1,npar);
          anint[m][i]=9999;    fclose(ficresprob);
          s[m][i]=-1;    fclose(ficresprobcov);
        }    fclose(ficresprobcor);
        fclose(ficgp);
     for (i=1; i<=imx; i++)  {    fclose(fichtm);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  }
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {  /******************* Printing html file ***********/
             if(agedc[i]>0)  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
               if(moisdc[i]!=99 && andc[i]!=9999)                    int lastpass, int stepm, int weightopt, char model[],\
               agev[m][i]=agedc[i];                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
             else {                    int popforecast, int estepm ,\
               if (andc[i]!=9999){                    double jprev1, double mprev1,double anprev1, \
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                    double jprev2, double mprev2,double anprev2){
               agev[m][i]=-1;    int jj1, k1, i1, cpt;
               }    /*char optionfilehtm[FILENAMELENGTH];*/
             }    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
           }      printf("Problem with %s \n",optionfilehtm), exit(0);
           else if(s[m][i] !=9){ /* Should no more exist */      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    }
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
             else if(agev[m][i] <agemin){   - 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
               agemin=agev[m][i];   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   - 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): 
             else if(agev[m][i] >agemax){     <a href=\"e%s\">e%s</a> <br>\n</li>", \
               agemax=agev[m][i];    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/   m=cptcoveff;
           }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           else { /* =9 */  
             agev[m][i]=1;   jj1=0;
             s[m][i]=-1;   for(k1=1; k1<=m;k1++){
           }     for(i1=1; i1<=ncodemax[k1];i1++){
         }       jj1++;
         else /*= 0 Unknown */       if (cptcovn > 0) {
           agev[m][i]=1;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       }         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for (i=1; i<=imx; i++)  {       }
       for(m=1; (m<= maxwav); m++){       /* Pij */
         if (s[m][i] > (nlstate+ndeath)) {       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>
           printf("Error: Wrong value in nlstate or ndeath\n");    <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           goto end;       /* Quasi-incidences */
         }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
       }  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     }         /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     free_vector(severity,1,maxwav);         }
     free_imatrix(outcome,1,maxwav+1,1,n);       for(cpt=1; cpt<=nlstate;cpt++) {
     free_vector(moisnais,1,n);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
     free_vector(annais,1,n);  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
     /* free_matrix(mint,1,maxwav,1,n);       }
        free_matrix(anint,1,maxwav,1,n);*/       fprintf(fichtm,"\n<br>- Total life expectancy by age and
     free_vector(moisdc,1,n);  health expectancies in states (1) and (2): e%s%d.png<br>
     free_vector(andc,1,n);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
       }/* End k1 */
     wav=ivector(1,imx);   fprintf(fichtm,"</ul>");
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
       fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     /* Concatenates waves */   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
       Tcode=ivector(1,100);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
       ncodemax[1]=1;   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
        /*  if(popforecast==1) fprintf(fichtm,"\n */
    codtab=imatrix(1,100,1,10);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    h=0;  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    m=pow(2,cptcoveff);  /*      <br>",fileres,fileres,fileres,fileres); */
    /*  else  */
    for(k=1;k<=cptcoveff; k++){  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
      for(i=1; i <=(m/pow(2,k));i++){  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   m=cptcoveff;
            h++;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
            if (h>m) h=1;codtab[h][k]=j;  
          }   jj1=0;
        }   for(k1=1; k1<=m;k1++){
      }     for(i1=1; i1<=ncodemax[k1];i1++){
    }       jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
    /*for(i=1; i <=m ;i++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
      for(k=1; k <=cptcovn; k++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      printf("\n");       for(cpt=1; cpt<=nlstate;cpt++) {
    }         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
    scanf("%d",i);*/  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);  
    /* Calculates basic frequencies. Computes observed prevalence at single age       }
        and prints on file fileres'p'. */     } /* end i1 */
    }/* End k1 */
       fprintf(fichtm,"</ul>");
      fclose(fichtm);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /******************* Gnuplot file **************/
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
          int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     /* For Powell, parameters are in a vector p[] starting at p[1]    int ng;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     if(mle==1){    }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    /*#ifdef windows */
          fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*--------- results files --------------*/      /*#endif */
     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);  m=pow(2,cptcoveff);
      
    /* 1eme*/
    jk=1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
    fprintf(ficres,"# Parameters\n");     for (k1=1; k1<= m ; k1 ++) {
    printf("# Parameters\n");       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
    for(i=1,jk=1; i <=nlstate; i++){       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)       for (i=1; i<= nlstate ; i ++) {
          {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
            printf("%d%d ",i,k);         else fprintf(ficgp," \%%*lf (\%%*lf)");
            fprintf(ficres,"%1d%1d ",i,k);       }
            for(j=1; j <=ncovmodel; j++){       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("%f ",p[jk]);       for (i=1; i<= nlstate ; i ++) {
              fprintf(ficres,"%f ",p[jk]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
              jk++;         else fprintf(ficgp," \%%*lf (\%%*lf)");
            }       } 
            printf("\n");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
            fprintf(ficres,"\n");       for (i=1; i<= nlstate ; i ++) {
          }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      }         else fprintf(ficgp," \%%*lf (\%%*lf)");
    }       }  
  if(mle==1){       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     /* Computing hessian and covariance matrix */     }
     ftolhess=ftol; /* Usually correct */    }
     hesscov(matcov, p, npar, delti, ftolhess, func);    /*2 eme*/
  }    
     fprintf(ficres,"# Scales\n");    for (k1=1; k1<= m ; k1 ++) { 
     printf("# Scales\n");      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       for(j=1; j <=nlstate+ndeath; j++){      
         if (j!=i) {      for (i=1; i<= nlstate+1 ; i ++) {
           fprintf(ficres,"%1d%1d",i,j);        k=2*i;
           printf("%1d%1d",i,j);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
           for(k=1; k<=ncovmodel;k++){        for (j=1; j<= nlstate+1 ; j ++) {
             printf(" %.5e",delti[jk]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             fprintf(ficres," %.5e",delti[jk]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
             jk++;        }   
           }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           printf("\n");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           fprintf(ficres,"\n");        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         }        for (j=1; j<= nlstate+1 ; j ++) {
       }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      }          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
     k=1;        fprintf(ficgp,"\" t\"\" w l 0,");
     fprintf(ficres,"# Covariance\n");        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
     printf("# Covariance\n");        for (j=1; j<= nlstate+1 ; j ++) {
     for(i=1;i<=npar;i++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       /*  if (k>nlstate) k=1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
       i1=(i-1)/(ncovmodel*nlstate)+1;        }   
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       printf("%s%d%d",alph[k],i1,tab[i]);*/        else fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficres,"%3d",i);      }
       printf("%3d",i);    }
       for(j=1; j<=i;j++){    
         fprintf(ficres," %.5e",matcov[i][j]);    /*3eme*/
         printf(" %.5e",matcov[i][j]);    
       }    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficres,"\n");      for (cpt=1; cpt<= nlstate ; cpt ++) {
       printf("\n");        k=2+nlstate*(2*cpt-2);
       k++;        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     }        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
            /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       ungetc(c,ficpar);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       fgets(line, MAXLINE, ficpar);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       puts(line);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       fputs(line,ficparo);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     }          
     ungetc(c,ficpar);        */
          for (i=1; i< nlstate ; i ++) {
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
              
     if (fage <= 2) {        } 
       bage = agemin;      }
       fage = agemaxpar;    }
     }    
        /* CV preval stable (period) */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);      for (cpt=1; cpt<=nlstate ; cpt ++) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        k=3;
          fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     while((c=getc(ficpar))=='#' && c!= EOF){        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     ungetc(c,ficpar);        
     fgets(line, MAXLINE, ficpar);        for (i=1; i<= nlstate ; i ++)
     puts(line);          fprintf(ficgp,"+$%d",k+i+1);
     fputs(line,ficparo);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   }        
   ungetc(c,ficpar);        l=3+(nlstate+ndeath)*cpt;
          fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for (i=1; i< nlstate ; i ++) {
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          l=3+(nlstate+ndeath)*cpt;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"+$%d",l+i+1);
              }
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     ungetc(c,ficpar);      } 
     fgets(line, MAXLINE, ficpar);    }  
     puts(line);    
     fputs(line,ficparo);    /* proba elementaires */
   }    for(i=1,jk=1; i <=nlstate; i++){
   ungetc(c,ficpar);      for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) {
           for(j=1; j <=ncovmodel; j++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            jk++; 
             fprintf(ficgp,"\n");
   fscanf(ficpar,"pop_based=%d\n",&popbased);          }
   fprintf(ficparo,"pop_based=%d\n",popbased);          }
   fprintf(ficres,"pop_based=%d\n",popbased);        }
       }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     fgets(line, MAXLINE, ficpar);       for(jk=1; jk <=m; jk++) {
     puts(line);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
     fputs(line,ficparo);         if (ng==2)
   }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   ungetc(c,ficpar);         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 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);         i=1;
 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);         for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
 while((c=getc(ficpar))=='#' && c!= EOF){             if (k != k2){
     ungetc(c,ficpar);               if(ng==2)
     fgets(line, MAXLINE, ficpar);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     puts(line);               else
     fputs(line,ficparo);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   }               ij=1;
   ungetc(c,ficpar);               for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   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,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   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++;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                 }
                  else
  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",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
 /*------------ gnuplot -------------*/               fprintf(ficgp,")/(1");
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);               
                 for(k1=1; k1 <=nlstate; k1++){   
 /*------------ free_vector  -------------*/                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  chdir(path);                 ij=1;
                   for(j=3; j <=ncovmodel; j++){
  free_ivector(wav,1,imx);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                       ij++;
  free_ivector(num,1,n);                   }
  free_vector(agedc,1,n);                   else
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  fclose(ficparo);                 }
  fclose(ficres);                 fprintf(ficgp,")");
                }
 /*--------- index.htm --------*/               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);               i=i+ncovmodel;
              }
             } /* end k */
   /*--------------- Prevalence limit --------------*/         } /* end k2 */
         } /* end jk */
   strcpy(filerespl,"pl");     } /* end ng */
   strcat(filerespl,fileres);     fclose(ficgp); 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  }  /* end gnuplot */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*************** Moving average **************/
   fprintf(ficrespl,"#Prevalence limit\n");  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int i, cpt, cptcod;
   fprintf(ficrespl,"\n");    int modcovmax =1;
      int mobilavrange, mob;
   prlim=matrix(1,nlstate,1,nlstate);    double age;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                             a covariate has 2 modalities */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   agebase=agemin;      if(mobilav==1) mobilavrange=5; /* default */
   agelim=agemaxpar;      else mobilavrange=mobilav;
   ftolpl=1.e-10;      for (age=bage; age<=fage; age++)
   i1=cptcoveff;        for (i=1; i<=nlstate;i++)
   if (cptcovn < 1){i1=1;}          for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   for(cptcov=1;cptcov<=i1;cptcov++){      /* We keep the original values on the extreme ages bage, fage and for 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
         k=k+1;         we use a 5 terms etc. until the borders are no more concerned. 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      */ 
         fprintf(ficrespl,"\n#******");      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for(j=1;j<=cptcoveff;j++)        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (i=1; i<=nlstate;i++){
         fprintf(ficrespl,"******\n");            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                      mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
         for (age=agebase; age<=agelim; age++){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
           fprintf(ficrespl,"%.0f",age );                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
           for(i=1; i<=nlstate;i++)                }
           fprintf(ficrespl," %.5f", prlim[i][i]);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
           fprintf(ficrespl,"\n");            }
         }          }
       }        }/* end age */
     }      }/* end mob */
   fclose(ficrespl);    }else return -1;
     return 0;
   /*------------- h Pij x at various ages ------------*/  }/* End movingaverage */
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /************** Forecasting ******************/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  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){
   }    /* proj1, year, month, day of starting projection 
   printf("Computing pij: result on file '%s' \n", filerespij);       agemin, agemax range of age
         dateprev1 dateprev2 range of dates during which prevalence is computed
   stepsize=(int) (stepm+YEARM-1)/YEARM;       anproj2 year of en of projection (same day and month as proj1).
   /*if (stepm<=24) stepsize=2;*/    */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   agelim=AGESUP;    int *popage;
   hstepm=stepsize*YEARM; /* Every year of age */    double agec; /* generic age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
      double *popeffectif,*popcount;
   k=0;    double ***p3mat;
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***mobaverage;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char fileresf[FILENAMELENGTH];
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");    agelim=AGESUP;
         for(j=1;j<=cptcoveff;j++)    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   
         fprintf(ficrespij,"******\n");    strcpy(fileresf,"f"); 
            strcat(fileresf,fileres);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if((ficresf=fopen(fileresf,"w"))==NULL) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("Problem with forecast resultfile: %s\n", fileresf);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
           oldm=oldms;savm=savms;    printf("Computing forecasting: result on file '%s' \n", fileresf);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    if (mobilav!=0) {
           fprintf(ficrespij,"\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           for (h=0; h<=nhstepm; h++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             for(i=1; i<=nlstate;i++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               for(j=1; j<=nlstate+ndeath;j++)      }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    }
             fprintf(ficrespij,"\n");  
           }    stepsize=(int) (stepm+YEARM-1)/YEARM;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (stepm<=12) stepsize=1;
           fprintf(ficrespij,"\n");    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
   }    else  hstepm=estepm;   
   
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   fclose(ficrespij);                                 fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
   /*---------- Forecasting ------------------*/    mprojmean=yp;
   if(stepm == 1) {    yp1=modf((yp2*30.5),&yp);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    jprojmean=yp;
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    if(jprojmean==0) jprojmean=1;
     free_matrix(mint,1,maxwav,1,n);    if(mprojmean==0) jprojmean=1;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);}    i1=cptcoveff;
   else{    if (cptcovn < 1){i1=1;}
     erreur=108;    
     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);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   }    
      fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*---------- Health expectancies and variances ------------*/  /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   strcpy(filerest,"t");      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   strcat(filerest,fileres);        k=k+1;
   if((ficrest=fopen(filerest,"w"))==NULL) {        fprintf(ficresf,"\n#******");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        for(j=1;j<=cptcoveff;j++) {
   }          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   strcpy(filerese,"e");        for(j=1; j<=nlstate+ndeath;j++){ 
   strcat(filerese,fileres);          for(i=1; i<=nlstate;i++)              
   if((ficreseij=fopen(filerese,"w"))==NULL) {            fprintf(ficresf," p%d%d",i,j);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          fprintf(ficresf," p.%d",j);
   }        }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
  strcpy(fileresv,"v");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
   k=0;            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
   for(cptcov=1;cptcov<=i1;cptcov++){          
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for (h=0; h<=nhstepm; h++){
       k=k+1;              if (h*hstepm/YEARM*stepm ==yearp) {
       fprintf(ficrest,"\n#****** ");                fprintf(ficresf,"\n");
       for(j=1;j<=cptcoveff;j++)                for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrest,"******\n");                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
       fprintf(ficreseij,"\n#****** ");              for(j=1; j<=nlstate+ndeath;j++) {
       for(j=1;j<=cptcoveff;j++)                ppij=0.;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                for(i=1; i<=nlstate;i++) {
       fprintf(ficreseij,"******\n");                  if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
       fprintf(ficresvij,"\n#****** ");                  else {
       for(j=1;j<=cptcoveff;j++)                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                  }
       fprintf(ficresvij,"******\n");                  if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  }
       oldm=oldms;savm=savms;                } /* end i */
       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", ppij);
       oldm=oldms;savm=savms;                }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              }/* end j */
                } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            } /* end agec */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        } /* end yearp */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      } /* end cptcod */
       fprintf(ficrest,"\n");    } /* end  cptcov */
          
       hf=1;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);    fclose(ficresf);
       for(age=bage; age <=fage ;age++){  }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {  /************** Forecasting *****not tested NB*************/
           for(i=1; i<=nlstate;i++)  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){
             prlim[i][i]=probs[(int)age][i][k];    
         }    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
            int *popage;
         fprintf(ficrest," %.0f",age);    double calagedatem, agelim, kk1, kk2;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double *popeffectif,*popcount;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double ***p3mat,***tabpop,***tabpopprev;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    double ***mobaverage;
           }    char filerespop[FILENAMELENGTH];
           epj[nlstate+1] +=epj[j];  
         }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(i=1, vepp=0.;i <=nlstate;i++)    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           for(j=1;j <=nlstate;j++)    agelim=AGESUP;
             vepp += vareij[i][j][(int)age];    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    
         for(j=1;j <=nlstate;j++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    
         }    
         fprintf(ficrest,"\n");    strcpy(filerespop,"pop"); 
       }    strcat(filerespop,fileres);
     }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   fclose(ficreseij);    }
   fclose(ficresvij);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   fclose(ficrest);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
   /*------- Variance limit prevalence------*/      if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresvpl,"vpl");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   strcat(fileresvpl,fileres);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      }
     exit(0);    }
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    agelim=AGESUP;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    hstepm=1;
       fprintf(ficresvpl,"\n#****** ");    hstepm=hstepm/stepm; 
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (popforecast==1) {
       fprintf(ficresvpl,"******\n");      if((ficpop=fopen(popfile,"r"))==NULL) {
              printf("Problem with population file : %s\n",popfile);exit(0);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       oldm=oldms;savm=savms;      } 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      popage=ivector(0,AGESUP);
     }      popeffectif=vector(0,AGESUP);
  }      popcount=vector(0,AGESUP);
       
   fclose(ficresvpl);      i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   /*---------- End : free ----------------*/     
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      imx=i;
        for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        k=k+1;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficrespop,"\n#******");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1;j<=cptcoveff;j++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          }
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficrespop,"******\n");
   free_vector(delti,1,npar);        fprintf(ficrespop,"# Age");
   free_matrix(agev,1,maxwav,1,imx);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        if (popforecast==1)  fprintf(ficrespop," [Population]");
         
   if(erreur >0)        for (cpt=0; cpt<=0;cpt++) { 
     printf("End of Imach with error %d\n",erreur);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   else   printf("End of Imach\n");          
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
              nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   /* 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);*/            nhstepm = nhstepm/hstepm; 
   /*printf("Total time was %d uSec.\n", total_usecs);*/            
   /*------ End -----------*/            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);  
  end:          
 #ifdef windows            for (h=0; h<=nhstepm; h++){
   /* chdir(pathcd);*/              if (h==(int) (calagedatem+YEARM*cpt)) {
 #endif                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
  /*system("wgnuplot graph.plt");*/              } 
  /*system("../gp37mgw/wgnuplot graph.plt");*/              for(j=1; j<=nlstate+ndeath;j++) {
  /*system("cd ../gp37mgw");*/                kk1=0.;kk2=0;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                for(i=1; i<=nlstate;i++) {              
  strcpy(plotcmd,GNUPLOTPROGRAM);                  if (mobilav==1) 
  strcat(plotcmd," ");                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
  strcat(plotcmd,optionfilegnuplot);                  else {
  system(plotcmd);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
 #ifdef windows                }
   while (z[0] != 'q') {                if (h==(int)(calagedatem+12*cpt)){
     chdir(path);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                    /*fprintf(ficrespop," %.3f", kk1);
     scanf("%s",z);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     if (z[0] == 'c') system("./imach");                }
     else if (z[0] == 'e') {              }
       chdir(path);              for(i=1; i<=nlstate;i++){
       system(optionfilehtm);                kk1=0.;
     }                  for(j=1; j<=nlstate;j++){
     else if (z[0] == 'q') exit(0);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   }                  }
 #endif                    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\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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  Added in v.1.82


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