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version 1.41.2.2, 2003/06/13 07:45:28 version 1.79, 2003/06/05 15:17:23
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 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "wgnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
     print results files
 /*#define windows*/    if mle==1 
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */       computes hessian
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    open gnuplot file
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open html file
     stable prevalence
 #define NINTERVMAX 8     for age prevalim()
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    h Pij x
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    variance of p varprob
 #define NCOVMAX 8 /* Maximum number of covariates */    forecasting if prevfcast==1 prevforecast call prevalence()
 #define MAXN 20000    health expectancies
 #define YEARM 12. /* Number of months per year */    Variance-covariance of DFLE
 #define AGESUP 130    prevalence()
 #define AGEBASE 40     movingaverage()
     varevsij() 
     if popbased==1 varevsij(,popbased)
 int erreur; /* Error number */    total life expectancies
 int nvar;    Variance of stable prevalence
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;   end
 int npar=NPARMAX;  */
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;   
   #include <math.h>
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <stdio.h>
 int maxwav; /* Maxim number of waves */  #include <stdlib.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <unistd.h>
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define MAXLINE 256
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GNUPLOTPROGRAM "gnuplot"
 double jmean; /* Mean space between 2 waves */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define FILENAMELENGTH 80
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  /*#define DEBUG*/
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  #define windows
 FILE *ficgp,*ficresprob,*ficpop;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 FILE *ficreseij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   char fileresv[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NR_END 1  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define FREE_ARG char*  #define NCOVMAX 8 /* Maximum number of covariates */
 #define FTOL 1.0e-10  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 #define NRANSI  #define AGESUP 130
 #define ITMAX 200  #define AGEBASE 40
   #ifdef windows
 #define TOL 2.0e-4  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #define CGOLD 0.3819660  #else
 #define ZEPS 1.0e-10  #define DIRSEPARATOR '/'
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define ODIRSEPARATOR '\\'
   #endif
 #define GOLD 1.618034  
 #define GLIMIT 100.0  /* $Id$ */
 #define TINY 1.0e-20  /* $Log$
    * Revision 1.79  2003/06/05 15:17:23  brouard
 static double maxarg1,maxarg2;   * *** empty log message ***
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   * */
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
    int erreur; /* Error number */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int nvar;
 #define rint(a) floor(a+0.5)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 static double sqrarg;  int nlstate=2; /* Number of live states */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int ndeath=1; /* Number of dead states */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 int imx;  
 int stepm;  int *wav; /* Number of waves for this individuual 0 is possible */
 /* Stepm, step in month: minimum step interpolation*/  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 int estepm;  int mle, weightopt;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  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 */
 int m,nb;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double jmean; /* Mean space between 2 waves */
 double **pmmij, ***probs, ***mobaverage;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double dateintmean=0;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double *weight;  FILE *ficlog, *ficrespow;
 int **s; /* Status */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double *agedc, **covar, idx;  FILE *ficresprobmorprev;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char filerese[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 /**************** split *************************/  FILE  *ficresvpl;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
    char *s;                             /* pointer */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
    l1 = strlen( path );                 /* length of path */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char filelog[FILENAMELENGTH]; /* Log file */
 #ifdef windows  char filerest[FILENAMELENGTH];
    s = strrchr( path, '\\' );           /* find last / */  char fileregp[FILENAMELENGTH];
 #else  char popfile[FILENAMELENGTH];
    s = strrchr( path, '/' );            /* find last / */  
 #endif  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  #define NR_END 1
       extern char       *getwd( );  #define FREE_ARG char*
   #define FTOL 1.0e-10
       if ( getwd( dirc ) == NULL ) {  
 #else  #define NRANSI 
       extern char       *getcwd( );  #define ITMAX 200 
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define TOL 2.0e-4 
 #endif  
          return( GLOCK_ERROR_GETCWD );  #define CGOLD 0.3819660 
       }  #define ZEPS 1.0e-10 
       strcpy( name, path );             /* we've got it */  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  #define GOLD 1.618034 
       l2 = strlen( s );                 /* length of filename */  #define GLIMIT 100.0 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define TINY 1.0e-20 
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  static double maxarg1,maxarg2;
       dirc[l1-l2] = 0;                  /* add zero */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
    l1 = strlen( dirc );                 /* length of directory */    
 #ifdef windows  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define rint(a) floor(a+0.5)
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  static double sqrarg;
 #endif  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    s = strrchr( name, '.' );            /* find last / */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    s++;  
    strcpy(ext,s);                       /* save extension */  int imx; 
    l1= strlen( name);  int stepm;
    l2= strlen( s)+1;  /* Stepm, step in month: minimum step interpolation*/
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;  int estepm;
    return( 0 );                         /* we're done */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
   int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 /******************************************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 void replace(char *s, char*t)  double dateintmean=0;
 {  
   int i;  double *weight;
   int lg=20;  int **s; /* Status */
   i=0;  double *agedc, **covar, idx;
   lg=strlen(t);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     if (t[i]== '\\') s[i]='/';  double ftolhess; /* Tolerance for computing hessian */
   }  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 int nbocc(char *s, char occ)  {
 {    char  *ss;                            /* pointer */
   int i,j=0;    int   l1, l2;                         /* length counters */
   int lg=20;  
   i=0;    l1 = strlen(path );                   /* length of path */
   lg=strlen(s);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(i=0; i<= lg; i++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if  (s[i] == occ ) j++;    if ( ss == NULL ) {                   /* no directory, so use current */
   }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   return j;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 void cutv(char *u,char *v, char*t, char occ)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   int i,lg,j,p=0;      }
   i=0;      strcpy( name, path );               /* we've got it */
   for(j=0; j<=strlen(t)-1; j++) {    } else {                              /* strip direcotry from path */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      ss++;                               /* after this, the filename */
   }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   lg=strlen(t);      strcpy( name, ss );         /* save file name */
   for(j=0; j<p; j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     (u[j] = t[j]);      dirc[l1-l2] = 0;                    /* add zero */
   }    }
      u[p]='\0';    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
    for(j=0; j<= lg; j++) {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     if (j>=(p+1))(v[j-p-1] = t[j]);  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     ss = strrchr( name, '.' );            /* find last / */
 /********************** nrerror ********************/    ss++;
     strcpy(ext,ss);                       /* save extension */
 void nrerror(char error_text[])    l1= strlen( name);
 {    l2= strlen(ss)+1;
   fprintf(stderr,"ERREUR ...\n");    strncpy( finame, name, l1-l2);
   fprintf(stderr,"%s\n",error_text);    finame[l1-l2]= 0;
   exit(1);    return( 0 );                          /* we're done */
 }  }
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  
 {  /******************************************/
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  void replace(char *s, char*t)
   if (!v) nrerror("allocation failure in vector");  {
   return v-nl+NR_END;    int i;
 }    int lg=20;
     i=0;
 /************************ free vector ******************/    lg=strlen(t);
 void free_vector(double*v, int nl, int nh)    for(i=0; i<= lg; i++) {
 {      (s[i] = t[i]);
   free((FREE_ARG)(v+nl-NR_END));      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  int nbocc(char *s, char occ)
 {  {
   int *v;    int i,j=0;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    int lg=20;
   if (!v) nrerror("allocation failure in ivector");    i=0;
   return v-nl+NR_END;    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /******************free ivector **************************/    }
 void free_ivector(int *v, long nl, long nh)    return j;
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /******************* imatrix *******************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 int **imatrix(long nrl, long nrh, long ncl, long nch)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    i=0;
   int **m;    for(j=0; j<=strlen(t)-1; j++) {
        if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   /* allocate pointers to rows */    }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    lg=strlen(t);
   m += NR_END;    for(j=0; j<p; j++) {
   m -= nrl;      (u[j] = t[j]);
      }
         u[p]='\0';
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));     for(j=0; j<= lg; j++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if (j>=(p+1))(v[j-p-1] = t[j]);
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;  }
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /********************** nrerror ********************/
    
   /* return pointer to array of pointers to rows */  void nrerror(char error_text[])
   return m;  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /****************** free_imatrix *************************/    exit(EXIT_FAILURE);
 void free_imatrix(m,nrl,nrh,ncl,nch)  }
       int **m;  /*********************** vector *******************/
       long nch,ncl,nrh,nrl;  double *vector(int nl, int nh)
      /* free an int matrix allocated by imatrix() */  {
 {    double *v;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free((FREE_ARG) (m+nrl-NR_END));    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  {
   double **m;    free((FREE_ARG)(v+nl-NR_END));
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  char *cvector(long nl,long nh)
   m -= nrl;  {
     char *v;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in cvector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /******************free ivector **************************/
   return m;  void free_cvector(char *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*************************free matrix ************************/  }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  /************************ivector *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int *ivector(long nl,long nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /******************* ma3x *******************************/    if (!v) nrerror("allocation failure in ivector");
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    return v-nl+NR_END;
 {  }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m += NR_END;  }
   m -= nrl;  
   /******************* imatrix *******************************/
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   m[nrl] += NR_END;  { 
   m[nrl] -= ncl;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
     /* allocate pointers to rows */ 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    if (!m) nrerror("allocation failure 1 in matrix()"); 
   m[nrl][ncl] += NR_END;    m += NR_END; 
   m[nrl][ncl] -= nll;    m -= nrl; 
   for (j=ncl+1; j<=nch; j++)    
     m[nrl][j]=m[nrl][j-1]+nlay;    
      /* allocate rows and set pointers to them */ 
   for (i=nrl+1; i<=nrh; i++) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (j=ncl+1; j<=nch; j++)    m[nrl] += NR_END; 
       m[i][j]=m[i][j-1]+nlay;    m[nrl] -= ncl; 
   }    
   return m;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
 /*************************free ma3x ************************/    return m; 
 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));  /****************** free_imatrix *************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void free_imatrix(m,nrl,nrh,ncl,nch)
   free((FREE_ARG)(m+nrl-NR_END));        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /***************** f1dim *************************/  { 
 extern int ncom;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 extern double *pcom,*xicom;    free((FREE_ARG) (m+nrl-NR_END)); 
 extern double (*nrfunc)(double []);  } 
    
 double f1dim(double x)  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   int j;  {
   double f;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double *xt;    double **m;
    
   xt=vector(1,ncom);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (!m) nrerror("allocation failure 1 in matrix()");
   f=(*nrfunc)(xt);    m += NR_END;
   free_vector(xt,1,ncom);    m -= nrl;
   return f;  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /*****************brent *************************/    m[nrl] += NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m[nrl] -= ncl;
 {  
   int iter;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double a,b,d,etemp;    return m;
   double fu,fv,fw,fx;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   double ftemp;     */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /*************************free matrix ************************/
   a=(ax < cx ? ax : cx);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   fw=fv=fx=(*f)(x);    free((FREE_ARG)(m+nrl-NR_END));
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /******************* ma3x *******************************/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     printf(".");fflush(stdout);  {
 #ifdef DEBUG    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    double ***m;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!m) nrerror("allocation failure 1 in matrix()");
       *xmin=x;    m += NR_END;
       return fx;    m -= nrl;
     }  
     ftemp=fu;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (fabs(e) > tol1) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       r=(x-w)*(fx-fv);    m[nrl] += NR_END;
       q=(x-v)*(fx-fw);    m[nrl] -= ncl;
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (q > 0.0) p = -p;  
       q=fabs(q);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       etemp=e;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       e=d;    m[nrl][ncl] += NR_END;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl][ncl] -= nll;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    for (j=ncl+1; j<=nch; j++) 
       else {      m[nrl][j]=m[nrl][j-1]+nlay;
         d=p/q;    
         u=x+d;    for (i=nrl+1; i<=nrh; i++) {
         if (u-a < tol2 || b-u < tol2)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           d=SIGN(tol1,xm-x);      for (j=ncl+1; j<=nch; j++) 
       }        m[i][j]=m[i][j-1]+nlay;
     } else {    }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     fu=(*f)(u);    */
     if (fu <= fx) {  }
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  /*************************free ma3x ************************/
         SHFT(fv,fw,fx,fu)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         } else {  {
           if (u < x) a=u; else b=u;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           if (fu <= fw || w == x) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             v=w;    free((FREE_ARG)(m+nrl-NR_END));
             w=u;  }
             fv=fw;  
             fw=fu;  /***************** f1dim *************************/
           } else if (fu <= fv || v == x || v == w) {  extern int ncom; 
             v=u;  extern double *pcom,*xicom;
             fv=fu;  extern double (*nrfunc)(double []); 
           }   
         }  double f1dim(double x) 
   }  { 
   nrerror("Too many iterations in brent");    int j; 
   *xmin=x;    double f;
   return fx;    double *xt; 
 }   
     xt=vector(1,ncom); 
 /****************** mnbrak ***********************/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    free_vector(xt,1,ncom); 
             double (*func)(double))    return f; 
 {  } 
   double ulim,u,r,q, dum;  
   double fu;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *fa=(*func)(*ax);  { 
   *fb=(*func)(*bx);    int iter; 
   if (*fb > *fa) {    double a,b,d,etemp;
     SHFT(dum,*ax,*bx,dum)    double fu,fv,fw,fx;
       SHFT(dum,*fb,*fa,dum)    double ftemp;
       }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *cx=(*bx)+GOLD*(*bx-*ax);    double e=0.0; 
   *fc=(*func)(*cx);   
   while (*fb > *fc) {    a=(ax < cx ? ax : cx); 
     r=(*bx-*ax)*(*fb-*fc);    b=(ax > cx ? ax : cx); 
     q=(*bx-*cx)*(*fb-*fa);    x=w=v=bx; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    fw=fv=fx=(*f)(x); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    for (iter=1;iter<=ITMAX;iter++) { 
     ulim=(*bx)+GLIMIT*(*cx-*bx);      xm=0.5*(a+b); 
     if ((*bx-u)*(u-*cx) > 0.0) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       fu=(*func)(u);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     } else if ((*cx-u)*(u-ulim) > 0.0) {      printf(".");fflush(stdout);
       fu=(*func)(u);      fprintf(ficlog,".");fflush(ficlog);
       if (fu < *fc) {  #ifdef DEBUG
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      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);
           SHFT(*fb,*fc,fu,(*func)(u))      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)))) { */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #endif
       u=ulim;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       fu=(*func)(u);        *xmin=x; 
     } else {        return fx; 
       u=(*cx)+GOLD*(*cx-*bx);      } 
       fu=(*func)(u);      ftemp=fu;
     }      if (fabs(e) > tol1) { 
     SHFT(*ax,*bx,*cx,u)        r=(x-w)*(fx-fv); 
       SHFT(*fa,*fb,*fc,fu)        q=(x-v)*(fx-fw); 
       }        p=(x-v)*q-(x-w)*r; 
 }        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
 /*************** linmin ************************/        q=fabs(q); 
         etemp=e; 
 int ncom;        e=d; 
 double *pcom,*xicom;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 double (*nrfunc)(double []);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          else { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))          d=p/q; 
 {          u=x+d; 
   double brent(double ax, double bx, double cx,          if (u-a < tol2 || b-u < tol2) 
                double (*f)(double), double tol, double *xmin);            d=SIGN(tol1,xm-x); 
   double f1dim(double x);        } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      } else { 
               double *fc, double (*func)(double));        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int j;      } 
   double xx,xmin,bx,ax;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double fx,fb,fa;      fu=(*f)(u); 
        if (fu <= fx) { 
   ncom=n;        if (u >= x) a=x; else b=x; 
   pcom=vector(1,n);        SHFT(v,w,x,u) 
   xicom=vector(1,n);          SHFT(fv,fw,fx,fu) 
   nrfunc=func;          } else { 
   for (j=1;j<=n;j++) {            if (u < x) a=u; else b=u; 
     pcom[j]=p[j];            if (fu <= fw || w == x) { 
     xicom[j]=xi[j];              v=w; 
   }              w=u; 
   ax=0.0;              fv=fw; 
   xx=1.0;              fw=fu; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);            } else if (fu <= fv || v == x || v == w) { 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);              v=u; 
 #ifdef DEBUG              fv=fu; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);            } 
 #endif          } 
   for (j=1;j<=n;j++) {    } 
     xi[j] *= xmin;    nrerror("Too many iterations in brent"); 
     p[j] += xi[j];    *xmin=x; 
   }    return fx; 
   free_vector(xicom,1,n);  } 
   free_vector(pcom,1,n);  
 }  /****************** mnbrak ***********************/
   
 /*************** powell ************************/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,              double (*func)(double)) 
             double (*func)(double []))  { 
 {    double ulim,u,r,q, dum;
   void linmin(double p[], double xi[], int n, double *fret,    double fu; 
               double (*func)(double []));   
   int i,ibig,j;    *fa=(*func)(*ax); 
   double del,t,*pt,*ptt,*xit;    *fb=(*func)(*bx); 
   double fp,fptt;    if (*fb > *fa) { 
   double *xits;      SHFT(dum,*ax,*bx,dum) 
   pt=vector(1,n);        SHFT(dum,*fb,*fa,dum) 
   ptt=vector(1,n);        } 
   xit=vector(1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
   xits=vector(1,n);    *fc=(*func)(*cx); 
   *fret=(*func)(p);    while (*fb > *fc) { 
   for (j=1;j<=n;j++) pt[j]=p[j];      r=(*bx-*ax)*(*fb-*fc); 
   for (*iter=1;;++(*iter)) {      q=(*bx-*cx)*(*fb-*fa); 
     fp=(*fret);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     ibig=0;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     del=0.0;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (i=1;i<=n;i++)        fu=(*func)(u); 
       printf(" %d %.12f",i, p[i]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     printf("\n");        fu=(*func)(u); 
     for (i=1;i<=n;i++) {        if (fu < *fc) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       fptt=(*fret);            SHFT(*fb,*fc,fu,(*func)(u)) 
 #ifdef DEBUG            } 
       printf("fret=%lf \n",*fret);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 #endif        u=ulim; 
       printf("%d",i);fflush(stdout);        fu=(*func)(u); 
       linmin(p,xit,n,fret,func);      } else { 
       if (fabs(fptt-(*fret)) > del) {        u=(*cx)+GOLD*(*cx-*bx); 
         del=fabs(fptt-(*fret));        fu=(*func)(u); 
         ibig=i;      } 
       }      SHFT(*ax,*bx,*cx,u) 
 #ifdef DEBUG        SHFT(*fa,*fb,*fc,fu) 
       printf("%d %.12e",i,(*fret));        } 
       for (j=1;j<=n;j++) {  } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /*************** linmin ************************/
       }  
       for(j=1;j<=n;j++)  int ncom; 
         printf(" p=%.12e",p[j]);  double *pcom,*xicom;
       printf("\n");  double (*nrfunc)(double []); 
 #endif   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  { 
 #ifdef DEBUG    double brent(double ax, double bx, double cx, 
       int k[2],l;                 double (*f)(double), double tol, double *xmin); 
       k[0]=1;    double f1dim(double x); 
       k[1]=-1;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("Max: %.12e",(*func)(p));                double *fc, double (*func)(double)); 
       for (j=1;j<=n;j++)    int j; 
         printf(" %.12e",p[j]);    double xx,xmin,bx,ax; 
       printf("\n");    double fx,fb,fa;
       for(l=0;l<=1;l++) {   
         for (j=1;j<=n;j++) {    ncom=n; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    pcom=vector(1,n); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    xicom=vector(1,n); 
         }    nrfunc=func; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for (j=1;j<=n;j++) { 
       }      pcom[j]=p[j]; 
 #endif      xicom[j]=xi[j]; 
     } 
     ax=0.0; 
       free_vector(xit,1,n);    xx=1.0; 
       free_vector(xits,1,n);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       free_vector(ptt,1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       free_vector(pt,1,n);  #ifdef DEBUG
       return;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #endif
     for (j=1;j<=n;j++) {    for (j=1;j<=n;j++) { 
       ptt[j]=2.0*p[j]-pt[j];      xi[j] *= xmin; 
       xit[j]=p[j]-pt[j];      p[j] += xi[j]; 
       pt[j]=p[j];    } 
     }    free_vector(xicom,1,n); 
     fptt=(*func)(ptt);    free_vector(pcom,1,n); 
     if (fptt < fp) {  } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  /*************** powell ************************/
         linmin(p,xit,n,fret,func);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         for (j=1;j<=n;j++) {              double (*func)(double [])) 
           xi[j][ibig]=xi[j][n];  { 
           xi[j][n]=xit[j];    void linmin(double p[], double xi[], int n, double *fret, 
         }                double (*func)(double [])); 
 #ifdef DEBUG    int i,ibig,j; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double del,t,*pt,*ptt,*xit;
         for(j=1;j<=n;j++)    double fp,fptt;
           printf(" %.12e",xit[j]);    double *xits;
         printf("\n");    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
       }    xit=vector(1,n); 
     }    xits=vector(1,n); 
   }    *fret=(*func)(p); 
 }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
 /**** Prevalence limit ****************/      fp=(*fret); 
       ibig=0; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      del=0.0; 
 {      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
      matrix by transitions matrix until convergence is reached */      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       for (i=1;i<=n;i++) {
   int i, ii,j,k;        printf(" %d %.12f",i, p[i]);
   double min, max, maxmin, maxmax,sumnew=0.;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **matprod2();        fprintf(ficrespow," %.12lf", p[i]);
   double **out, cov[NCOVMAX], **pmij();      }
   double **newm;      printf("\n");
   double agefin, delaymax=50 ; /* Max number of years to converge */      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");
   for (ii=1;ii<=nlstate+ndeath;ii++)      for (i=1;i<=n;i++) { 
     for (j=1;j<=nlstate+ndeath;j++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fptt=(*fret); 
     }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
    cov[1]=1.;        fprintf(ficlog,"fret=%lf \n",*fret);
    #endif
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        printf("%d",i);fflush(stdout);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        fprintf(ficlog,"%d",i);fflush(ficlog);
     newm=savm;        linmin(p,xit,n,fret,func); 
     /* Covariates have to be included here again */        if (fabs(fptt-(*fret)) > del) { 
      cov[2]=agefin;          del=fabs(fptt-(*fret)); 
            ibig=i; 
       for (k=1; k<=cptcovn;k++) {        } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #ifdef DEBUG
         /*      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]]);*/        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (j=1;j<=n;j++) {
       for (k=1; k<=cptcovprod;k++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        for(j=1;j<=n;j++) {
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/          printf(" p=%.12e",p[j]);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);          fprintf(ficlog," p=%.12e",p[j]);
         }
     savm=oldm;        printf("\n");
     oldm=newm;        fprintf(ficlog,"\n");
     maxmax=0.;  #endif
     for(j=1;j<=nlstate;j++){      } 
       min=1.;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       max=0.;  #ifdef DEBUG
       for(i=1; i<=nlstate; i++) {        int k[2],l;
         sumnew=0;        k[0]=1;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        k[1]=-1;
         prlim[i][j]= newm[i][j]/(1-sumnew);        printf("Max: %.12e",(*func)(p));
         max=FMAX(max,prlim[i][j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         min=FMIN(min,prlim[i][j]);        for (j=1;j<=n;j++) {
       }          printf(" %.12e",p[j]);
       maxmin=max-min;          fprintf(ficlog," %.12e",p[j]);
       maxmax=FMAX(maxmax,maxmin);        }
     }        printf("\n");
     if(maxmax < ftolpl){        fprintf(ficlog,"\n");
       return prlim;        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
   }            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]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /*************** transition probabilities ***************/          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 {        }
   double s1, s2;  #endif
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  
         free_vector(xit,1,n); 
     for(i=1; i<= nlstate; i++){        free_vector(xits,1,n); 
     for(j=1; j<i;j++){        free_vector(ptt,1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        free_vector(pt,1,n); 
         /*s2 += param[i][j][nc]*cov[nc];*/        return; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      } 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       }      for (j=1;j<=n;j++) { 
       ps[i][j]=s2;        ptt[j]=2.0*p[j]-pt[j]; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
     for(j=i+1; j<=nlstate+ndeath;j++){      } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fptt=(*func)(ptt); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (fptt < fp) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       }        if (t < 0.0) { 
       ps[i][j]=s2;          linmin(p,xit,n,fret,func); 
     }          for (j=1;j<=n;j++) { 
   }            xi[j][ibig]=xi[j][n]; 
     /*ps[3][2]=1;*/            xi[j][n]=xit[j]; 
           }
   for(i=1; i<= nlstate; i++){  #ifdef DEBUG
      s1=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=1; j<i; j++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       s1+=exp(ps[i][j]);          for(j=1;j<=n;j++){
     for(j=i+1; j<=nlstate+ndeath; j++)            printf(" %.12e",xit[j]);
       s1+=exp(ps[i][j]);            fprintf(ficlog," %.12e",xit[j]);
     ps[i][i]=1./(s1+1.);          }
     for(j=1; j<i; j++)          printf("\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];          fprintf(ficlog,"\n");
     for(j=i+1; j<=nlstate+ndeath; j++)  #endif
       ps[i][j]= exp(ps[i][j])*ps[i][i];        }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      } 
   } /* end i */    } 
   } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /**** Prevalence limit (stable prevalence)  ****************/
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     }  {
   }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    int i, ii,j,k;
     for(jj=1; jj<= nlstate+ndeath; jj++){    double min, max, maxmin, maxmax,sumnew=0.;
      printf("%lf ",ps[ii][jj]);    double **matprod2();
    }    double **out, cov[NCOVMAX], **pmij();
     printf("\n ");    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*    for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      for (j=1;j<=nlstate+ndeath;j++){
   goto end;*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     return ps;      }
 }  
      cov[1]=1.;
 /**************** Product of 2 matrices ******************/   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      /* Covariates have to be included here again */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */       cov[2]=agefin;
   /* in, b, out are matrice of pointers which should have been initialized    
      before: only the contents of out is modified. The function returns        for (k=1; k<=cptcovn;k++) {
      a pointer to pointers identical to out */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   long i, j, k;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   for(i=nrl; i<= nrh; i++)        }
     for(k=ncolol; k<=ncoloh; k++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        for (k=1; k<=cptcovprod;k++)
         out[i][k] +=in[i][j]*b[j][k];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   return out;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 /************* Higher Matrix Product ***************/  
       savm=oldm;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      oldm=newm;
 {      maxmax=0.;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for(j=1;j<=nlstate;j++){
      duration (i.e. until        min=1.;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        max=0.;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        for(i=1; i<=nlstate; i++) {
      (typically every 2 years instead of every month which is too big).          sumnew=0;
      Model is determined by parameters x and covariates have to be          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      included manually here.          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
      */          min=FMIN(min,prlim[i][j]);
         }
   int i, j, d, h, k;        maxmin=max-min;
   double **out, cov[NCOVMAX];        maxmax=FMAX(maxmax,maxmin);
   double **newm;      }
       if(maxmax < ftolpl){
   /* Hstepm could be zero and should return the unit matrix */        return prlim;
   for (i=1;i<=nlstate+ndeath;i++)      }
     for (j=1;j<=nlstate+ndeath;j++){    }
       oldm[i][j]=(i==j ? 1.0 : 0.0);  }
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  /*************** transition probabilities ***************/ 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(d=1; d <=hstepm; d++){  {
       newm=savm;    double s1, s2;
       /* Covariates have to be included here again */    /*double t34;*/
       cov[1]=1.;    int i,j,j1, nc, ii, jj;
       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(i=1; i<= nlstate; i++){
       for (k=1; k<=cptcovage;k++)      for(j=1; j<i;j++){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1; k<=cptcovprod;k++)          /*s2 += param[i][j][nc]*cov[nc];*/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        ps[i][j]=s2;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      for(j=i+1; j<=nlstate+ndeath;j++){
       savm=oldm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       oldm=newm;          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);*/
     for(i=1; i<=nlstate+ndeath; i++)        }
       for(j=1;j<=nlstate+ndeath;j++) {        ps[i][j]=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[3][2]=1;*/
       }  
   } /* end h */    for(i=1; i<= nlstate; i++){
   return po;       s1=0;
 }      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
 /*************** log-likelihood *************/        s1+=exp(ps[i][j]);
 double func( double *x)      ps[i][i]=1./(s1+1.);
 {      for(j=1; j<i; j++)
   int i, ii, j, k, mi, d, kk;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(j=i+1; j<=nlstate+ndeath; j++)
   double **out;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double sw; /* Sum of weights */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   double lli; /* Individual log likelihood */    } /* end i */
   int s1, s2;  
   long ipmx;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   /*extern weight */      for(jj=1; jj<= nlstate+ndeath; jj++){
   /* We are differentiating ll according to initial status */        ps[ii][jj]=0;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        ps[ii][ii]=1;
   /*for(i=1;i<imx;i++)      }
     printf(" %d\n",s[4][i]);    }
   */  
   cov[1]=1.;  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   for(k=1; k<=nlstate; k++) ll[k]=0.;      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){       printf("%lf ",ps[ii][jj]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];     }
     for(mi=1; mi<= wav[i]-1; mi++){      printf("\n ");
       for (ii=1;ii<=nlstate+ndeath;ii++)      }
         for (j=1;j<=nlstate+ndeath;j++){      printf("\n ");printf("%lf ",cov[2]);*/
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*
           savm[ii][j]=(ii==j ? 1.0 : 0.0);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
         }    goto end;*/
       for(d=0; d<dh[mi][i]; d++){      return ps;
         newm=savm;  }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /**************** Product of 2 matrices ******************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         savm=oldm;    /* in, b, out are matrice of pointers which should have been initialized 
         oldm=newm;       before: only the contents of out is modified. The function returns
               a pointer to pointers identical to out */
            long i, j, k;
       } /* end mult */    for(i=nrl; i<= nrh; i++)
            for(k=ncolol; k<=ncoloh; k++)
       s1=s[mw[mi][i]][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       s2=s[mw[mi+1][i]][i];          out[i][k] +=in[i][j]*b[j][k];
       if( s2 > nlstate){  
         /* i.e. if s2 is a death state and if the date of death is known then the contribution    return out;
            to the likelihood is the probability to die between last step unit time and current  }
            step unit time, which is also the differences between probability to die before dh  
            and probability to die before dh-stepm .  
            In version up to 0.92 likelihood was computed  /************* Higher Matrix Product ***************/
            as if date of death was unknown. Death was treated as any other  
            health state: the date of the interview describes the actual state  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
            and not the date of a change in health state. The former idea was  {
            to consider that at each interview the state was recorded    /* Computes the transition matrix starting at age 'age' over 
            (healthy, disable or death) and IMaCh was corrected; but when we       'nhstepm*hstepm*stepm' months (i.e. until
            introduced the exact date of death then we should have modified       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            the contribution of an exact death to the likelihood. This new       nhstepm*hstepm matrices. 
            contribution is smaller and very dependent of the step unit       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
            stepm. It is no more the probability to die between last interview       (typically every 2 years instead of every month which is too big 
            and month of death but the probability to survive from last       for the memory).
            interview up to one month before death multiplied by the       Model is determined by parameters x and covariates have to be 
            probability to die within a month. Thanks to Chris       included manually here. 
            Jackson for correcting this bug.  Former versions increased  
            mortality artificially. The bad side is that we add another loop       */
            which slows down the processing. The difference can be up to 10%  
            lower mortality.    int i, j, d, h, k;
         */    double **out, cov[NCOVMAX];
         lli=log(out[s1][s2] - savm[s1][s2]);    double **newm;
       }else{  
         lli=log(out[s1][s2]); /* or     lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); */    /* Hstepm could be zero and should return the unit matrix */
         /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    for (i=1;i<=nlstate+ndeath;i++)
       }      for (j=1;j<=nlstate+ndeath;j++){
       ipmx +=1;        oldm[i][j]=(i==j ? 1.0 : 0.0);
       sw += weight[i];        po[i][j][0]=(i==j ? 1.0 : 0.0);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      }
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d lli=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],lli,weight[i],out[s1][s2],savm[s1][s2]);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     } /* end of wave */    for(h=1; h <=nhstepm; h++){
   } /* end of individual */      for(d=1; d <=hstepm; d++){
         newm=savm;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        /* Covariates have to be included here again */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        cov[1]=1.;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   /*exit(0);*/        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   return -l;        for (k=1; k<=cptcovage;k++)
 }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 /*********** Maximum Likelihood Estimation ***************/  
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   int i,j, iter;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double **xi,*delti;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double fret;        savm=oldm;
   xi=matrix(1,npar,1,npar);        oldm=newm;
   for (i=1;i<=npar;i++)      }
     for (j=1;j<=npar;j++)      for(i=1; i<=nlstate+ndeath; i++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        for(j=1;j<=nlstate+ndeath;j++) {
   printf("Powell\n");          po[i][j][h]=newm[i][j];
   powell(p,xi,npar,ftol,&iter,&fret,func);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    } /* end h */
     return po;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*************** log-likelihood *************/
 {  double func( double *x)
   double  **a,**y,*x,pd;  {
   double **hess;    int i, ii, j, k, mi, d, kk;
   int i, j,jk;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   int *indx;    double **out;
     double sw; /* Sum of weights */
   double hessii(double p[], double delta, int theta, double delti[]);    double lli; /* Individual log likelihood */
   double hessij(double p[], double delti[], int i, int j);    int s1, s2;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double bbh, survp;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    long ipmx;
     /*extern weight */
   hess=matrix(1,npar,1,npar);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   printf("\nCalculation of the hessian matrix. Wait...\n");    /*for(i=1;i<imx;i++) 
   for (i=1;i<=npar;i++){      printf(" %d\n",s[4][i]);
     printf("%d",i);fflush(stdout);    */
     hess[i][i]=hessii(p,ftolhess,i,delti);    cov[1]=1.;
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
      if(mle==1){
   for (i=1;i<=npar;i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (j=1;j<=npar;j++)  {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if (j>i) {        for(mi=1; mi<= wav[i]-1; mi++){
         printf(".%d%d",i,j);fflush(stdout);          for (ii=1;ii<=nlstate+ndeath;ii++)
         hess[i][j]=hessij(p,delti,i,j);            for (j=1;j<=nlstate+ndeath;j++){
         hess[j][i]=hess[i][j];                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         /*printf(" %lf ",hess[i][j]);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          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++) {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   a=matrix(1,npar,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   y=matrix(1,npar,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   x=vector(1,npar);            savm=oldm;
   indx=ivector(1,npar);            oldm=newm;
   for (i=1;i<=npar;i++)          } /* end mult */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        
   ludcmp(a,npar,indx,&pd);          /*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.
   for (j=1;j<=npar;j++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<=npar;i++) x[i]=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     x[j]=1;           * the nearest (and in case of equal distance, to the lowest) interval but now
     lubksb(a,npar,indx,x);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (i=1;i<=npar;i++){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       matcov[i][j]=x[i];           * 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
   }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
   printf("\n#Hessian matrix#\n");           * For stepm > 1 the results are less biased than in previous versions. 
   for (i=1;i<=npar;i++) {           */
     for (j=1;j<=npar;j++) {          s1=s[mw[mi][i]][i];
       printf("%.3e ",hess[i][j]);          s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
     printf("\n");          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
            */
   /* Recompute Inverse */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for (i=1;i<=npar;i++)          if( s2 > nlstate){ 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   ludcmp(a,npar,indx,&pd);               to the likelihood is the probability to die between last step unit time and current 
                step unit time, which is also the differences between probability to die before dh 
   /*  printf("\n#Hessian matrix recomputed#\n");               and probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   for (j=1;j<=npar;j++) {          as if date of death was unknown. Death was treated as any other
     for (i=1;i<=npar;i++) x[i]=0;          health state: the date of the interview describes the actual state
     x[j]=1;          and not the date of a change in health state. The former idea was
     lubksb(a,npar,indx,x);          to consider that at each interview the state was recorded
     for (i=1;i<=npar;i++){          (healthy, disable or death) and IMaCh was corrected; but when we
       y[i][j]=x[i];          introduced the exact date of death then we should have modified
       printf("%.3e ",y[i][j]);          the contribution of an exact death to the likelihood. This new
     }          contribution is smaller and very dependent of the step unit
     printf("\n");          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
   */          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
   free_matrix(a,1,npar,1,npar);          Jackson for correcting this bug.  Former versions increased
   free_matrix(y,1,npar,1,npar);          mortality artificially. The bad side is that we add another loop
   free_vector(x,1,npar);          which slows down the processing. The difference can be up to 10%
   free_ivector(indx,1,npar);          lower mortality.
   free_matrix(hess,1,npar,1,npar);            */
             lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
 }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
 /*************** hessian matrix ****************/          } 
 double hessii( double x[], double delta, int theta, double delti[])          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int i;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int l=1, lmax=20;          ipmx +=1;
   double k1,k2;          sw += weight[i];
   double p2[NPARMAX+1];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double res;        } /* end of wave */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } /* end of individual */
   double fx;    }  else if(mle==2){
   int k=0,kmax=10;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double l1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   fx=func(x);          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++) p2[i]=x[i];            for (j=1;j<=nlstate+ndeath;j++){
   for(l=0 ; l <=lmax; l++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     l1=pow(10,l);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     delts=delt;            }
     for(k=1 ; k <kmax; k=k+1){          for(d=0; d<=dh[mi][i]; d++){
       delt = delta*(l1*k);            newm=savm;
       p2[theta]=x[theta] +delt;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       k1=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
       p2[theta]=x[theta]-delt;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       k2=func(p2)-fx;            }
       /*res= (k1-2.0*fx+k2)/delt/delt; */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
 #ifdef DEBUG            oldm=newm;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          } /* end mult */
 #endif        
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /* But now since version 0.9 we anticipate for bias and large stepm.
         k=kmax;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */           * the nearest (and in case of equal distance, to the lowest) interval but now
         k=kmax; l=lmax*10.;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * probability in order to take into account the bias as a fraction of the way
         delts=delt;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
   delti[theta]=delts;           */
   return res;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 double hessij( double x[], double delti[], int thetai,int thetaj)           * is higher than the multiple of stepm and negative otherwise.
 {           */
   int i;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   int l=1, l1, lmax=20;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double k1,k2,k3,k4,res,fx;          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
   double p2[NPARMAX+1];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int k;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   fx=func(x);          ipmx +=1;
   for (k=1; k<=2; k++) {          sw += weight[i];
     for (i=1;i<=npar;i++) p2[i]=x[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     p2[thetai]=x[thetai]+delti[thetai]/k;        } /* end of wave */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } /* end of individual */
     k1=func(p2)-fx;    }  else if(mle==3){  /* exponential inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     k2=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]-delti[thetai]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     k3=func(p2)-fx;            }
            for(d=0; d<dh[mi][i]; d++){
     p2[thetai]=x[thetai]-delti[thetai]/k;            newm=savm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     k4=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 #ifdef DEBUG            }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   return res;            oldm=newm;
 }          } /* end mult */
         
 /************** Inverse of matrix **************/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 void ludcmp(double **a, int n, int *indx, double *d)          /* But now since version 0.9 we anticipate for bias and large stepm.
 {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int i,imax,j,k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double big,dum,sum,temp;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double *vv;           * 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
   vv=vector(1,n);           * probability in order to take into account the bias as a fraction of the way
   *d=1.0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=n;i++) {           * -stepm/2 to stepm/2 .
     big=0.0;           * For stepm=1 the results are the same as for previous versions of Imach.
     for (j=1;j<=n;j++)           * For stepm > 1 the results are less biased than in previous versions. 
       if ((temp=fabs(a[i][j])) > big) big=temp;           */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          s1=s[mw[mi][i]][i];
     vv[i]=1.0/big;          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   for (j=1;j<=n;j++) {          /* bias is positive if real duration
     for (i=1;i<j;i++) {           * is higher than the multiple of stepm and negative otherwise.
       sum=a[i][j];           */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][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 */
       a[i][j]=sum;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     big=0.0;          /*if(lli ==000.0)*/
     for (i=j;i<=n;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<j;k++)          sw += weight[i];
         sum -= a[i][k]*a[k][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       a[i][j]=sum;        } /* end of wave */
       if ( (dum=vv[i]*fabs(sum)) >= big) {      } /* end of individual */
         big=dum;    }else{  /* ml=4 no inter-extrapolation */
         imax=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(mi=1; mi<= wav[i]-1; mi++){
     if (j != imax) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1;k<=n;k++) {            for (j=1;j<=nlstate+ndeath;j++){
         dum=a[imax][k];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         a[imax][k]=a[j][k];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         a[j][k]=dum;            }
       }          for(d=0; d<dh[mi][i]; d++){
       *d = -(*d);            newm=savm;
       vv[imax]=vv[j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     indx[j]=imax;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (a[j][j] == 0.0) a[j][j]=TINY;            }
     if (j != n) {          
       dum=1.0/(a[j][j]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (i=j+1;i<=n;i++) a[i][j] *= dum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   free_vector(vv,1,n);  /* Doesn't work */          } /* end mult */
 ;        
 }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
 void lubksb(double **a, int n, int *indx, double b[])          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i,ii=0,ip,j;        } /* end of wave */
   double sum;      } /* end of individual */
      } /* End of if */
   for (i=1;i<=n;i++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     ip=indx[i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     sum=b[ip];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     b[ip]=b[i];    return -l;
     if (ii)  }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  
     b[i]=sum;  /*********** Maximum Likelihood Estimation ***************/
   }  
   for (i=n;i>=1;i--) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     sum=b[i];  {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int i,j, iter;
     b[i]=sum/a[i][i];    double **xi;
   }    double fret;
 }    char filerespow[FILENAMELENGTH];
     xi=matrix(1,npar,1,npar);
 /************ Frequencies ********************/    for (i=1;i<=npar;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 (j=1;j<=npar;j++)
 {  /* Some frequencies */        xi[i][j]=(i==j ? 1.0 : 0.0);
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    strcpy(filerespow,"pow"); 
   double ***freq; /* Frequencies */    strcat(filerespow,fileres);
   double *pp;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double pos, k2, dateintsum=0,k2cpt=0;      printf("Problem with resultfile: %s\n", filerespow);
   FILE *ficresp;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   char fileresp[FILENAMELENGTH];    }
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   pp=vector(1,nlstate);    for (i=1;i<=nlstate;i++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(j=1;j<=nlstate+ndeath;j++)
   strcpy(fileresp,"p");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   strcat(fileresp,fileres);    fprintf(ficrespow,"\n");
   if((ficresp=fopen(fileresp,"w"))==NULL) {    powell(p,xi,npar,ftol,&iter,&fret,func);
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);    fclose(ficrespow);
   }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   j1=0;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    
   j=cptcoveff;  }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    /**** Computes Hessian and covariance matrix ***/
   for(k1=1; k1<=j;k1++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(i1=1; i1<=ncodemax[k1];i1++){  {
       j1++;    double  **a,**y,*x,pd;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double **hess;
         scanf("%d", i);*/    int i, j,jk;
       for (i=-1; i<=nlstate+ndeath; i++)      int *indx;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)    double hessii(double p[], double delta, int theta, double delti[]);
             freq[i][jk][m]=0;    double hessij(double p[], double delti[], int i, int j);
          void lubksb(double **a, int npar, int *indx, double b[]) ;
       dateintsum=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
       k2cpt=0;  
       for (i=1; i<=imx; i++) {    hess=matrix(1,npar,1,npar);
         bool=1;  
         if  (cptcovn>0) {    printf("\nCalculation of the hessian matrix. Wait...\n");
           for (z1=1; z1<=cptcoveff; z1++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (i=1;i<=npar;i++){
               bool=0;      printf("%d",i);fflush(stdout);
         }      fprintf(ficlog,"%d",i);fflush(ficlog);
         if (bool==1) {      hess[i][i]=hessii(p,ftolhess,i,delti);
           for(m=firstpass; m<=lastpass; m++){      /*printf(" %f ",p[i]);*/
             k2=anint[m][i]+(mint[m][i]/12.);      /*printf(" %lf ",hess[i][i]);*/
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    }
               if(agev[m][i]==0) agev[m][i]=agemax+1;    
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=npar;i++) {
               if (m<lastpass) {      for (j=1;j<=npar;j++)  {
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        if (j>i) { 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          printf(".%d%d",i,j);fflush(stdout);
               }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                        hess[i][j]=hessij(p,delti,i,j);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          hess[j][i]=hess[i][j];    
                 dateintsum=dateintsum+k2;          /*printf(" %lf ",hess[i][j]);*/
                 k2cpt++;        }
               }      }
             }    }
           }    printf("\n");
         }    fprintf(ficlog,"\n");
       }  
            printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
       if  (cptcovn>0) {    a=matrix(1,npar,1,npar);
         fprintf(ficresp, "\n#********** Variable ");    y=matrix(1,npar,1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    x=vector(1,npar);
         fprintf(ficresp, "**********\n#");    indx=ivector(1,npar);
       }    for (i=1;i<=npar;i++)
       for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    ludcmp(a,npar,indx,&pd);
       fprintf(ficresp, "\n");  
          for (j=1;j<=npar;j++) {
       for(i=(int)agemin; i <= (int)agemax+3; i++){      for (i=1;i<=npar;i++) x[i]=0;
         if(i==(int)agemax+3)      x[j]=1;
           printf("Total");      lubksb(a,npar,indx,x);
         else      for (i=1;i<=npar;i++){ 
           printf("Age %d", i);        matcov[i][j]=x[i];
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    }
             pp[jk] += freq[jk][m][i];  
         }    printf("\n#Hessian matrix#\n");
         for(jk=1; jk <=nlstate ; jk++){    fprintf(ficlog,"\n#Hessian matrix#\n");
           for(m=-1, pos=0; m <=0 ; m++)    for (i=1;i<=npar;i++) { 
             pos += freq[jk][m][i];      for (j=1;j<=npar;j++) { 
           if(pp[jk]>=1.e-10)        printf("%.3e ",hess[i][j]);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        fprintf(ficlog,"%.3e ",hess[i][j]);
           else      }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      printf("\n");
         }      fprintf(ficlog,"\n");
     }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /* Recompute Inverse */
             pp[jk] += freq[jk][m][i];    for (i=1;i<=npar;i++)
         }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
         for(jk=1,pos=0; jk <=nlstate ; jk++)  
           pos += pp[jk];    /*  printf("\n#Hessian matrix recomputed#\n");
         for(jk=1; jk <=nlstate ; jk++){  
           if(pos>=1.e-5)    for (j=1;j<=npar;j++) {
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for (i=1;i<=npar;i++) x[i]=0;
           else      x[j]=1;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      lubksb(a,npar,indx,x);
           if( i <= (int) agemax){      for (i=1;i<=npar;i++){ 
             if(pos>=1.e-5){        y[i][j]=x[i];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        printf("%.3e ",y[i][j]);
               probs[i][jk][j1]= pp[jk]/pos;        fprintf(ficlog,"%.3e ",y[i][j]);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      }
             }      printf("\n");
             else      fprintf(ficlog,"\n");
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    }
           }    */
         }  
            free_matrix(a,1,npar,1,npar);
         for(jk=-1; jk <=nlstate+ndeath; jk++)    free_matrix(y,1,npar,1,npar);
           for(m=-1; m <=nlstate+ndeath; m++)    free_vector(x,1,npar);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    free_ivector(indx,1,npar);
         if(i <= (int) agemax)    free_matrix(hess,1,npar,1,npar);
           fprintf(ficresp,"\n");  
         printf("\n");  
       }  }
     }  
   }  /*************** hessian matrix ****************/
   dateintmean=dateintsum/k2cpt;  double hessii( double x[], double delta, int theta, double delti[])
    {
   fclose(ficresp);    int i;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int l=1, lmax=20;
   free_vector(pp,1,nlstate);    double k1,k2;
      double p2[NPARMAX+1];
   /* End of Freq */    double res;
 }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
 /************ Prevalence ********************/    int k=0,kmax=10;
 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)    double l1;
 {  /* Some frequencies */  
      fx=func(x);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double ***freq; /* Frequencies */    for(l=0 ; l <=lmax; l++){
   double *pp;      l1=pow(10,l);
   double pos, k2;      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   pp=vector(1,nlstate);        delt = delta*(l1*k);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        p2[theta]=x[theta] +delt;
          k1=func(p2)-fx;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        p2[theta]=x[theta]-delt;
   j1=0;        k2=func(p2)-fx;
          /*res= (k1-2.0*fx+k2)/delt/delt; */
   j=cptcoveff;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        
    #ifdef DEBUG
  for(k1=1; k1<=j;k1++){        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);
     for(i1=1; i1<=ncodemax[k1];i1++){        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);
       j1++;  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for (i=-1; i<=nlstate+ndeath; i++)          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for (jk=-1; jk<=nlstate+ndeath; jk++)            k=kmax;
           for(m=agemin; m <= agemax+3; m++)        }
             freq[i][jk][m]=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                k=kmax; l=lmax*10.;
       for (i=1; i<=imx; i++) {        }
         bool=1;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         if  (cptcovn>0) {          delts=delt;
           for (z1=1; z1<=cptcoveff; z1++)        }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      }
               bool=0;    }
         }    delti[theta]=delts;
         if (bool==1) {    return res; 
           for(m=firstpass; m<=lastpass; m++){    
             k2=anint[m][i]+(mint[m][i]/12.);  }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  double hessij( double x[], double delti[], int thetai,int thetaj)
               if(agev[m][i]==1) agev[m][i]=agemax+2;  {
               if (m<lastpass)    int i;
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    int l=1, l1, lmax=20;
               else    double k1,k2,k3,k4,res,fx;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double p2[NPARMAX+1];
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    int k;
             }  
           }    fx=func(x);
         }    for (k=1; k<=2; k++) {
       }      for (i=1;i<=npar;i++) p2[i]=x[i];
         for(i=(int)agemin; i <= (int)agemax+3; i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
           for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      k1=func(p2)-fx;
               pp[jk] += freq[jk][m][i];    
           }      p2[thetai]=x[thetai]+delti[thetai]/k;
           for(jk=1; jk <=nlstate ; jk++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             for(m=-1, pos=0; m <=0 ; m++)      k2=func(p2)-fx;
             pos += freq[jk][m][i];    
         }      p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          for(jk=1; jk <=nlstate ; jk++){      k3=func(p2)-fx;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    
              pp[jk] += freq[jk][m][i];      p2[thetai]=x[thetai]-delti[thetai]/k;
          }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                k4=func(p2)-fx;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
          for(jk=1; jk <=nlstate ; jk++){                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( i <= (int) agemax){      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);
              if(pos>=1.e-5){  #endif
                probs[i][jk][j1]= pp[jk]/pos;    }
              }    return res;
            }  }
          }  
            /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
     }  { 
   }    int i,imax,j,k; 
     double big,dum,sum,temp; 
      double *vv; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);   
   free_vector(pp,1,nlstate);    vv=vector(1,n); 
      *d=1.0; 
 }  /* End of Freq */    for (i=1;i<=n;i++) { 
       big=0.0; 
 /************* Waves Concatenation ***************/      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 {      vv[i]=1.0/big; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    } 
      Death is a valid wave (if date is known).    for (j=1;j<=n;j++) { 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for (i=1;i<j;i++) { 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        sum=a[i][j]; 
      and mw[mi+1][i]. dh depends on stepm.        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      */        a[i][j]=sum; 
       } 
   int i, mi, m;      big=0.0; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (i=j;i<=n;i++) { 
      double sum=0., jmean=0.;*/        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   int j, k=0,jk, ju, jl;          sum -= a[i][k]*a[k][j]; 
   double sum=0.;        a[i][j]=sum; 
   jmin=1e+5;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   jmax=-1;          big=dum; 
   jmean=0.;          imax=i; 
   for(i=1; i<=imx; i++){        } 
     mi=0;      } 
     m=firstpass;      if (j != imax) { 
     while(s[m][i] <= nlstate){        for (k=1;k<=n;k++) { 
       if(s[m][i]>=1)          dum=a[imax][k]; 
         mw[++mi][i]=m;          a[imax][k]=a[j][k]; 
       if(m >=lastpass)          a[j][k]=dum; 
         break;        } 
       else        *d = -(*d); 
         m++;        vv[imax]=vv[j]; 
     }/* end while */      } 
     if (s[m][i] > nlstate){      indx[j]=imax; 
       mi++;     /* Death is another wave */      if (a[j][j] == 0.0) a[j][j]=TINY; 
       /* if(mi==0)  never been interviewed correctly before death */      if (j != n) { 
          /* Only death is a correct wave */        dum=1.0/(a[j][j]); 
       mw[mi][i]=m;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     } 
     wav[i]=mi;    free_vector(vv,1,n);  /* Doesn't work */
     if(mi==0)  ;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  } 
   }  
   void lubksb(double **a, int n, int *indx, double b[]) 
   for(i=1; i<=imx; i++){  { 
     for(mi=1; mi<wav[i];mi++){    int i,ii=0,ip,j; 
       if (stepm <=0)    double sum; 
         dh[mi][i]=1;   
       else{    for (i=1;i<=n;i++) { 
         if (s[mw[mi+1][i]][i] > nlstate) {      ip=indx[i]; 
           if (agedc[i] < 2*AGESUP) {      sum=b[ip]; 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      b[ip]=b[i]; 
           if(j==0) j=1;  /* Survives at least one month after exam */      if (ii) 
           k=k+1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           if (j >= jmax) jmax=j;      else if (sum) ii=i; 
           if (j <= jmin) jmin=j;      b[i]=sum; 
           sum=sum+j;    } 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    for (i=n;i>=1;i--) { 
           }      sum=b[i]; 
         }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         else{      b[i]=sum/a[i][i]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    } 
           k=k+1;  } 
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  /************ Frequencies ********************/
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  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)
           sum=sum+j;  {  /* Some frequencies */
         }    
         jk= j/stepm;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         jl= j -jk*stepm;    int first;
         ju= j -(jk+1)*stepm;    double ***freq; /* Frequencies */
         if(jl <= -ju)    double *pp, **prop;
           dh[mi][i]=jk;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         else    FILE *ficresp;
           dh[mi][i]=jk+1;    char fileresp[FILENAMELENGTH];
         if(dh[mi][i]==0)    
           dh[mi][i]=1; /* At least one step */    pp=vector(1,nlstate);
       }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     }    strcpy(fileresp,"p");
   }    strcat(fileresp,fileres);
   jmean=sum/k;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      printf("Problem with prevalence resultfile: %s\n", fileresp);
  }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 /*********** Tricode ****************************/      exit(0);
 void tricode(int *Tvar, int **nbcode, int imx)    }
 {    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   int Ndum[20],ij=1, k, j, i;    j1=0;
   int cptcode=0;    
   cptcoveff=0;    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;    first=1;
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for(k1=1; k1<=j;k1++){
     for (i=1; i<=imx; i++) {      for(i1=1; i1<=ncodemax[k1];i1++){
       ij=(int)(covar[Tvar[j]][i]);        j1++;
       Ndum[ij]++;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          scanf("%d", i);*/
       if (ij > cptcode) cptcode=ij;        for (i=-1; i<=nlstate+ndeath; i++)  
     }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
     for (i=0; i<=cptcode; i++) {              freq[i][jk][m]=0;
       if(Ndum[i]!=0) ncodemax[j]++;  
     }      for (i=1; i<=nlstate; i++)  
     ij=1;        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
         
     for (i=1; i<=ncodemax[j]; i++) {        dateintsum=0;
       for (k=0; k<=19; k++) {        k2cpt=0;
         if (Ndum[k] != 0) {        for (i=1; i<=imx; i++) {
           nbcode[Tvar[j]][ij]=k;          bool=1;
                    if  (cptcovn>0) {
           ij++;            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         if (ij > ncodemax[j]) break;                bool=0;
       }            }
     }          if (bool==1){
   }              for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
  for (k=0; k<19; k++) Ndum[k]=0;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
  for (i=1; i<=ncovmodel-2; i++) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       ij=Tvar[i];                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       Ndum[ij]++;                if (m<lastpass) {
     }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
  ij=1;                }
  for (i=1; i<=10; i++) {                
    if((Ndum[i]!=0) && (i<=ncovcol)){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
      Tvaraff[ij]=i;                  dateintsum=dateintsum+k2;
      ij++;                  k2cpt++;
    }                }
  }              }
              }
     cptcoveff=ij-1;          }
 }        }
          
 /*********** Health Expectancies ****************/        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Health expectancies */          fprintf(ficresp, "**********\n#");
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        }
   double age, agelim, hf;        for(i=1; i<=nlstate;i++) 
   double ***p3mat,***varhe;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double **dnewm,**doldm;        fprintf(ficresp, "\n");
   double *xp;        
   double **gp, **gm;        for(i=iagemin; i <= iagemax+3; i++){
   double ***gradg, ***trgradg;          if(i==iagemax+3){
   int theta;            fprintf(ficlog,"Total");
           }else{
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            if(first==1){
   xp=vector(1,npar);              first=0;
   dnewm=matrix(1,nlstate*2,1,npar);              printf("See log file for details...\n");
   doldm=matrix(1,nlstate*2,1,nlstate*2);            }
              fprintf(ficlog,"Age %d", i);
   fprintf(ficreseij,"# Health expectancies\n");          }
   fprintf(ficreseij,"# Age");          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for(j=1; j<=nlstate;j++)              pp[jk] += freq[jk][m][i]; 
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          }
   fprintf(ficreseij,"\n");          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   if(estepm < stepm){              pos += freq[jk][m][i];
     printf ("Problem %d lower than %d\n",estepm, stepm);            if(pp[jk]>=1.e-10){
   }              if(first==1){
   else  hstepm=estepm;                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* We compute the life expectancy from trapezoids spaced every estepm months              }
    * This is mainly to measure the difference between two models: for example              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    * if stepm=24 months pijx are given only every 2 years and by summing them            }else{
    * we are calculating an estimate of the Life Expectancy assuming a linear              if(first==1)
    * progression inbetween and thus overestimating or underestimating according                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * to the curvature of the survival function. If, for the same date, we              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            }
    * to compare the new estimate of Life expectancy with the same linear          }
    * hypothesis. A more precise result, taking into account a more precise  
    * curvature will be obtained if estepm is as small as stepm. */          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   /* For example we decided to compute the life expectancy with the smallest unit */              pp[jk] += freq[jk][m][i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          }       
      nhstepm is the number of hstepm from age to agelim          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
      nstepm is the number of stepm from age to agelin.            pos += pp[jk];
      Look at hpijx to understand the reason of that which relies in memory size            posprop += prop[jk][i];
      and note for a fixed period like estepm months */          }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(jk=1; jk <=nlstate ; jk++){
      survival function given by stepm (the optimization length). Unfortunately it            if(pos>=1.e-5){
      means that if the survival funtion is printed only each two years of age and if              if(first==1)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      results. So we changed our mind and took the option of the best precision.              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   */            }else{
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   agelim=AGESUP;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     /* nhstepm age range expressed in number of stepm */            if( i <= iagemax){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);              if(pos>=1.e-5){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     /* if (stepm >= YEARM) hstepm=1;*/                probs[i][jk][j1]= pp[jk]/pos;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);              else
     gp=matrix(0,nhstepm,1,nlstate*2);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     gm=matrix(0,nhstepm,1,nlstate*2);            }
           }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(jk=-1; jk <=nlstate+ndeath; jk++)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
               if(first==1)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     /* Computing Variances of health expectancies */              }
           if(i <= iagemax)
      for(theta=1; theta <=npar; theta++){            fprintf(ficresp,"\n");
       for(i=1; i<=npar; i++){          if(first==1)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
        }
       cptj=0;    }
       for(j=1; j<= nlstate; j++){    dateintmean=dateintsum/k2cpt; 
         for(i=1; i<=nlstate; i++){   
           cptj=cptj+1;    fclose(ficresp);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    free_vector(pp,1,nlstate);
           }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         }    /* End of Freq */
       }  }
        
        /************ Prevalence ********************/
       for(i=1; i<=npar; i++)  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             in each health status at the date of interview (if between dateprev1 and dateprev2).
       cptj=0;       We still use firstpass and lastpass as another selection.
       for(j=1; j<= nlstate; j++){    */
         for(i=1;i<=nlstate;i++){   
           cptj=cptj+1;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    double ***freq; /* Frequencies */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double *pp, **prop;
           }    double pos,posprop; 
         }    double  y2; /* in fractional years */
       }    int iagemin, iagemax;
        
        iagemin= (int) agemin;
     iagemax= (int) agemax;
       for(j=1; j<= nlstate*2; j++)    /*pp=vector(1,nlstate);*/
         for(h=0; h<=nhstepm-1; h++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         }    j1=0;
     
      }    j=cptcoveff;
        if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /* End theta */    
     for(k1=1; k1<=j;k1++){
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
      for(h=0; h<=nhstepm-1; h++)        
       for(j=1; j<=nlstate*2;j++)        for (i=1; i<=nlstate; i++)  
         for(theta=1; theta <=npar; theta++)          for(m=iagemin; m <= iagemax+3; m++)
         trgradg[h][j][theta]=gradg[h][theta][j];            prop[i][m]=0.0;
        
         for (i=1; i<=imx; i++) { /* Each individual */
      for(i=1;i<=nlstate*2;i++)          bool=1;
       for(j=1;j<=nlstate*2;j++)          if  (cptcovn>0) {
         varhe[i][j][(int)age] =0.;            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for(h=0;h<=nhstepm-1;h++){                bool=0;
       for(k=0;k<=nhstepm-1;k++){          } 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          if (bool==1) { 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         for(i=1;i<=nlstate*2;i++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           for(j=1;j<=nlstate*2;j++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                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) { 
                        /*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]]);*/
     /* Computing expectancies */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1; i<=nlstate;i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for(j=1; j<=nlstate;j++)                } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){              }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            } /* end selection of waves */
                    }
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        }
         for(i=iagemin; i <= iagemax+3; i++){  
         }          
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficreseij,"%3.0f",age );            posprop += prop[jk][i]; 
     cptj=0;          } 
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){     
         cptj++;            if( i <=  iagemax){ 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );              if(posprop>=1.e-5){ 
       }                probs[i][jk][j1]= prop[jk][i]/posprop;
     fprintf(ficreseij,"\n");              } 
                } 
     free_matrix(gm,0,nhstepm,1,nlstate*2);          }/* end jk */ 
     free_matrix(gp,0,nhstepm,1,nlstate*2);        }/* end i */ 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      } /* end i1 */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    } /* end k1 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
   }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   free_vector(xp,1,npar);    /*free_vector(pp,1,nlstate);*/
   free_matrix(dnewm,1,nlstate*2,1,npar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  }  /* End of prevalence */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  
 }  /************* Waves Concatenation ***************/
   
 /************ Variance ******************/  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)
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  {
 {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   /* Variance of health expectancies */       Death is a valid wave (if date is known).
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   double **newm;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   double **dnewm,**doldm;       and mw[mi+1][i]. dh depends on stepm.
   int i, j, nhstepm, hstepm, h, nstepm ;       */
   int k, cptcode;  
   double *xp;    int i, mi, m;
   double **gp, **gm;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   double ***gradg, ***trgradg;       double sum=0., jmean=0.;*/
   double ***p3mat;    int first;
   double age,agelim, hf;    int j, k=0,jk, ju, jl;
   int theta;    double sum=0.;
     first=0;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    jmin=1e+5;
   fprintf(ficresvij,"# Age");    jmax=-1;
   for(i=1; i<=nlstate;i++)    jmean=0.;
     for(j=1; j<=nlstate;j++)    for(i=1; i<=imx; i++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      mi=0;
   fprintf(ficresvij,"\n");      m=firstpass;
       while(s[m][i] <= nlstate){
   xp=vector(1,npar);        if(s[m][i]>=1)
   dnewm=matrix(1,nlstate,1,npar);          mw[++mi][i]=m;
   doldm=matrix(1,nlstate,1,nlstate);        if(m >=lastpass)
            break;
   if(estepm < stepm){        else
     printf ("Problem %d lower than %d\n",estepm, stepm);          m++;
   }      }/* end while */
   else  hstepm=estepm;        if (s[m][i] > nlstate){
   /* For example we decided to compute the life expectancy with the smallest unit */        mi++;     /* Death is another wave */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        /* if(mi==0)  never been interviewed correctly before death */
      nhstepm is the number of hstepm from age to agelim           /* Only death is a correct wave */
      nstepm is the number of stepm from age to agelin.        mw[mi][i]=m;
      Look at hpijx to understand the reason of that which relies in memory size      }
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      wav[i]=mi;
      survival function given by stepm (the optimization length). Unfortunately it      if(mi==0){
      means that if the survival funtion is printed only each two years of age and if        if(first==0){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
      results. So we changed our mind and took the option of the best precision.          first=1;
   */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        if(first==1){
   agelim = AGESUP;          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* end mi==0 */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    } /* End individuals */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    for(i=1; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);      for(mi=1; mi<wav[i];mi++){
     gm=matrix(0,nhstepm,1,nlstate);        if (stepm <=0)
           dh[mi][i]=1;
     for(theta=1; theta <=npar; theta++){        else{
       for(i=1; i<=npar; i++){ /* Computes gradient */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (agedc[i] < 2*AGESUP) {
       }            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              if(j==0) j=1;  /* Survives at least one month after exam */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            k=k+1;
             if (j >= jmax) jmax=j;
       if (popbased==1) {            if (j <= jmin) jmin=j;
         for(i=1; i<=nlstate;i++)            sum=sum+j;
           prlim[i][i]=probs[(int)age][i][ij];            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          else{
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       }            k=k+1;
                if (j >= jmax) jmax=j;
       for(i=1; i<=npar; i++) /* Computes gradient */            else if (j <= jmin)jmin=j;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              /*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]);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
              sum=sum+j;
       if (popbased==1) {          }
         for(i=1; i<=nlstate;i++)          jk= j/stepm;
           prlim[i][i]=probs[(int)age][i][ij];          jl= j -jk*stepm;
       }          ju= j -(jk+1)*stepm;
           if(mle <=1){ 
       for(j=1; j<= nlstate; j++){            if(jl==0){
         for(h=0; h<=nhstepm; h++){              dh[mi][i]=jk;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              bh[mi][i]=0;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            }else{ /* We want a negative bias in order to only have interpolation ie
         }                    * at the price of an extra matrix product in likelihood */
       }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
       for(j=1; j<= nlstate; j++)            }
         for(h=0; h<=nhstepm; h++){          }else{
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            if(jl <= -ju){
         }              dh[mi][i]=jk;
     } /* End theta */              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);                                   */
             }
     for(h=0; h<=nhstepm; h++)            else{
       for(j=1; j<=nlstate;j++)              dh[mi][i]=jk+1;
         for(theta=1; theta <=npar; theta++)              bh[mi][i]=ju;
           trgradg[h][j][theta]=gradg[h][theta][j];            }
             if(dh[mi][i]==0){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              dh[mi][i]=1; /* At least one step */
     for(i=1;i<=nlstate;i++)              bh[mi][i]=ju; /* At least one step */
       for(j=1;j<=nlstate;j++)              /*  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);*/
         vareij[i][j][(int)age] =0.;            }
           }
     for(h=0;h<=nhstepm;h++){        } /* end if mle */
       for(k=0;k<=nhstepm;k++){      } /* end wave */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    jmean=sum/k;
         for(i=1;i<=nlstate;i++)    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           for(j=1;j<=nlstate;j++)    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;   }
       }  
     }  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
     fprintf(ficresvij,"%.0f ",age );  {
     for(i=1; i<=nlstate;i++)    
       for(j=1; j<=nlstate;j++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    int cptcode=0;
       }    cptcoveff=0; 
     fprintf(ficresvij,"\n");   
     free_matrix(gp,0,nhstepm,1,nlstate);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     free_matrix(gm,0,nhstepm,1,nlstate);    for (k=1; k<=7; k++) ncodemax[k]=0;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   } /* End age */                                 modality*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   free_vector(xp,1,npar);        Ndum[ij]++; /*store the modality */
   free_matrix(doldm,1,nlstate,1,npar);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   free_matrix(dnewm,1,nlstate,1,nlstate);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
 }                                         female is 1, then  cptcode=1.*/
       }
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      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 */
   /* Variance of prevalence limit */      }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;      ij=1; 
   double **dnewm,**doldm;      for (i=1; i<=ncodemax[j]; i++) {
   int i, j, nhstepm, hstepm;        for (k=0; k<= maxncov; k++) {
   int k, cptcode;          if (Ndum[k] != 0) {
   double *xp;            nbcode[Tvar[j]][ij]=k; 
   double *gp, *gm;            /* 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; */
   double **gradg, **trgradg;            
   double age,agelim;            ij++;
   int theta;          }
              if (ij > ncodemax[j]) break; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        }  
   fprintf(ficresvpl,"# Age");      } 
   for(i=1; i<=nlstate;i++)    }  
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
   xp=vector(1,npar);   for (i=1; i<=ncovmodel-2; i++) { 
   dnewm=matrix(1,nlstate,1,npar);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   doldm=matrix(1,nlstate,1,nlstate);     ij=Tvar[i];
       Ndum[ij]++;
   hstepm=1*YEARM; /* Every year of age */   }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;   ij=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   for (i=1; i<= maxncov; i++) {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     if((Ndum[i]!=0) && (i<=ncovcol)){
     if (stepm >= YEARM) hstepm=1;       Tvaraff[ij]=i; /*For printing */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       ij++;
     gradg=matrix(1,npar,1,nlstate);     }
     gp=vector(1,nlstate);   }
     gm=vector(1,nlstate);   
    cptcoveff=ij-1; /*Number of simple covariates*/
     for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*********** Health Expectancies ****************/
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  {
        /* Health expectancies */
       for(i=1; i<=npar; i++) /* Computes gradient */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double age, agelim, hf;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***p3mat,***varhe;
       for(i=1;i<=nlstate;i++)    double **dnewm,**doldm;
         gm[i] = prlim[i][i];    double *xp;
     double **gp, **gm;
       for(i=1;i<=nlstate;i++)    double ***gradg, ***trgradg;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int theta;
     } /* End theta */  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     trgradg =matrix(1,nlstate,1,npar);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     for(j=1; j<=nlstate;j++)    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       for(theta=1; theta <=npar; theta++)    
         trgradg[j][theta]=gradg[theta][j];    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
     for(i=1;i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       varpl[i][(int)age] =0.;      for(j=1; j<=nlstate;j++)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    fprintf(ficreseij,"\n");
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     fprintf(ficresvpl,"%.0f ",age );    }
     for(i=1; i<=nlstate;i++)    else  hstepm=estepm;   
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    /* We compute the life expectancy from trapezoids spaced every estepm months
     fprintf(ficresvpl,"\n");     * This is mainly to measure the difference between two models: for example
     free_vector(gp,1,nlstate);     * if stepm=24 months pijx are given only every 2 years and by summing them
     free_vector(gm,1,nlstate);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     free_matrix(gradg,1,npar,1,nlstate);     * progression in between and thus overestimating or underestimating according
     free_matrix(trgradg,1,nlstate,1,npar);     * to the curvature of the survival function. If, for the same date, we 
   } /* End age */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
   free_vector(xp,1,npar);     * hypothesis. A more precise result, taking into account a more precise
   free_matrix(doldm,1,nlstate,1,npar);     * curvature will be obtained if estepm is as small as stepm. */
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     /* For example we decided to compute the life expectancy with the smallest unit */
 }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
 /************ Variance of one-step probabilities  ******************/       nstepm is the number of stepm from age to agelin. 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)       Look at hpijx to understand the reason of that which relies in memory size
 {       and note for a fixed period like estepm months */
   int i, j, i1, k1, j1, z1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int k=0, cptcode;       survival function given by stepm (the optimization length). Unfortunately it
   double **dnewm,**doldm;       means that if the survival funtion is printed only each two years of age and if
   double *xp;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double *gp, *gm;       results. So we changed our mind and took the option of the best precision.
   double **gradg, **trgradg;    */
   double age,agelim, cov[NCOVMAX];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int theta;  
   char fileresprob[FILENAMELENGTH];    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   strcpy(fileresprob,"prob");      /* nhstepm age range expressed in number of stepm */
   strcat(fileresprob,fileres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("Problem with resultfile: %s\n", fileresprob);      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   fprintf(ficresprob,"# Age");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   fprintf(ficresprob,"\n");  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
   xp=vector(1,npar);      /* Computing Variances of health expectancies */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));       for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ 
   cov[1]=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   j1=0;    
   for(k1=1; k1<=1;k1++){        cptj=0;
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=1; j<= nlstate; j++){
     j1++;          for(i=1; i<=nlstate; i++){
             cptj=cptj+1;
     if  (cptcovn>0) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       fprintf(ficresprob, "\n#********** Variable ");              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            }
       fprintf(ficresprob, "**********\n#");          }
     }        }
           
       for (age=bage; age<=fage; age ++){       
         cov[2]=age;        for(i=1; i<=npar; i++) 
         for (k=1; k<=cptcovn;k++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                  
         }        cptj=0;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=1; j<= nlstate; j++){
         for (k=1; k<=cptcovprod;k++)          for(i=1;i<=nlstate;i++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            cptj=cptj+1;
                    for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         gradg=matrix(1,npar,1,9);  
         trgradg=matrix(1,9,1,npar);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
            }
         for(theta=1; theta <=npar; theta++){        for(j=1; j<= nlstate*nlstate; j++)
           for(i=1; i<=npar; i++)          for(h=0; h<=nhstepm-1; h++){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                    }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       } 
               
           k=0;  /* End theta */
           for(i=1; i<= (nlstate+ndeath); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
               k=k+1;  
               gp[k]=pmmij[i][j];       for(h=0; h<=nhstepm-1; h++)
             }        for(j=1; j<=nlstate*nlstate;j++)
           }          for(theta=1; theta <=npar; theta++)
                      trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<=npar; i++)       
             xp[i] = x[i] - (i==theta ?delti[theta]:0);  
           for(i=1;i<=nlstate*nlstate;i++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(j=1;j<=nlstate*nlstate;j++)
           k=0;          varhe[i][j][(int)age] =0.;
           for(i=1; i<=(nlstate+ndeath); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){       printf("%d|",(int)age);fflush(stdout);
               k=k+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               gm[k]=pmmij[i][j];       for(h=0;h<=nhstepm-1;h++){
             }        for(k=0;k<=nhstepm-1;k++){
           }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          for(i=1;i<=nlstate*nlstate;i++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              for(j=1;j<=nlstate*nlstate;j++)
         }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      }
           for(theta=1; theta <=npar; theta++)      /* Computing expectancies */
             trgradg[j][theta]=gradg[theta][j];      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                    
         pmij(pmmij,cov,ncovmodel,x,nlstate);  /* 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]);*/
          
         k=0;          }
         for(i=1; i<=(nlstate+ndeath); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficreseij,"%3.0f",age );
             k=k+1;      cptj=0;
             gm[k]=pmmij[i][j];      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++){
         }          cptj++;
                fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
      /*printf("\n%d ",(int)age);        }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      fprintf(ficreseij,"\n");
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));     
      }*/      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficresprob,"\n%d ",(int)age);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    }
      printf("\n");
       }    fprintf(ficlog,"\n");
     }  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(xp,1,npar);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }  }
   free_vector(xp,1,npar);  
   fclose(ficresprob);  /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
 }  {
     /* Variance of health expectancies */
 /******************* Printing html file ***********/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    /* double **newm;*/
  int lastpass, int stepm, int weightopt, char model[],\    double **dnewm,**doldm;
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    double **dnewmp,**doldmp;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    int i, j, nhstepm, hstepm, h, nstepm ;
  char version[], int popforecast, int estepm ){    int k, cptcode;
   int jj1, k1, i1, cpt;    double *xp;
   FILE *fichtm;    double **gp, **gm;  /* for var eij */
   /*char optionfilehtm[FILENAMELENGTH];*/    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   strcpy(optionfilehtm,optionfile);    double *gpp, *gmp; /* for var p point j */
   strcat(optionfilehtm,".htm");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    double ***p3mat;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double age,agelim, hf;
   }    double ***mobaverage;
     int theta;
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    char digit[4];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    char digitp[25];
 \n  
 Total number of observations=%d <br>\n    char fileresprobmorprev[FILENAMELENGTH];
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  
 <hr  size=\"2\" color=\"#EC5E5E\">    if(popbased==1){
  <ul><li>Outputs files<br>\n      if(mobilav!=0)
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        strcpy(digitp,"-populbased-mobilav-");
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n      else strcpy(digitp,"-populbased-nomobil-");
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    else 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n      strcpy(digitp,"-stablbased-");
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  
     if (mobilav!=0) {
  fprintf(fichtm,"\n      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      }
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    }
   
  if(popforecast==1) fprintf(fichtm,"\n    strcpy(fileresprobmorprev,"prmorprev"); 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    sprintf(digit,"%-d",ij);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         <br>",fileres,fileres,fileres,fileres);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
  else    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
    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);    strcat(fileresprobmorprev,fileres);
 fprintf(fichtm," <li>Graphs</li><p>");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
  m=cptcoveff;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  jj1=0;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  for(k1=1; k1<=m;k1++){    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);
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
        jj1++;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        if (cptcovn > 0) {      fprintf(ficresprobmorprev," p.%-d SE",j);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      for(i=1; i<=nlstate;i++)
          for (cpt=1; cpt<=cptcoveff;cpt++)        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    }  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficresprobmorprev,"\n");
        }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        for(cpt=1; cpt<nlstate;cpt++){      exit(0);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    else{
        }      fprintf(ficgp,"\n# Routine varevsij");
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
 interval) in state (%d): v%s%d%d.gif <br>      printf("Problem with html file: %s\n", optionfilehtm);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      }      exit(0);
      for(cpt=1; cpt<=nlstate;cpt++) {    }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    else{
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      }      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    }
 health expectancies in states (1) and (2): e%s%d.gif<br>    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
 fprintf(fichtm,"\n</body>");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
    }    fprintf(ficresvij,"# Age");
    }    for(i=1; i<=nlstate;i++)
 fclose(fichtm);      for(j=1; j<=nlstate;j++)
 }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   strcpy(optionfilegnuplot,optionfilefiname);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(optionfilegnuplot,".gp.txt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     printf("Problem with file %s",optionfilegnuplot);    gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 #ifdef windows    
     fprintf(ficgp,"cd \"%s\" \n",pathc);    if(estepm < stepm){
 #endif      printf ("Problem %d lower than %d\n",estepm, stepm);
 m=pow(2,cptcoveff);    }
      else  hstepm=estepm;   
  /* 1eme*/    /* For example we decided to compute the life expectancy with the smallest unit */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    for (k1=1; k1<= m ; k1 ++) {       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
 for (i=1; i<= nlstate ; i ++) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       survival function given by stepm (the optimization length). Unfortunately it
   else fprintf(ficgp," \%%*lf (\%%*lf)");       means that if the survival funtion is printed every two years of age and if
 }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       results. So we changed our mind and took the option of the best precision.
     for (i=1; i<= nlstate ; i ++) {    */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    agelim = AGESUP;
 }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      for (i=1; i<= nlstate ; i ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 }        gp=matrix(0,nhstepm,1,nlstate);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      gm=matrix(0,nhstepm,1,nlstate);
   
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   /*2 eme*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   for (k1=1; k1<= m ; k1 ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      
     for (i=1; i<= nlstate+1 ; i ++) {        if (popbased==1) {
       k=2*i;          if(mobilav ==0){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            for(i=1; i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {              prlim[i][i]=probs[(int)age][i][ij];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }else{ /* mobilav */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1; i<=nlstate;i++)
 }                prlim[i][i]=mobaverage[(int)age][i][ij];
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {        for(j=1; j<= nlstate; j++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(h=0; h<=nhstepm; h++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 }                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       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 ++) {        /* This for computing probability of death (h=1 means
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           computed over hstepm matrices product = hstepm*stepm months) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");           as a weighted average of prlim.
 }          */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       else fprintf(ficgp,"\" t\"\" w l 0,");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        }    
   }        /* end probability of death */
    
   /*3eme*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   for (k1=1; k1<= m ; k1 ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for (cpt=1; cpt<= nlstate ; cpt ++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       k=2+nlstate*(2*cpt-2);   
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        if (popbased==1) {
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          if(mobilav ==0){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              prlim[i][i]=probs[(int)age][i][ij];
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          }else{ /* mobilav */ 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
 */        }
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
       }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     }          }
     }        }
          /* This for computing probability of death (h=1 means
   /* CV preval stat */           computed over hstepm matrices product = hstepm*stepm months) 
     for (k1=1; k1<= m ; k1 ++) {           as a weighted average of prlim.
     for (cpt=1; cpt<nlstate ; cpt ++) {        */
       k=3;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
       for (i=1; i< nlstate ; i ++)        }    
         fprintf(ficgp,"+$%d",k+i+1);        /* end probability of death */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
              for(j=1; j<= nlstate; j++) /* vareij */
       l=3+(nlstate+ndeath)*cpt;          for(h=0; h<=nhstepm; h++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for (i=1; i< nlstate ; i ++) {          }
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       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);  
     }      } /* End theta */
   }    
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){      for(h=0; h<=nhstepm; h++) /* veij */
     for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<=nlstate;j++)
       if (k != i) {          for(theta=1; theta <=npar; theta++)
         for(j=1; j <=ncovmodel; j++){            trgradg[h][j][theta]=gradg[h][theta][j];
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           jk++;        for(theta=1; theta <=npar; theta++)
           fprintf(ficgp,"\n");          trgradgp[j][theta]=gradgp[theta][j];
         }    
       }  
     }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
     for(jk=1; jk <=m; jk++) {          vareij[i][j][(int)age] =0.;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);  
    i=1;      for(h=0;h<=nhstepm;h++){
    for(k2=1; k2<=nlstate; k2++) {        for(k=0;k<=nhstepm;k++){
      k3=i;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      for(k=1; k<=(nlstate+ndeath); k++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
        if (k != k2){          for(i=1;i<=nlstate;i++)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            for(j=1;j<=nlstate;j++)
 ij=1;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for(j=3; j <=ncovmodel; j++) {        }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    
             ij++;      /* pptj */
           }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           else      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           fprintf(ficgp,")/(1");          varppt[j][i]=doldmp[j][i];
              /* end ppptj */
         for(k1=1; k1 <=nlstate; k1++){        /*  x centered again */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 ij=1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           for(j=3; j <=ncovmodel; j++){   
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      if (popbased==1) {
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if(mobilav ==0){
             ij++;          for(i=1; i<=nlstate;i++)
           }            prlim[i][i]=probs[(int)age][i][ij];
           else        }else{ /* mobilav */ 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(i=1; i<=nlstate;i++)
           }            prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficgp,")");        }
         }      }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);               
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      /* This for computing probability of death (h=1 means
         i=i+ncovmodel;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
        }         as a weighted average of prlim.
      }      */
    }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
    }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
          }    
   fclose(ficgp);      /* end probability of death */
 }  /* end gnuplot */  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 /*************** Moving average **************/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   int i, cpt, cptcod;        }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      } 
       for (i=1; i<=nlstate;i++)      fprintf(ficresprobmorprev,"\n");
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;      fprintf(ficresvij,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        for(j=1; j<=nlstate;j++){
       for (i=1; i<=nlstate;i++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
           for (cpt=0;cpt<=4;cpt++){      fprintf(ficresvij,"\n");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      free_matrix(gp,0,nhstepm,1,nlstate);
           }      free_matrix(gm,0,nhstepm,1,nlstate);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
 }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 /************** Forecasting ******************/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   int *popage;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   double *popeffectif,*popcount;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
   double ***p3mat;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   char fileresf[FILENAMELENGTH];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
  agelim=AGESUP;    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);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /*  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);
   */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
    
      free_vector(xp,1,npar);
   strcpy(fileresf,"f");    free_matrix(doldm,1,nlstate,1,nlstate);
   strcat(fileresf,fileres);    free_matrix(dnewm,1,nlstate,1,npar);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("Problem with forecast resultfile: %s\n", fileresf);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fclose(ficgp);
     fclose(fichtm);
   if (mobilav==1) {  }  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);  /************ Variance of prevlim ******************/
   }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   {
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /* Variance of prevalence limit */
   if (stepm<=12) stepsize=1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
      double **newm;
   agelim=AGESUP;    double **dnewm,**doldm;
      int i, j, nhstepm, hstepm;
   hstepm=1;    int k, cptcode;
   hstepm=hstepm/stepm;    double *xp;
   yp1=modf(dateintmean,&yp);    double *gp, *gm;
   anprojmean=yp;    double **gradg, **trgradg;
   yp2=modf((yp1*12),&yp);    double age,agelim;
   mprojmean=yp;    int theta;
   yp1=modf((yp2*30.5),&yp);     
   jprojmean=yp;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   if(jprojmean==0) jprojmean=1;    fprintf(ficresvpl,"# Age");
   if(mprojmean==0) jprojmean=1;    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    fprintf(ficresvpl,"\n");
    
   for(cptcov=1;cptcov<=i2;cptcov++){    xp=vector(1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    dnewm=matrix(1,nlstate,1,npar);
       k=k+1;    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficresf,"\n#******");    
       for(j=1;j<=cptcoveff;j++) {    hstepm=1*YEARM; /* Every year of age */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       }    agelim = AGESUP;
       fprintf(ficresf,"******\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresf,"# StartingAge FinalAge");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      if (stepm >= YEARM) hstepm=1;
            nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
            gradg=matrix(1,npar,1,nlstate);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      gp=vector(1,nlstate);
         fprintf(ficresf,"\n");      gm=vector(1,nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
       for(theta=1; theta <=npar; theta++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=1; i<=npar; i++){ /* Computes gradient */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           nhstepm = nhstepm/hstepm;        }
                  prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1;i<=nlstate;i++)
           oldm=oldms;savm=savms;          gp[i] = prlim[i][i];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
                for(i=1; i<=npar; i++) /* Computes gradient */
           for (h=0; h<=nhstepm; h++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             if (h==(int) (calagedate+YEARM*cpt)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        for(i=1;i<=nlstate;i++)
             }          gm[i] = prlim[i][i];
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;        for(i=1;i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                 if (mobilav==1)      } /* End theta */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {      trgradg =matrix(1,nlstate,1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }      for(j=1; j<=nlstate;j++)
                        for(theta=1; theta <=npar; theta++)
               }          trgradg[j][theta]=gradg[theta][j];
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);      for(i=1;i<=nlstate;i++)
                                varpl[i][(int)age] =0.;
               }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
             }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           }      for(i=1;i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         }  
       }      fprintf(ficresvpl,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
              fprintf(ficresvpl,"\n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
   fclose(ficresf);      free_matrix(gradg,1,npar,1,nlstate);
 }      free_matrix(trgradg,1,nlstate,1,npar);
 /************** Forecasting ******************/    } /* End age */
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  
      free_vector(xp,1,npar);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_matrix(doldm,1,nlstate,1,npar);
   int *popage;    free_matrix(dnewm,1,nlstate,1,nlstate);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;  }
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, j=0,  i1, k1, l1, t, tj;
   agelim=AGESUP;    int k2, l2, j1,  z1;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    int k=0,l, cptcode;
      int first=1, first1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
      double *xp;
   strcpy(filerespop,"pop");    double *gp, *gm;
   strcat(filerespop,fileres);    double **gradg, **trgradg;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    double **mu;
     printf("Problem with forecast resultfile: %s\n", filerespop);    double age,agelim, cov[NCOVMAX];
   }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int theta;
     char fileresprob[FILENAMELENGTH];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double ***varpij;
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if (stepm<=12) stepsize=1;      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   agelim=AGESUP;    }
      strcpy(fileresprobcov,"probcov"); 
   hstepm=1;    strcat(fileresprobcov,fileres);
   hstepm=hstepm/stepm;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   if (popforecast==1) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     if((ficpop=fopen(popfile,"r"))==NULL) {    }
       printf("Problem with population file : %s\n",popfile);exit(0);    strcpy(fileresprobcor,"probcor"); 
     }    strcat(fileresprobcor,fileres);
     popage=ivector(0,AGESUP);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     popeffectif=vector(0,AGESUP);      printf("Problem with resultfile: %s\n", fileresprobcor);
     popcount=vector(0,AGESUP);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
        }
     i=1;      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     imx=i;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresprob,"# Age");
       k=k+1;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       fprintf(ficrespop,"\n#******");    fprintf(ficresprobcov,"# Age");
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcov,"# Age");
       }  
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      for(j=1; j<=(nlstate+ndeath);j++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
              fprintf(ficresprobcov," p%1d-%1d ",i,j);
       for (cpt=0; cpt<=0;cpt++) {        fprintf(ficresprobcor," p%1d-%1d ",i,j);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        }  
           /* fprintf(ficresprob,"\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresprobcov,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficresprobcor,"\n");
           nhstepm = nhstepm/hstepm;   */
             xp=vector(1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           oldm=oldms;savm=savms;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
            varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           for (h=0; h<=nhstepm; h++){    first=1;
             if (h==(int) (calagedate+YEARM*cpt)) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
             }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
             for(j=1; j<=nlstate+ndeath;j++) {      exit(0);
               kk1=0.;kk2=0;    }
               for(i=1; i<=nlstate;i++) {                  else{
                 if (mobilav==1)      fprintf(ficgp,"\n# Routine varprob");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      printf("Problem with html file: %s\n", optionfilehtm);
                 }      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
               }      exit(0);
               if (h==(int)(calagedate+12*cpt)){    }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    else{
                   /*fprintf(ficrespop," %.3f", kk1);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      fprintf(fichtm,"\n");
               }  
             }      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
             for(i=1; i<=nlstate;i++){      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");
               kk1=0.;      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");
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    }
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    cov[1]=1;
             }    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    j1=0;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    for(t=1; t<=tj;t++){
           }      for(i1=1; i1<=ncodemax[t];i1++){ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;
         }        if  (cptcovn>0) {
       }          fprintf(ficresprob, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /******/          fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficresprobcov, "**********\n#\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          fprintf(ficgp, "\n#********** Variable "); 
           nhstepm = nhstepm/hstepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                    fprintf(ficgp, "**********\n#\n");
           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(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (h=0; h<=nhstepm; h++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          
             }          fprintf(ficresprobcor, "\n#********** Variable ");    
             for(j=1; j<=nlstate+ndeath;j++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               kk1=0.;kk2=0;          fprintf(ficresprobcor, "**********\n#");    
               for(i=1; i<=nlstate;i++) {                      }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            
               }        for (age=bage; age<=fage; age ++){ 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          cov[2]=age;
             }          for (k=1; k<=cptcovn;k++) {
           }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }          for (k=1; k<=cptcovprod;k++)
    }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }          
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
   if (popforecast==1) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
     free_ivector(popage,0,AGESUP);      
     free_vector(popeffectif,0,AGESUP);          for(theta=1; theta <=npar; theta++){
     free_vector(popcount,0,AGESUP);            for(i=1; i<=npar; i++)
   }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   fclose(ficrespop);            
 }            k=0;
             for(i=1; i<= (nlstate); i++){
 /***********************************************/              for(j=1; j<=(nlstate+ndeath);j++){
 /**************** Main Program *****************/                k=k+1;
 /***********************************************/                gp[k]=pmmij[i][j];
               }
 int main(int argc, char *argv[])            }
 {            
             for(i=1; i<=npar; i++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   double agedeb, agefin,hf;      
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   double fret;            for(i=1; i<=(nlstate); i++){
   double **xi,tmp,delta;              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   double dum; /* Dummy variable */                gm[k]=pmmij[i][j];
   double ***p3mat;              }
   int *indx;            }
   char line[MAXLINE], linepar[MAXLINE];       
   char title[MAXLINE];            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          }
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
   char filerest[FILENAMELENGTH];              trgradg[j][theta]=gradg[theta][j];
   char fileregp[FILENAMELENGTH];          
   char popfile[FILENAMELENGTH];          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   int firstobs=1, lastobs=10;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   int sdeb, sfin; /* Status at beginning and end */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   int c,  h , cpt,l;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   int ju,jl, mi;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   int mobilav=0,popforecast=0;          
   int hstepm, nhstepm;          k=0;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
   double bage, fage, age, agelim, agebase;              k=k+1;
   double ftolpl=FTOL;              mu[k][(int) age]=pmmij[i][j];
   double **prlim;            }
   double *severity;          }
   double ***param; /* Matrix of parameters */          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   double  *p;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   double **matcov; /* Matrix of covariance */              varpij[i][j][(int)age] = doldm[i][j];
   double ***delti3; /* Scale */  
   double *delti; /* Scale */          /*printf("\n%d ",(int)age);
   double ***eij, ***vareij;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   double **varpl; /* Variances of prevalence limits by age */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double *epj, vepp;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   double kk1, kk2;            }*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
            fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   char version[80]="Imach version 0.8a1, June 2003, INED-EUROREVES ";          fprintf(ficresprobcor,"\n%d ",(int)age);
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   char z[1]="c", occ;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 #include <sys/time.h>            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 #include <time.h>            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          }
            i=0;
   /* long total_usecs;          for (k=1; k<=(nlstate);k++){
   struct timeval start_time, end_time;            for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   getcwd(pathcd, size);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
   printf("\n%s",version);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   if(argc <=1){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     printf("\nEnter the parameter file name: ");              }
     scanf("%s",pathtot);            }
   }          }/* end of loop for state */
   else{        } /* end of loop for age */
     strcpy(pathtot,argv[1]);  
   }        /* Confidence intervalle of pij  */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        /*
   /*cygwin_split_path(pathtot,path,optionfile);          fprintf(ficgp,"\nset noparametric;unset label");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   /* cutv(path,optionfile,pathtot,'\\');*/          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);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   chdir(path);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   replace(pathc,path);        */
   
 /*-------- arguments in the command line --------*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
   strcpy(fileres,"r");        for (k2=1; k2<=(nlstate);k2++){
   strcat(fileres, optionfilefiname);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   strcat(fileres,".txt");    /* Other files have txt extension */            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   /*---------arguments file --------*/            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                if(l1==k1) continue;
     printf("Problem with optionfile %s\n",optionfile);                i=(k1-1)*(nlstate+ndeath)+l1;
     goto end;                if(i<=j) continue;
   }                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   strcpy(filereso,"o");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   strcat(filereso,fileres);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   if((ficparo=fopen(filereso,"w"))==NULL) {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   }                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
   /* Reads comments: lines beginning with '#' */                    /* Computing eigen value of matrix of covariance */
   while((c=getc(ficpar))=='#' && c!= EOF){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ungetc(c,ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fgets(line, MAXLINE, ficpar);                    /* Eigen vectors */
     puts(line);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     fputs(line,ficparo);                    /*v21=sqrt(1.-v11*v11); *//* error */
   }                    v21=(lc1-v1)/cv12*v11;
   ungetc(c,ficpar);                    v12=-v21;
                     v22=v11;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                    tnalp=v21/v11;
   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);                    if(first1==1){
   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);                      first1=0;
 while((c=getc(ficpar))=='#' && c!= EOF){                      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);
     ungetc(c,ficpar);                    }
     fgets(line, MAXLINE, ficpar);                    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);
     puts(line);                    /*printf(fignu*/
     fputs(line,ficparo);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   ungetc(c,ficpar);                    if(first==1){
                        first=0;
                          fprintf(ficgp,"\nset parametric;unset label");
   covar=matrix(0,NCOVMAX,1,n);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   cptcovn=0;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
   ncovmodel=2+cptcovn;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   /* Read guess parameters */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   /* Reads comments: lines beginning with '#' */                      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",\
   while((c=getc(ficpar))=='#' && c!= EOF){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     ungetc(c,ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     fgets(line, MAXLINE, ficpar);                    }else{
     puts(line);                      first=0;
     fputs(line,ficparo);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   ungetc(c,ficpar);                      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",\
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     for(i=1; i <=nlstate; i++)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     for(j=1; j <=nlstate+ndeath-1; j++){                    }/* if first */
       fscanf(ficpar,"%1d%1d",&i1,&j1);                  } /* age mod 5 */
       fprintf(ficparo,"%1d%1d",i1,j1);                } /* end loop age */
       printf("%1d%1d",i,j);                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
       for(k=1; k<=ncovmodel;k++){                first=1;
         fscanf(ficpar," %lf",&param[i][j][k]);              } /*l12 */
         printf(" %lf",param[i][j][k]);            } /* k12 */
         fprintf(ficparo," %lf",param[i][j][k]);          } /*l1 */
       }        }/* k1 */
       fscanf(ficpar,"\n");      } /* loop covariates */
       printf("\n");    }
       fprintf(ficparo,"\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_vector(xp,1,npar);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fclose(ficresprob);
     fclose(ficresprobcov);
   p=param[1][1];    fclose(ficresprobcor);
      fclose(ficgp);
   /* Reads comments: lines beginning with '#' */    fclose(fichtm);
   while((c=getc(ficpar))=='#' && c!= EOF){  }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /******************* Printing html file ***********/
     fputs(line,ficparo);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   }                    int lastpass, int stepm, int weightopt, char model[],\
   ungetc(c,ficpar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                    double jprev1, double mprev1,double anprev1, \
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                    double jprev2, double mprev2,double anprev2){
   for(i=1; i <=nlstate; i++){    int jj1, k1, i1, cpt;
     for(j=1; j <=nlstate+ndeath-1; j++){    /*char optionfilehtm[FILENAMELENGTH];*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
       printf("%1d%1d",i,j);      printf("Problem with %s \n",optionfilehtm), exit(0);
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
         fprintf(ficparo," %le",delti3[i][j][k]);   - 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
       }   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
       fscanf(ficpar,"\n");   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
       printf("\n");   - Life expectancies by age and initial health status (estepm=%2d months): 
       fprintf(ficparo,"\n");     <a href=\"e%s\">e%s</a> <br>\n</li>", \
     }    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   }  
   delti=delti3[1][1];  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    
   /* Reads comments: lines beginning with '#' */   m=cptcoveff;
   while((c=getc(ficpar))=='#' && c!= EOF){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   jj1=0;
     puts(line);   for(k1=1; k1<=m;k1++){
     fputs(line,ficparo);     for(i1=1; i1<=ncodemax[k1];i1++){
   }       jj1++;
   ungetc(c,ficpar);       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   matcov=matrix(1,npar,1,npar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   for(i=1; i <=npar; i++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fscanf(ficpar,"%s",&str);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("%s",str);       }
     fprintf(ficparo,"%s",str);       /* Pij */
     for(j=1; j <=i; j++){       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>
       fscanf(ficpar," %le",&matcov[i][j]);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
       printf(" %.5le",matcov[i][j]);       /* Quasi-incidences */
       fprintf(ficparo," %.5le",matcov[i][j]);       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); 
     fscanf(ficpar,"\n");         /* Stable prevalence in each health state */
     printf("\n");         for(cpt=1; cpt<nlstate;cpt++){
     fprintf(ficparo,"\n");           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);
   for(i=1; i <=npar; i++)         }
     for(j=i+1;j<=npar;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
       matcov[i][j]=matcov[j][i];          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
      <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   printf("\n");       }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and
   health expectancies in states (1) and (2): e%s%d.png<br>
     /*-------- Rewriting paramater file ----------*/  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      strcpy(rfileres,"r");    /* "Rparameterfile */     } /* end i1 */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/   }/* End k1 */
      strcat(rfileres,".");    /* */   fprintf(fichtm,"</ul>");
      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(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
     }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
     fprintf(ficres,"#%s\n",version);   - 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
     /*-------- data file ----------*/   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     if((fic=fopen(datafile,"r"))==NULL)    {   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
       printf("Problem with datafile: %s\n", datafile);goto end;   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     }   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
     n= lastobs;  /*  if(popforecast==1) fprintf(fichtm,"\n */
     severity = vector(1,maxwav);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     outcome=imatrix(1,maxwav+1,1,n);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     num=ivector(1,n);  /*      <br>",fileres,fileres,fileres,fileres); */
     moisnais=vector(1,n);  /*  else  */
     annais=vector(1,n);  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     moisdc=vector(1,n);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     andc=vector(1,n);  
     agedc=vector(1,n);   m=cptcoveff;
     cod=ivector(1,n);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */   jj1=0;
     mint=matrix(1,maxwav,1,n);   for(k1=1; k1<=m;k1++){
     anint=matrix(1,maxwav,1,n);     for(i1=1; i1<=ncodemax[k1];i1++){
     s=imatrix(1,maxwav+1,1,n);       jj1++;
     adl=imatrix(1,maxwav+1,1,n);           if (cptcovn > 0) {
     tab=ivector(1,NCOVMAX);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     ncodemax=ivector(1,8);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     i=1;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     while (fgets(line, MAXLINE, fic) != NULL)    {       }
       if ((i >= firstobs) && (i <=lastobs)) {       for(cpt=1; cpt<=nlstate;cpt++) {
                 fprintf(fichtm,"<br>- Observed and period prevalence (with confident
         for (j=maxwav;j>=1;j--){  interval) in state (%d): v%s%d%d.png <br>
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
           strcpy(line,stra);       }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);     } /* end i1 */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   }/* End k1 */
         }   fprintf(fichtm,"</ul>");
          fclose(fichtm);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /******************* Gnuplot file **************/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    int ng;
         for (j=ncovcol;j>=1;j--){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      printf("Problem with file %s",optionfilegnuplot);
         }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
         num[i]=atol(stra);    }
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    /*#ifdef windows */
           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(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
         i=i+1;  m=pow(2,cptcoveff);
       }    
     }   /* 1eme*/
     /* printf("ii=%d", ij);    for (cpt=1; cpt<= nlstate ; cpt ++) {
        scanf("%d",i);*/     for (k1=1; k1<= m ; k1 ++) {
   imx=i-1; /* Number of individuals */       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;       for (i=1; i<= nlstate ; i ++) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;         else fprintf(ficgp," \%%*lf (\%%*lf)");
     }*/       }
    /*  for (i=1; i<=imx; i++){       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);
      if (s[4][i]==9)  s[4][i]=-1;       for (i=1; i<= nlstate ; 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]));}*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
   /* Calculation of the number of parameter from char model*/       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
   Tvar=ivector(1,15);       for (i=1; i<= nlstate ; i ++) {
   Tprod=ivector(1,15);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   Tvaraff=ivector(1,15);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   Tvard=imatrix(1,15,1,2);       }  
   Tage=ivector(1,15);             fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
         }
   if (strlen(model) >1){    }
     j=0, j1=0, k1=1, k2=1;    /*2 eme*/
     j=nbocc(model,'+');    
     j1=nbocc(model,'*');    for (k1=1; k1<= m ; k1 ++) { 
     cptcovn=j+1;      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     cptcovprod=j1;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
          
     strcpy(modelsav,model);      for (i=1; i<= nlstate+1 ; i ++) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        k=2*i;
       printf("Error. Non available option model=%s ",model);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
       goto end;        for (j=1; j<= nlstate+1 ; j ++) {
     }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(i=(j+1); i>=1;i--){        }   
       cutv(stra,strb,modelsav,'+');        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
       /*scanf("%d",i);*/        for (j=1; j<= nlstate+1 ; j ++) {
       if (strchr(strb,'*')) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         cutv(strd,strc,strb,'*');          else fprintf(ficgp," \%%*lf (\%%*lf)");
         if (strcmp(strc,"age")==0) {        }   
           cptcovprod--;        fprintf(ficgp,"\" t\"\" w l 0,");
           cutv(strb,stre,strd,'V');        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
           Tvar[i]=atoi(stre);        for (j=1; j<= nlstate+1 ; j ++) {
           cptcovage++;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
             Tage[cptcovage]=i;          else fprintf(ficgp," \%%*lf (\%%*lf)");
             /*printf("stre=%s ", stre);*/        }   
         }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else if (strcmp(strd,"age")==0) {        else fprintf(ficgp,"\" t\"\" w l 0,");
           cptcovprod--;      }
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=atoi(stre);    
           cptcovage++;    /*3eme*/
           Tage[cptcovage]=i;    
         }    for (k1=1; k1<= m ; k1 ++) { 
         else {      for (cpt=1; cpt<= nlstate ; cpt ++) {
           cutv(strb,stre,strc,'V');        k=2+nlstate*(2*cpt-2);
           Tvar[i]=ncovcol+k1;        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           cutv(strb,strc,strd,'V');        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
           Tprod[k1]=i;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           Tvard[k1][1]=atoi(strc);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           Tvard[k1][2]=atoi(stre);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           Tvar[cptcovn+k2]=Tvard[k1][1];          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           for (k=1; k<=lastobs;k++)          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          
           k1++;        */
           k2=k2+2;        for (i=1; i< nlstate ; i ++) {
         }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
       }          
       else {        } 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      }
        /*  scanf("%d",i);*/    }
       cutv(strd,strc,strb,'V');    
       Tvar[i]=atoi(strc);    /* CV preval stable (period) */
       }    for (k1=1; k1<= m ; k1 ++) { 
       strcpy(modelsav,stra);        for (cpt=1; cpt<=nlstate ; cpt ++) {
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        k=3;
         scanf("%d",i);*/        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     }        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
 }        
          for (i=1; i<= nlstate ; i ++)
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          fprintf(ficgp,"+$%d",k+i+1);
   printf("cptcovprod=%d ", cptcovprod);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   scanf("%d ",i);*/        
     fclose(fic);        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
     /*  if(mle==1){*/        for (i=1; i< nlstate ; i ++) {
     if (weightopt != 1) { /* Maximisation without weights*/          l=3+(nlstate+ndeath)*cpt;
       for(i=1;i<=n;i++) weight[i]=1.0;          fprintf(ficgp,"+$%d",l+i+1);
     }        }
     /*-calculation of age at interview from date of interview and age at death -*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     agev=matrix(1,maxwav,1,imx);      } 
     }  
     for (i=1; i<=imx; i++) {    
       for(m=2; (m<= maxwav); m++) {    /* proba elementaires */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    for(i=1,jk=1; i <=nlstate; i++){
          anint[m][i]=9999;      for(k=1; k <=(nlstate+ndeath); k++){
          s[m][i]=-1;        if (k != i) {
        }          for(j=1; j <=ncovmodel; j++){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       }            jk++; 
     }            fprintf(ficgp,"\n");
           }
     for (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      }
       for(m=1; (m<= maxwav); m++){     }
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
             if(agedc[i]>0)       for(jk=1; jk <=m; jk++) {
               if(moisdc[i]!=99 && andc[i]!=9999)         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
                 agev[m][i]=agedc[i];         if (ng==2)
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
            else {         else
               if (andc[i]!=9999){           fprintf(ficgp,"\nset title \"Probability\"\n");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
               agev[m][i]=-1;         i=1;
               }         for(k2=1; k2<=nlstate; k2++) {
             }           k3=i;
           }           for(k=1; k<=(nlstate+ndeath); k++) {
           else if(s[m][i] !=9){ /* Should no more exist */             if (k != k2){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);               if(ng==2)
             if(mint[m][i]==99 || anint[m][i]==9999)                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
               agev[m][i]=1;               else
             else if(agev[m][i] <agemin){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
               agemin=agev[m][i];               ij=1;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/               for(j=3; j <=ncovmodel; j++) {
             }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
             else if(agev[m][i] >agemax){                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
               agemax=agev[m][i];                   ij++;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                 }
             }                 else
             /*agev[m][i]=anint[m][i]-annais[i];*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             /*   agev[m][i] = age[i]+2*m;*/               }
           }               fprintf(ficgp,")/(1");
           else { /* =9 */               
             agev[m][i]=1;               for(k1=1; k1 <=nlstate; k1++){   
             s[m][i]=-1;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
           }                 ij=1;
         }                 for(j=3; j <=ncovmodel; j++){
         else /*= 0 Unknown */                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           agev[m][i]=1;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       }                     ij++;
                       }
     }                   else
     for (i=1; i<=imx; i++)  {                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       for(m=1; (m<= maxwav); m++){                 }
         if (s[m][i] > (nlstate+ndeath)) {                 fprintf(ficgp,")");
           printf("Error: Wrong value in nlstate or ndeath\n");                 }
           goto end;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
         }               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       }               i=i+ncovmodel;
     }             }
            } /* end k */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);         } /* end k2 */
        } /* end jk */
     free_vector(severity,1,maxwav);     } /* end ng */
     free_imatrix(outcome,1,maxwav+1,1,n);     fclose(ficgp); 
     free_vector(moisnais,1,n);  }  /* end gnuplot */
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/  /*************** Moving average **************/
     free_vector(moisdc,1,n);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     free_vector(andc,1,n);  
     int i, cpt, cptcod;
        int modcovmax =1;
     wav=ivector(1,imx);    int mobilavrange, mob;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double age;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
        modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     /* Concatenates waves */                             a covariate has 2 modalities */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       Tcode=ivector(1,100);      if(mobilav==1) mobilavrange=5; /* default */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      else mobilavrange=mobilav;
       ncodemax[1]=1;      for (age=bage; age<=fage; age++)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for (i=1; i<=nlstate;i++)
                for (cptcod=1;cptcod<=modcovmax;cptcod++)
    codtab=imatrix(1,100,1,10);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
    h=0;      /* We keep the original values on the extreme ages bage, fage and for 
    m=pow(2,cptcoveff);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
    for(k=1;k<=cptcoveff; k++){      */ 
      for(i=1; i <=(m/pow(2,k));i++){      for (mob=3;mob <=mobilavrange;mob=mob+2){
        for(j=1; j <= ncodemax[k]; j++){        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for (i=1; i<=nlstate;i++){
            h++;            for (cptcod=1;cptcod<=modcovmax;cptcod++){
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                for (cpt=1;cpt<=(mob-1)/2;cpt++){
          }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
        }                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
      }                }
    }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
    /* 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++){        }/* end age */
       for(k=1; k <=cptcovn; k++){      }/* end mob */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    }else return -1;
       }    return 0;
       printf("\n");  }/* End movingaverage */
       }  
       scanf("%d",i);*/  
      /************** Forecasting ******************/
    /* Calculates basic frequencies. Computes observed prevalence at single age  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){
        and prints on file fileres'p'. */    /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
           dateprev1 dateprev2 range of dates during which prevalence is computed
           anproj2 year of en of projection (same day and month as proj1).
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int *popage;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double agec; /* generic age */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
          double *popeffectif,*popcount;
     /* For Powell, parameters are in a vector p[] starting at p[1]    double ***p3mat;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    double ***mobaverage;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    char fileresf[FILENAMELENGTH];
   
     if(mle==1){    agelim=AGESUP;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     }   
        strcpy(fileresf,"f"); 
     /*--------- results files --------------*/    strcat(fileresf,fileres);
     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);    if((ficresf=fopen(fileresf,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    jk=1;    }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("Computing forecasting: result on file '%s' \n", fileresf);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
        if (k != i)  
          {    if (mobilav!=0) {
            printf("%d%d ",i,k);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            fprintf(ficres,"%1d%1d ",i,k);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
            for(j=1; j <=ncovmodel; j++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              printf("%f ",p[jk]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
              fprintf(ficres,"%f ",p[jk]);      }
              jk++;    }
            }  
            printf("\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
            fprintf(ficres,"\n");    if (stepm<=12) stepsize=1;
          }    if(estepm < stepm){
      }      printf ("Problem %d lower than %d\n",estepm, stepm);
    }    }
  if(mle==1){    else  hstepm=estepm;   
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    hstepm=hstepm/stepm; 
     hesscov(matcov, p, npar, delti, ftolhess, func);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
  }                                 fractional in yp1 */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    anprojmean=yp;
     printf("# Scales (for hessian or gradient estimation)\n");    yp2=modf((yp1*12),&yp);
      for(i=1,jk=1; i <=nlstate; i++){    mprojmean=yp;
       for(j=1; j <=nlstate+ndeath; j++){    yp1=modf((yp2*30.5),&yp);
         if (j!=i) {    jprojmean=yp;
           fprintf(ficres,"%1d%1d",i,j);    if(jprojmean==0) jprojmean=1;
           printf("%1d%1d",i,j);    if(mprojmean==0) jprojmean=1;
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);    i1=cptcoveff;
             fprintf(ficres," %.5e",delti[jk]);    if (cptcovn < 1){i1=1;}
             jk++;    
           }    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
           printf("\n");    
           fprintf(ficres,"\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
         }  
       }  /*            if (h==(int)(YEARM*yearp)){ */
      }    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
          for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     k=1;        k=k+1;
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        fprintf(ficresf,"\n#******");
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        for(j=1;j<=cptcoveff;j++) {
     for(i=1;i<=npar;i++){          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]]);
       /*  if (k>nlstate) k=1;        }
       i1=(i-1)/(ncovmodel*nlstate)+1;        fprintf(ficresf,"******\n");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(j=1; j<=nlstate+ndeath;j++){ 
       fprintf(ficres,"%3d",i);          for(i=1; i<=nlstate;i++)              
       printf("%3d",i);            fprintf(ficresf," p%d%d",i,j);
       for(j=1; j<=i;j++){          fprintf(ficresf," p.%d",j);
         fprintf(ficres," %.5e",matcov[i][j]);        }
         printf(" %.5e",matcov[i][j]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       }          fprintf(ficresf,"\n");
       fprintf(ficres,"\n");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       printf("\n");  
       k++;          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     }            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                nhstepm = nhstepm/hstepm; 
     while((c=getc(ficpar))=='#' && c!= EOF){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       ungetc(c,ficpar);            oldm=oldms;savm=savms;
       fgets(line, MAXLINE, ficpar);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       puts(line);          
       fputs(line,ficparo);            for (h=0; h<=nhstepm; h++){
     }              if (h*hstepm/YEARM*stepm ==yearp) {
     ungetc(c,ficpar);                fprintf(ficresf,"\n");
     estepm=0;                for(j=1;j<=cptcoveff;j++) 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     if (estepm==0 || estepm < stepm) estepm=stepm;                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     if (fage <= 2) {              } 
       bage = ageminpar;              for(j=1; j<=nlstate+ndeath;j++) {
       fage = agemaxpar;                ppij=0.;
     }                for(i=1; i<=nlstate;i++) {
                      if (mobilav==1) 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                  else {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                    }
     while((c=getc(ficpar))=='#' && c!= EOF){                  if (h*hstepm/YEARM*stepm== yearp) {
     ungetc(c,ficpar);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
     fgets(line, MAXLINE, ficpar);                  }
     puts(line);                } /* end i */
     fputs(line,ficparo);                if (h*hstepm/YEARM*stepm==yearp) {
   }                  fprintf(ficresf," %.3f", ppij);
   ungetc(c,ficpar);                }
                }/* end j */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            } /* end h */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          } /* end agec */
              } /* end yearp */
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* end cptcod */
     ungetc(c,ficpar);    } /* end  cptcov */
     fgets(line, MAXLINE, ficpar);         
     puts(line);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fputs(line,ficparo);  
   }    fclose(ficresf);
   ungetc(c,ficpar);  }
    
   /************** Forecasting *****not tested NB*************/
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  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){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   fscanf(ficpar,"pop_based=%d\n",&popbased);    int *popage;
   fprintf(ficparo,"pop_based=%d\n",popbased);      double calagedatem, agelim, kk1, kk2;
   fprintf(ficres,"pop_based=%d\n",popbased);      double *popeffectif,*popcount;
      double ***p3mat,***tabpop,***tabpopprev;
   while((c=getc(ficpar))=='#' && c!= EOF){    double ***mobaverage;
     ungetc(c,ficpar);    char filerespop[FILENAMELENGTH];
     fgets(line, MAXLINE, ficpar);  
     puts(line);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fputs(line,ficparo);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }    agelim=AGESUP;
   ungetc(c,ficpar);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
   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);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
 while((c=getc(ficpar))=='#' && c!= EOF){    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     ungetc(c,ficpar);      printf("Problem with forecast resultfile: %s\n", filerespop);
     fgets(line, MAXLINE, ficpar);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     puts(line);    }
     fputs(line,ficparo);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   ungetc(c,ficpar);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   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);    if (mobilav!=0) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
 /*------------ gnuplot -------------*/      }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    }
    
 /*------------ free_vector  -------------*/    stepsize=(int) (stepm+YEARM-1)/YEARM;
  chdir(path);    if (stepm<=12) stepsize=1;
      
  free_ivector(wav,1,imx);    agelim=AGESUP;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      hstepm=1;
  free_ivector(num,1,n);    hstepm=hstepm/stepm; 
  free_vector(agedc,1,n);    
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    if (popforecast==1) {
  fclose(ficparo);      if((ficpop=fopen(popfile,"r"))==NULL) {
  fclose(ficres);        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
 /*--------- index.htm --------*/      } 
       popage=ivector(0,AGESUP);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
        
   /*--------------- Prevalence limit --------------*/      i=1;   
        while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
   strcpy(filerespl,"pl");     
   strcat(filerespl,fileres);      imx=i;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   fprintf(ficrespl,"#Prevalence limit\n");     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   fprintf(ficrespl,"#Age ");        k=k+1;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        fprintf(ficrespop,"\n#******");
   fprintf(ficrespl,"\n");        for(j=1;j<=cptcoveff;j++) {
            fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   prlim=matrix(1,nlstate,1,nlstate);        }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficrespop,"******\n");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficrespop,"# Age");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (popforecast==1)  fprintf(ficrespop," [Population]");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        
   k=0;        for (cpt=0; cpt<=0;cpt++) { 
   agebase=ageminpar;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   agelim=agemaxpar;          
   ftolpl=1.e-10;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   i1=cptcoveff;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   if (cptcovn < 1){i1=1;}            nhstepm = nhstepm/hstepm; 
             
   for(cptcov=1;cptcov<=i1;cptcov++){            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            oldm=oldms;savm=savms;
         k=k+1;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          
         fprintf(ficrespl,"\n#******");            for (h=0; h<=nhstepm; h++){
         for(j=1;j<=cptcoveff;j++)              if (h==(int) (calagedatem+YEARM*cpt)) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         fprintf(ficrespl,"******\n");              } 
                      for(j=1; j<=nlstate+ndeath;j++) {
         for (age=agebase; age<=agelim; age++){                kk1=0.;kk2=0;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                for(i=1; i<=nlstate;i++) {              
           fprintf(ficrespl,"%.0f",age );                  if (mobilav==1) 
           for(i=1; i<=nlstate;i++)                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
           fprintf(ficrespl," %.5f", prlim[i][i]);                  else {
           fprintf(ficrespl,"\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
         }                  }
       }                }
     }                if (h==(int)(calagedatem+12*cpt)){
   fclose(ficrespl);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
   /*------------- h Pij x at various ages ------------*/                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                  }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              for(i=1; i<=nlstate;i++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                kk1=0.;
   }                  for(j=1; j<=nlstate;j++){
   printf("Computing pij: result on file '%s' \n", filerespij);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                    }
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
   /*if (stepm<=24) stepsize=2;*/              }
   
   agelim=AGESUP;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   hstepm=stepsize*YEARM; /* Every year of age */                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
       k=k+1;    /******/
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         fprintf(ficrespij,"******\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
                    nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            nhstepm = nhstepm/hstepm; 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=oldms;savm=savms;
           oldm=oldms;savm=savms;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (h=0; h<=nhstepm; h++){
           fprintf(ficrespij,"# Age");              if (h==(int) (calagedatem+YEARM*cpt)) {
           for(i=1; i<=nlstate;i++)                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
             for(j=1; j<=nlstate+ndeath;j++)              } 
               fprintf(ficrespij," %1d-%1d",i,j);              for(j=1; j<=nlstate+ndeath;j++) {
           fprintf(ficrespij,"\n");                kk1=0.;kk2=0;
            for (h=0; h<=nhstepm; h++){                for(i=1; i<=nlstate;i++) {              
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
             for(i=1; i<=nlstate;i++)                }
               for(j=1; j<=nlstate+ndeath;j++)                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              }
             fprintf(ficrespij,"\n");            }
              }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           fprintf(ficrespij,"\n");        }
         }     } 
     }    }
   }   
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  
     if (popforecast==1) {
   fclose(ficrespij);      free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
   /*---------- Forecasting ------------------*/    }
   if((stepm == 1) && (strcmp(model,".")==0)){    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    fclose(ficrespop);
   }  }
   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);  /**************** Main Program *****************/
   }  /***********************************************/
    
   int main(int argc, char *argv[])
   /*---------- Health expectancies and variances ------------*/  {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   strcpy(filerest,"t");    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   strcat(filerest,fileres);    double agedeb, agefin,hf;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }    double fret;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
   strcpy(filerese,"e");    double ***p3mat;
   strcat(filerese,fileres);    double ***mobaverage;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    int *indx;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    char line[MAXLINE], linepar[MAXLINE];
   }    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
  strcpy(fileresv,"v");    int c,  h , cpt,l;
   strcat(fileresv,fileres);    int ju,jl, mi;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   }    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    int mobilav=0,popforecast=0;
   calagedate=-1;    int hstepm, nhstepm;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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;
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    double bage, fage, age, agelim, agebase;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double ftolpl=FTOL;
       k=k+1;    double **prlim;
       fprintf(ficrest,"\n#****** ");    double *severity;
       for(j=1;j<=cptcoveff;j++)    double ***param; /* Matrix of parameters */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double  *p;
       fprintf(ficrest,"******\n");    double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
       fprintf(ficreseij,"\n#****** ");    double *delti; /* Scale */
       for(j=1;j<=cptcoveff;j++)    double ***eij, ***vareij;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **varpl; /* Variances of prevalence limits by age */
       fprintf(ficreseij,"******\n");    double *epj, vepp;
     double kk1, kk2;
       fprintf(ficresvij,"\n#****** ");    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char *alph[]={"a","a","b","c","d","e"}, str[4];
       fprintf(ficresvij,"******\n");  
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    char z[1]="c", occ;
       oldm=oldms;savm=savms;  #include <sys/time.h>
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    #include <time.h>
      char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   
       oldm=oldms;savm=savms;    /* long total_usecs;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);       struct timeval start_time, end_time;
        
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
      getcwd(pathcd, size);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    printf("\n%s",version);
       fprintf(ficrest,"\n");    if(argc <=1){
       printf("\nEnter the parameter file name: ");
       epj=vector(1,nlstate+1);      scanf("%s",pathtot);
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    else{
         if (popbased==1) {      strcpy(pathtot,argv[1]);
           for(i=1; i<=nlstate;i++)    }
             prlim[i][i]=probs[(int)age][i][k];    /*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);*/
         fprintf(ficrest," %4.0f",age);    /* cutv(path,optionfile,pathtot,'\\');*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    chdir(path);
           }    replace(pathc,path);
           epj[nlstate+1] +=epj[j];  
         }    /*-------- arguments in the command line --------*/
   
         for(i=1, vepp=0.;i <=nlstate;i++)    /* Log file */
           for(j=1;j <=nlstate;j++)    strcat(filelog, optionfilefiname);
             vepp += vareij[i][j][(int)age];    strcat(filelog,".log");    /* */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    if((ficlog=fopen(filelog,"w"))==NULL)    {
         for(j=1;j <=nlstate;j++){      printf("Problem with logfile %s\n",filelog);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      goto end;
         }    }
         fprintf(ficrest,"\n");    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);
 free_matrix(mint,1,maxwav,1,n);    fflush(ficlog);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);    /* */
   fclose(ficreseij);    strcpy(fileres,"r");
   fclose(ficresvij);    strcat(fileres, optionfilefiname);
   fclose(ficrest);    strcat(fileres,".txt");    /* Other files have txt extension */
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    /*---------arguments file --------*/
    
   /*------- Variance limit prevalence------*/      if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
   strcpy(fileresvpl,"vpl");      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
   strcat(fileresvpl,fileres);      goto end;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);    strcpy(filereso,"o");
   }    strcat(filereso,fileres);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
   k=0;      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
   for(cptcov=1;cptcov<=i1;cptcov++){      goto end;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");    /* Reads comments: lines beginning with '#' */
       for(j=1;j<=cptcoveff;j++)    while((c=getc(ficpar))=='#' && c!= EOF){
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      ungetc(c,ficpar);
       fprintf(ficresvpl,"******\n");      fgets(line, MAXLINE, ficpar);
            puts(line);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      fputs(line,ficparo);
       oldm=oldms;savm=savms;    }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    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);
   fclose(ficresvpl);    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){
   /*---------- End : free ----------------*/      ungetc(c,ficpar);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      fgets(line, MAXLINE, ficpar);
        puts(line);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fputs(line,ficparo);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
      ungetc(c,ficpar);
      
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    covar=matrix(0,NCOVMAX,1,n); 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
    
   free_matrix(matcov,1,npar,1,npar);    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   free_vector(delti,1,npar);    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   free_matrix(agev,1,maxwav,1,imx);    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
   if(erreur >0)    while((c=getc(ficpar))=='#' && c!= EOF){
     printf("End of Imach with error or warning %d\n",erreur);      ungetc(c,ficpar);
   else   printf("End of Imach\n");      fgets(line, MAXLINE, ficpar);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      puts(line);
        fputs(line,ficparo);
   /* 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);*/    ungetc(c,ficpar);
   /*------ End -----------*/    
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
  end:      for(j=1; j <=nlstate+ndeath-1; j++){
   /* chdir(pathcd);*/        fscanf(ficpar,"%1d%1d",&i1,&j1);
  /*system("wgnuplot graph.plt");*/        fprintf(ficparo,"%1d%1d",i1,j1);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        if(mle==1)
  /*system("cd ../gp37mgw");*/          printf("%1d%1d",i,j);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficlog,"%1d%1d",i,j);
  strcpy(plotcmd,GNUPLOTPROGRAM);        for(k=1; k<=ncovmodel;k++){
  strcat(plotcmd," ");          fscanf(ficpar," %lf",&param[i][j][k]);
  strcat(plotcmd,optionfilegnuplot);          if(mle==1){
  system(plotcmd);            printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
  /*#ifdef windows*/          }
   while (z[0] != 'q') {          else
     /* chdir(path); */            fprintf(ficlog," %lf",param[i][j][k]);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          fprintf(ficparo," %lf",param[i][j][k]);
     scanf("%s",z);        }
     if (z[0] == 'c') system("./imach");        fscanf(ficpar,"\n");
     else if (z[0] == 'e') system(optionfilehtm);        if(mle==1)
     else if (z[0] == 'g') system(plotcmd);          printf("\n");
     else if (z[0] == 'q') exit(0);        fprintf(ficlog,"\n");
   }        fprintf(ficparo,"\n");
   /*#endif */      }
 }    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.41.2.2  
changed lines
  Added in v.1.79

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