Diff for /imach/src/imach.c between versions 1.48 and 1.82

version 1.48, 2002/06/10 13:12:49 version 1.82, 2003/06/05 15:57:20
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  */
   first survey ("cross") where individuals from different ages are  /*
   interviewed on their health status or degree of disability (in the     Interpolated Markov Chain
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Short summary of the programme:
   (if any) in individual health status.  Health expectancies are    
   computed from the time spent in each health state according to a    This program computes Healthy Life Expectancies from
   model. More health states you consider, more time is necessary to reach the    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Maximum Likelihood of the parameters involved in the model.  The    first survey ("cross") where individuals from different ages are
   simplest model is the multinomial logistic model where pij is the    interviewed on their health status or degree of disability (in the
   probability to be observed in state j at the second wave    case of a health survey which is our main interest) -2- at least a
   conditional to be observed in state i at the first wave. Therefore    second wave of interviews ("longitudinal") which measure each change
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (if any) in individual health status.  Health expectancies are
   'age' is age and 'sex' is a covariate. If you want to have a more    computed from the time spent in each health state according to a
   complex model than "constant and age", you should modify the program    model. More health states you consider, more time is necessary to reach the
   where the markup *Covariates have to be included here again* invites    Maximum Likelihood of the parameters involved in the model.  The
   you to do it.  More covariates you add, slower the    simplest model is the multinomial logistic model where pij is the
   convergence.    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
   The advantage of this computer programme, compared to a simple    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   multinomial logistic model, is clear when the delay between waves is not    'age' is age and 'sex' is a covariate. If you want to have a more
   identical for each individual. Also, if a individual missed an    complex model than "constant and age", you should modify the program
   intermediate interview, the information is lost, but taken into    where the markup *Covariates have to be included here again* invites
   account using an interpolation or extrapolation.      you to do it.  More covariates you add, slower the
     convergence.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    The advantage of this computer programme, compared to a simple
   split into an exact number (nh*stepm) of unobserved intermediate    multinomial logistic model, is clear when the delay between waves is not
   states. This elementary transition (by month or quarter trimester,    identical for each individual. Also, if a individual missed an
   semester or year) is model as a multinomial logistic.  The hPx    intermediate interview, the information is lost, but taken into
   matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply  
   hPijx.    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
   Also this programme outputs the covariance matrix of the parameters but also    split into an exact number (nh*stepm) of unobserved intermediate
   of the life expectancies. It also computes the prevalence limits.    states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    matrix is simply the matrix product of nh*stepm elementary matrices
            Institut national d'études démographiques, Paris.    and the contribution of each individual to the likelihood is simply
   This software have been partly granted by Euro-REVES, a concerted action    hPijx.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Also this programme outputs the covariance matrix of the parameters but also
   software can be distributed freely for non commercial use. Latest version    of the life expectancies. It also computes the stable prevalence. 
   can be accessed at http://euroreves.ined.fr/imach .    
   **********************************************************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
 #include <math.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdio.h>    from the European Union.
 #include <stdlib.h>    It is copyrighted identically to a GNU software product, ie programme and
 #include <unistd.h>    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "gnuplot"    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define FILENAMELENGTH 80    
 /*#define DEBUG*/    **********************************************************************/
 #define windows  /*
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    main
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    read parameterfile
     read datafile
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    concatwav
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    if (mle >= 1)
       mlikeli
 #define NINTERVMAX 8    print results files
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    if mle==1 
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */       computes hessian
 #define NCOVMAX 8 /* Maximum number of covariates */    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXN 20000        begin-prev-date,...
 #define YEARM 12. /* Number of months per year */    open gnuplot file
 #define AGESUP 130    open html file
 #define AGEBASE 40    stable prevalence
 #ifdef windows     for age prevalim()
 #define DIRSEPARATOR '\\'    h Pij x
 #else    variance of p varprob
 #define DIRSEPARATOR '/'    forecasting if prevfcast==1 prevforecast call prevalence()
 #endif    health expectancies
     Variance-covariance of DFLE
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    prevalence()
 int erreur; /* Error number */     movingaverage()
 int nvar;    varevsij() 
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    if popbased==1 varevsij(,popbased)
 int npar=NPARMAX;    total life expectancies
 int nlstate=2; /* Number of live states */    Variance of stable prevalence
 int ndeath=1; /* Number of dead states */   end
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  */
 int popbased=0;  
   
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */   
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <math.h>
 int mle, weightopt;  #include <stdio.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #include <stdlib.h>
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #include <unistd.h>
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define MAXLINE 256
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define GNUPLOTPROGRAM "gnuplot"
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #define FILENAMELENGTH 80
 FILE *fichtm; /* Html File */  /*#define DEBUG*/
 FILE *ficreseij;  #define windows
 char filerese[FILENAMELENGTH];  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 FILE  *ficresvij;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 char fileresvpl[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 char title[MAXLINE];  
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #define NINTERVMAX 8
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 char filerest[FILENAMELENGTH];  #define YEARM 12. /* Number of months per year */
 char fileregp[FILENAMELENGTH];  #define AGESUP 130
 char popfile[FILENAMELENGTH];  #define AGEBASE 40
   #ifdef windows
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #define NR_END 1  #else
 #define FREE_ARG char*  #define DIRSEPARATOR '/'
 #define FTOL 1.0e-10  #define ODIRSEPARATOR '\\'
   #endif
 #define NRANSI  
 #define ITMAX 200  /* $Id$ */
   /* $State$ */
 #define TOL 2.0e-4  
   char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 #define CGOLD 0.3819660  char fullversion[]="$Revision$ $Date$"; 
 #define ZEPS 1.0e-10  int erreur; /* Error number */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define GOLD 1.618034  int npar=NPARMAX;
 #define GLIMIT 100.0  int nlstate=2; /* Number of live states */
 #define TINY 1.0e-20  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 static double maxarg1,maxarg2;  int popbased=0;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int *wav; /* Number of waves for this individuual 0 is possible */
    int maxwav; /* Maxim number of waves */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int jmin, jmax; /* min, max spacing between 2 waves */
 #define rint(a) floor(a+0.5)  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 static double sqrarg;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 int imx;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 int stepm;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 /* Stepm, step in month: minimum step interpolation*/  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 int estepm;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 int m,nb;  FILE *ficreseij;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  char filerese[FILENAMELENGTH];
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  FILE  *ficresvij;
 double **pmmij, ***probs, ***mobaverage;  char fileresv[FILENAMELENGTH];
 double dateintmean=0;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 double *weight;  char title[MAXLINE];
 int **s; /* Status */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 double *agedc, **covar, idx;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char filelog[FILENAMELENGTH]; /* Log file */
 double ftolhess; /* Tolerance for computing hessian */  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 /**************** split *************************/  char popfile[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  #define NR_END 1
   #define FREE_ARG char*
    l1 = strlen( path );                 /* length of path */  #define FTOL 1.0e-10
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  #define NRANSI 
    if ( s == NULL ) {                   /* no directory, so use current */  #define ITMAX 200 
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  #define TOL 2.0e-4 
   
       if ( getwd( dirc ) == NULL ) {  #define CGOLD 0.3819660 
 #else  #define ZEPS 1.0e-10 
       extern char       *getcwd( );  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define GOLD 1.618034 
 #endif  #define GLIMIT 100.0 
          return( GLOCK_ERROR_GETCWD );  #define TINY 1.0e-20 
       }  
       strcpy( name, path );             /* we've got it */  static double maxarg1,maxarg2;
    } else {                             /* strip direcotry from path */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       s++;                              /* after this, the filename */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       l2 = strlen( s );                 /* length of filename */    
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       strcpy( name, s );                /* save file name */  #define rint(a) floor(a+0.5)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  static double sqrarg;
    }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    l1 = strlen( dirc );                 /* length of directory */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int imx; 
 #else  int stepm;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  /* Stepm, step in month: minimum step interpolation*/
 #endif  
    s = strrchr( name, '.' );            /* find last / */  int estepm;
    s++;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  int m,nb;
    l2= strlen( s)+1;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    strncpy( finame, name, l1-l2);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    finame[l1-l2]= 0;  double **pmmij, ***probs;
    return( 0 );                         /* we're done */  double dateintmean=0;
 }  
   double *weight;
   int **s; /* Status */
 /******************************************/  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 void replace(char *s, char*t)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int i;  double ftolhess; /* Tolerance for computing hessian */
   int lg=20;  
   i=0;  /**************** split *************************/
   lg=strlen(t);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for(i=0; i<= lg; i++) {  {
     (s[i] = t[i]);    char  *ss;                            /* pointer */
     if (t[i]== '\\') s[i]='/';    int   l1, l2;                         /* length counters */
   }  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 int nbocc(char *s, char occ)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 {    if ( ss == NULL ) {                   /* no directory, so use current */
   int i,j=0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   int lg=20;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   i=0;      /* get current working directory */
   lg=strlen(s);      /*    extern  char* getcwd ( char *buf , int len);*/
   for(i=0; i<= lg; i++) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   if  (s[i] == occ ) j++;        return( GLOCK_ERROR_GETCWD );
   }      }
   return j;      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 void cutv(char *u,char *v, char*t, char occ)      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,lg,j,p=0;      strcpy( name, ss );         /* save file name */
   i=0;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for(j=0; j<=strlen(t)-1; j++) {      dirc[l1-l2] = 0;                    /* add zero */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    }
   }    l1 = strlen( dirc );                  /* length of directory */
   #ifdef windows
   lg=strlen(t);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   for(j=0; j<p; j++) {  #else
     (u[j] = t[j]);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   }  #endif
      u[p]='\0';    ss = strrchr( name, '.' );            /* find last / */
     ss++;
    for(j=0; j<= lg; j++) {    strcpy(ext,ss);                       /* save extension */
     if (j>=(p+1))(v[j-p-1] = t[j]);    l1= strlen( name);
   }    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /********************** nrerror ********************/    return( 0 );                          /* we're done */
   }
 void nrerror(char error_text[])  
 {  
   fprintf(stderr,"ERREUR ...\n");  /******************************************/
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  void replace(char *s, char*t)
 }  {
 /*********************** vector *******************/    int i;
 double *vector(int nl, int nh)    int lg=20;
 {    i=0;
   double *v;    lg=strlen(t);
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    for(i=0; i<= lg; i++) {
   if (!v) nrerror("allocation failure in vector");      (s[i] = t[i]);
   return v-nl+NR_END;      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  int nbocc(char *s, char occ)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    int i,j=0;
 }    int lg=20;
     i=0;
 /************************ivector *******************************/    lg=strlen(s);
 int *ivector(long nl,long nh)    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   int *v;    }
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    return j;
   if (!v) nrerror("allocation failure in ivector");  }
   return v-nl+NR_END;  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /******************free ivector **************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 void free_ivector(int *v, long nl, long nh)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   free((FREE_ARG)(v+nl-NR_END));    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /******************* imatrix *******************************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 int **imatrix(long nrl, long nrh, long ncl, long nch)    }
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    lg=strlen(t);
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    for(j=0; j<p; j++) {
   int **m;      (u[j] = t[j]);
      }
   /* allocate pointers to rows */       u[p]='\0';
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");     for(j=0; j<= lg; j++) {
   m += NR_END;      if (j>=(p+1))(v[j-p-1] = t[j]);
   m -= nrl;    }
    }
    
   /* allocate rows and set pointers to them */  /********************** nrerror ********************/
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void nrerror(char error_text[])
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    exit(EXIT_FAILURE);
    }
   /* return pointer to array of pointers to rows */  /*********************** vector *******************/
   return m;  double *vector(int nl, int nh)
 }  {
     double *v;
 /****************** free_imatrix *************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 void free_imatrix(m,nrl,nrh,ncl,nch)    if (!v) nrerror("allocation failure in vector");
       int **m;    return v-nl+NR_END;
       long nch,ncl,nrh,nrl;  }
      /* free an int matrix allocated by imatrix() */  
 {  /************************ free vector ******************/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  void free_vector(double*v, int nl, int nh)
   free((FREE_ARG) (m+nrl-NR_END));  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /************************ivector *******************************/
 {  char *cvector(long nl,long nh)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  {
   double **m;    char *v;
     v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (!v) nrerror("allocation failure in cvector");
   if (!m) nrerror("allocation failure 1 in matrix()");    return v-nl+NR_END;
   m += NR_END;  }
   m -= nrl;  
   /******************free ivector **************************/
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void free_cvector(char *v, long nl, long nh)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /************************ivector *******************************/
   return m;  int *ivector(long nl,long nh)
 }  {
     int *v;
 /*************************free matrix ************************/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
 /******************* ma3x *******************************/  {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   if (!m) nrerror("allocation failure 1 in matrix()");  { 
   m += NR_END;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   m -= nrl;    int **m; 
     
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    /* allocate pointers to rows */ 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   m[nrl] += NR_END;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   m[nrl] -= ncl;    m += NR_END; 
     m -= nrl; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
     
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    /* allocate rows and set pointers to them */ 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m[nrl][ncl] += NR_END;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   m[nrl][ncl] -= nll;    m[nrl] += NR_END; 
   for (j=ncl+1; j<=nch; j++)    m[nrl] -= ncl; 
     m[nrl][j]=m[nrl][j-1]+nlay;    
      for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   for (i=nrl+1; i<=nrh; i++) {    
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    /* return pointer to array of pointers to rows */ 
     for (j=ncl+1; j<=nch; j++)    return m; 
       m[i][j]=m[i][j-1]+nlay;  } 
   }  
   return m;  /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 /*************************free ma3x ************************/        long nch,ncl,nrh,nrl; 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)       /* free an int matrix allocated by imatrix() */ 
 {  { 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    free((FREE_ARG) (m+nrl-NR_END)); 
   free((FREE_ARG)(m+nrl-NR_END));  } 
 }  
   /******************* matrix *******************************/
 /***************** f1dim *************************/  double **matrix(long nrl, long nrh, long ncl, long nch)
 extern int ncom;  {
 extern double *pcom,*xicom;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 extern double (*nrfunc)(double []);    double **m;
    
 double f1dim(double x)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int j;    m += NR_END;
   double f;    m -= nrl;
   double *xt;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   xt=vector(1,ncom);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    m[nrl] += NR_END;
   f=(*nrfunc)(xt);    m[nrl] -= ncl;
   free_vector(xt,1,ncom);  
   return f;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }    return m;
     /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
 /*****************brent *************************/     */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /*************************free matrix ************************/
   double a,b,d,etemp;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double fu,fv,fw,fx;  {
   double ftemp;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    free((FREE_ARG)(m+nrl-NR_END));
   double e=0.0;  }
    
   a=(ax < cx ? ax : cx);  /******************* ma3x *******************************/
   b=(ax > cx ? ax : cx);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   x=w=v=bx;  {
   fw=fv=fx=(*f)(x);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (iter=1;iter<=ITMAX;iter++) {    double ***m;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    if (!m) nrerror("allocation failure 1 in matrix()");
     printf(".");fflush(stdout);    m += NR_END;
 #ifdef DEBUG    m -= nrl;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    m[nrl] += NR_END;
       *xmin=x;    m[nrl] -= ncl;
       return fx;  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     ftemp=fu;  
     if (fabs(e) > tol1) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       r=(x-w)*(fx-fv);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       q=(x-v)*(fx-fw);    m[nrl][ncl] += NR_END;
       p=(x-v)*q-(x-w)*r;    m[nrl][ncl] -= nll;
       q=2.0*(q-r);    for (j=ncl+1; j<=nch; j++) 
       if (q > 0.0) p = -p;      m[nrl][j]=m[nrl][j-1]+nlay;
       q=fabs(q);    
       etemp=e;    for (i=nrl+1; i<=nrh; i++) {
       e=d;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      for (j=ncl+1; j<=nch; j++) 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));        m[i][j]=m[i][j-1]+nlay;
       else {    }
         d=p/q;    return m; 
         u=x+d;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         if (u-a < tol2 || b-u < tol2)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
           d=SIGN(tol1,xm-x);    */
       }  }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     if (fu <= fx) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if (u >= x) a=x; else b=x;    free((FREE_ARG)(m+nrl-NR_END));
       SHFT(v,w,x,u)  }
         SHFT(fv,fw,fx,fu)  
         } else {  /***************** f1dim *************************/
           if (u < x) a=u; else b=u;  extern int ncom; 
           if (fu <= fw || w == x) {  extern double *pcom,*xicom;
             v=w;  extern double (*nrfunc)(double []); 
             w=u;   
             fv=fw;  double f1dim(double x) 
             fw=fu;  { 
           } else if (fu <= fv || v == x || v == w) {    int j; 
             v=u;    double f;
             fv=fu;    double *xt; 
           }   
         }    xt=vector(1,ncom); 
   }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   nrerror("Too many iterations in brent");    f=(*nrfunc)(xt); 
   *xmin=x;    free_vector(xt,1,ncom); 
   return fx;    return f; 
 }  } 
   
 /****************** mnbrak ***********************/  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  { 
             double (*func)(double))    int iter; 
 {    double a,b,d,etemp;
   double ulim,u,r,q, dum;    double fu,fv,fw,fx;
   double fu;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fa=(*func)(*ax);    double e=0.0; 
   *fb=(*func)(*bx);   
   if (*fb > *fa) {    a=(ax < cx ? ax : cx); 
     SHFT(dum,*ax,*bx,dum)    b=(ax > cx ? ax : cx); 
       SHFT(dum,*fb,*fa,dum)    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
   *cx=(*bx)+GOLD*(*bx-*ax);    for (iter=1;iter<=ITMAX;iter++) { 
   *fc=(*func)(*cx);      xm=0.5*(a+b); 
   while (*fb > *fc) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     r=(*bx-*ax)*(*fb-*fc);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     q=(*bx-*cx)*(*fb-*fa);      printf(".");fflush(stdout);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      fprintf(ficlog,".");fflush(ficlog);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #ifdef DEBUG
     ulim=(*bx)+GLIMIT*(*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);
     if ((*bx-u)*(u-*cx) > 0.0) {      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);
       fu=(*func)(u);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #endif
       fu=(*func)(u);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if (fu < *fc) {        *xmin=x; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        return fx; 
           SHFT(*fb,*fc,fu,(*func)(u))      } 
           }      ftemp=fu;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      if (fabs(e) > tol1) { 
       u=ulim;        r=(x-w)*(fx-fv); 
       fu=(*func)(u);        q=(x-v)*(fx-fw); 
     } else {        p=(x-v)*q-(x-w)*r; 
       u=(*cx)+GOLD*(*cx-*bx);        q=2.0*(q-r); 
       fu=(*func)(u);        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     SHFT(*ax,*bx,*cx,u)        etemp=e; 
       SHFT(*fa,*fb,*fc,fu)        e=d; 
       }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
 /*************** linmin ************************/          d=p/q; 
           u=x+d; 
 int ncom;          if (u-a < tol2 || b-u < tol2) 
 double *pcom,*xicom;            d=SIGN(tol1,xm-x); 
 double (*nrfunc)(double []);        } 
        } else { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   double brent(double ax, double bx, double cx,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                double (*f)(double), double tol, double *xmin);      fu=(*f)(u); 
   double f1dim(double x);      if (fu <= fx) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (u >= x) a=x; else b=x; 
               double *fc, double (*func)(double));        SHFT(v,w,x,u) 
   int j;          SHFT(fv,fw,fx,fu) 
   double xx,xmin,bx,ax;          } else { 
   double fx,fb,fa;            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
   ncom=n;              v=w; 
   pcom=vector(1,n);              w=u; 
   xicom=vector(1,n);              fv=fw; 
   nrfunc=func;              fw=fu; 
   for (j=1;j<=n;j++) {            } else if (fu <= fv || v == x || v == w) { 
     pcom[j]=p[j];              v=u; 
     xicom[j]=xi[j];              fv=fu; 
   }            } 
   ax=0.0;          } 
   xx=1.0;    } 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    nrerror("Too many iterations in brent"); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    *xmin=x; 
 #ifdef DEBUG    return fx; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  } 
 #endif  
   for (j=1;j<=n;j++) {  /****************** mnbrak ***********************/
     xi[j] *= xmin;  
     p[j] += xi[j];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   }              double (*func)(double)) 
   free_vector(xicom,1,n);  { 
   free_vector(pcom,1,n);    double ulim,u,r,q, dum;
 }    double fu; 
    
 /*************** powell ************************/    *fa=(*func)(*ax); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    *fb=(*func)(*bx); 
             double (*func)(double []))    if (*fb > *fa) { 
 {      SHFT(dum,*ax,*bx,dum) 
   void linmin(double p[], double xi[], int n, double *fret,        SHFT(dum,*fb,*fa,dum) 
               double (*func)(double []));        } 
   int i,ibig,j;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double del,t,*pt,*ptt,*xit;    *fc=(*func)(*cx); 
   double fp,fptt;    while (*fb > *fc) { 
   double *xits;      r=(*bx-*ax)*(*fb-*fc); 
   pt=vector(1,n);      q=(*bx-*cx)*(*fb-*fa); 
   ptt=vector(1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   xit=vector(1,n);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   xits=vector(1,n);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   *fret=(*func)(p);      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (j=1;j<=n;j++) pt[j]=p[j];        fu=(*func)(u); 
   for (*iter=1;;++(*iter)) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     fp=(*fret);        fu=(*func)(u); 
     ibig=0;        if (fu < *fc) { 
     del=0.0;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (i=1;i<=n;i++)            } 
       printf(" %d %.12f",i, p[i]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     printf("\n");        u=ulim; 
     for (i=1;i<=n;i++) {        fu=(*func)(u); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      } else { 
       fptt=(*fret);        u=(*cx)+GOLD*(*cx-*bx); 
 #ifdef DEBUG        fu=(*func)(u); 
       printf("fret=%lf \n",*fret);      } 
 #endif      SHFT(*ax,*bx,*cx,u) 
       printf("%d",i);fflush(stdout);        SHFT(*fa,*fb,*fc,fu) 
       linmin(p,xit,n,fret,func);        } 
       if (fabs(fptt-(*fret)) > del) {  } 
         del=fabs(fptt-(*fret));  
         ibig=i;  /*************** linmin ************************/
       }  
 #ifdef DEBUG  int ncom; 
       printf("%d %.12e",i,(*fret));  double *pcom,*xicom;
       for (j=1;j<=n;j++) {  double (*nrfunc)(double []); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);   
         printf(" x(%d)=%.12e",j,xit[j]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       }  { 
       for(j=1;j<=n;j++)    double brent(double ax, double bx, double cx, 
         printf(" p=%.12e",p[j]);                 double (*f)(double), double tol, double *xmin); 
       printf("\n");    double f1dim(double x); 
 #endif    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     }                double *fc, double (*func)(double)); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    int j; 
 #ifdef DEBUG    double xx,xmin,bx,ax; 
       int k[2],l;    double fx,fb,fa;
       k[0]=1;   
       k[1]=-1;    ncom=n; 
       printf("Max: %.12e",(*func)(p));    pcom=vector(1,n); 
       for (j=1;j<=n;j++)    xicom=vector(1,n); 
         printf(" %.12e",p[j]);    nrfunc=func; 
       printf("\n");    for (j=1;j<=n;j++) { 
       for(l=0;l<=1;l++) {      pcom[j]=p[j]; 
         for (j=1;j<=n;j++) {      xicom[j]=xi[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]);    ax=0.0; 
         }    xx=1.0; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 #endif  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       free_vector(xit,1,n);  #endif
       free_vector(xits,1,n);    for (j=1;j<=n;j++) { 
       free_vector(ptt,1,n);      xi[j] *= xmin; 
       free_vector(pt,1,n);      p[j] += xi[j]; 
       return;    } 
     }    free_vector(xicom,1,n); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    free_vector(pcom,1,n); 
     for (j=1;j<=n;j++) {  } 
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /*************** powell ************************/
       pt[j]=p[j];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
     fptt=(*func)(ptt);  { 
     if (fptt < fp) {    void linmin(double p[], double xi[], int n, double *fret, 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);                double (*func)(double [])); 
       if (t < 0.0) {    int i,ibig,j; 
         linmin(p,xit,n,fret,func);    double del,t,*pt,*ptt,*xit;
         for (j=1;j<=n;j++) {    double fp,fptt;
           xi[j][ibig]=xi[j][n];    double *xits;
           xi[j][n]=xit[j];    pt=vector(1,n); 
         }    ptt=vector(1,n); 
 #ifdef DEBUG    xit=vector(1,n); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    xits=vector(1,n); 
         for(j=1;j<=n;j++)    *fret=(*func)(p); 
           printf(" %.12e",xit[j]);    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf("\n");    for (*iter=1;;++(*iter)) { 
 #endif      fp=(*fret); 
       }      ibig=0; 
     }      del=0.0; 
   }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficrespow,"%d %.12f",*iter,*fret);
 /**** Prevalence limit ****************/      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        fprintf(ficlog," %d %.12lf",i, p[i]);
 {        fprintf(ficrespow," %.12lf", p[i]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      }
      matrix by transitions matrix until convergence is reached */      printf("\n");
       fprintf(ficlog,"\n");
   int i, ii,j,k;      fprintf(ficrespow,"\n");
   double min, max, maxmin, maxmax,sumnew=0.;      for (i=1;i<=n;i++) { 
   double **matprod2();        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double **out, cov[NCOVMAX], **pmij();        fptt=(*fret); 
   double **newm;  #ifdef DEBUG
   double agefin, delaymax=50 ; /* Max number of years to converge */        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   for (ii=1;ii<=nlstate+ndeath;ii++)  #endif
     for (j=1;j<=nlstate+ndeath;j++){        printf("%d",i);fflush(stdout);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fprintf(ficlog,"%d",i);fflush(ficlog);
     }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
    cov[1]=1.;          del=fabs(fptt-(*fret)); 
            ibig=i; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #ifdef DEBUG
     newm=savm;        printf("%d %.12e",i,(*fret));
     /* Covariates have to be included here again */        fprintf(ficlog,"%d %.12e",i,(*fret));
      cov[2]=agefin;        for (j=1;j<=n;j++) {
            xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for (k=1; k<=cptcovn;k++) {          printf(" x(%d)=%.12e",j,xit[j]);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        }
       }        for(j=1;j<=n;j++) {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          printf(" p=%.12e",p[j]);
       for (k=1; k<=cptcovprod;k++)          fprintf(ficlog," p=%.12e",p[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        }
         printf("\n");
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        fprintf(ficlog,"\n");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #endif
       /*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);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
     savm=oldm;        int k[2],l;
     oldm=newm;        k[0]=1;
     maxmax=0.;        k[1]=-1;
     for(j=1;j<=nlstate;j++){        printf("Max: %.12e",(*func)(p));
       min=1.;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       max=0.;        for (j=1;j<=n;j++) {
       for(i=1; i<=nlstate; i++) {          printf(" %.12e",p[j]);
         sumnew=0;          fprintf(ficlog," %.12e",p[j]);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        }
         prlim[i][j]= newm[i][j]/(1-sumnew);        printf("\n");
         max=FMAX(max,prlim[i][j]);        fprintf(ficlog,"\n");
         min=FMIN(min,prlim[i][j]);        for(l=0;l<=1;l++) {
       }          for (j=1;j<=n;j++) {
       maxmin=max-min;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       maxmax=FMAX(maxmax,maxmin);            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]);
     if(maxmax < ftolpl){          }
       return prlim;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }        }
 }  #endif
   
 /*************** transition probabilities ***************/  
         free_vector(xit,1,n); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        free_vector(xits,1,n); 
 {        free_vector(ptt,1,n); 
   double s1, s2;        free_vector(pt,1,n); 
   /*double t34;*/        return; 
   int i,j,j1, nc, ii, jj;      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for(i=1; i<= nlstate; i++){      for (j=1;j<=n;j++) { 
     for(j=1; j<i;j++){        ptt[j]=2.0*p[j]-pt[j]; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        xit[j]=p[j]-pt[j]; 
         /*s2 += param[i][j][nc]*cov[nc];*/        pt[j]=p[j]; 
         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);*/      fptt=(*func)(ptt); 
       }      if (fptt < fp) { 
       ps[i][j]=s2;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
     for(j=i+1; j<=nlstate+ndeath;j++){          for (j=1;j<=n;j++) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            xi[j][ibig]=xi[j][n]; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            xi[j][n]=xit[j]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          }
       }  #ifdef DEBUG
       ps[i][j]=s2;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }          for(j=1;j<=n;j++){
     /*ps[3][2]=1;*/            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   for(i=1; i<= nlstate; i++){          }
      s1=0;          printf("\n");
     for(j=1; j<i; j++)          fprintf(ficlog,"\n");
       s1+=exp(ps[i][j]);  #endif
     for(j=i+1; j<=nlstate+ndeath; j++)        }
       s1+=exp(ps[i][j]);      } 
     ps[i][i]=1./(s1+1.);    } 
     for(j=1; j<i; j++)  } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /**** Prevalence limit (stable prevalence)  ****************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   } /* end i */  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){       matrix by transitions matrix until convergence is reached */
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;    int i, ii,j,k;
       ps[ii][ii]=1;    double min, max, maxmin, maxmax,sumnew=0.;
     }    double **matprod2();
   }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (ii=1;ii<=nlstate+ndeath;ii++)
      printf("%lf ",ps[ii][jj]);      for (j=1;j<=nlstate+ndeath;j++){
    }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("\n ");      }
     }  
     printf("\n ");printf("%lf ",cov[2]);*/     cov[1]=1.;
 /*   
   for(i=1; i<= npar; i++) printf("%f ",x[i]);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   goto end;*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     return ps;      newm=savm;
 }      /* Covariates have to be included here again */
        cov[2]=agefin;
 /**************** Product of 2 matrices ******************/    
         for (k=1; k<=cptcovn;k++) {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* in, b, out are matrice of pointers which should have been initialized        for (k=1; k<=cptcovprod;k++)
      before: only the contents of out is modified. The function returns          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      a pointer to pointers identical to out */  
   long i, j, k;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for(i=nrl; i<= nrh; i++)        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(k=ncolol; k<=ncoloh; k++)        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         out[i][k] +=in[i][j]*b[j][k];  
       savm=oldm;
   return out;      oldm=newm;
 }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
         min=1.;
 /************* Higher Matrix Product ***************/        max=0.;
         for(i=1; i<=nlstate; i++) {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          sumnew=0;
 {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          prlim[i][j]= newm[i][j]/(1-sumnew);
      duration (i.e. until          max=FMAX(max,prlim[i][j]);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          min=FMIN(min,prlim[i][j]);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        }
      (typically every 2 years instead of every month which is too big).        maxmin=max-min;
      Model is determined by parameters x and covariates have to be        maxmax=FMAX(maxmax,maxmin);
      included manually here.      }
       if(maxmax < ftolpl){
      */        return prlim;
       }
   int i, j, d, h, k;    }
   double **out, cov[NCOVMAX];  }
   double **newm;  
   /*************** transition probabilities ***************/ 
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double s1, s2;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){      for(i=1; i<= nlstate; i++){
     for(d=1; d <=hstepm; d++){      for(j=1; j<i;j++){
       newm=savm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       /* Covariates have to be included here again */          /*s2 += param[i][j][nc]*cov[nc];*/
       cov[1]=1.;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        }
       for (k=1; k<=cptcovage;k++)        ps[i][j]=s2;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       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]]];      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        ps[i][j]=s2;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      }
       savm=oldm;    }
       oldm=newm;      /*ps[3][2]=1;*/
     }  
     for(i=1; i<=nlstate+ndeath; i++)    for(i=1; i<= nlstate; i++){
       for(j=1;j<=nlstate+ndeath;j++) {       s1=0;
         po[i][j][h]=newm[i][j];      for(j=1; j<i; j++)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        s1+=exp(ps[i][j]);
          */      for(j=i+1; j<=nlstate+ndeath; j++)
       }        s1+=exp(ps[i][j]);
   } /* end h */      ps[i][i]=1./(s1+1.);
   return po;      for(j=1; j<i; j++)
 }        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
 /*************** log-likelihood *************/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 double func( double *x)    } /* end i */
 {  
   int i, ii, j, k, mi, d, kk;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(jj=1; jj<= nlstate+ndeath; jj++){
   double **out;        ps[ii][jj]=0;
   double sw; /* Sum of weights */        ps[ii][ii]=1;
   double lli; /* Individual log likelihood */      }
   long ipmx;    }
   /*extern weight */  
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   /*for(i=1;i<imx;i++)      for(jj=1; jj<= nlstate+ndeath; jj++){
     printf(" %d\n",s[4][i]);       printf("%lf ",ps[ii][jj]);
   */     }
   cov[1]=1.;      printf("\n ");
       }
   for(k=1; k<=nlstate; k++) ll[k]=0.;      printf("\n ");printf("%lf ",cov[2]);*/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     for(mi=1; mi<= wav[i]-1; mi++){    goto end;*/
       for (ii=1;ii<=nlstate+ndeath;ii++)      return ps;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /**************** Product of 2 matrices ******************/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  {
         }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
               b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* in, b, out are matrice of pointers which should have been initialized 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       before: only the contents of out is modified. The function returns
         savm=oldm;       a pointer to pointers identical to out */
         oldm=newm;    long i, j, k;
            for(i=nrl; i<= nrh; i++)
              for(k=ncolol; k<=ncoloh; k++)
       } /* end mult */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                out[i][k] +=in[i][j]*b[j][k];
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    return out;
       ipmx +=1;  }
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  /************* Higher Matrix Product ***************/
   } /* end of individual */  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* Computes the transition matrix starting at age 'age' over 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */       'nhstepm*hstepm*stepm' months (i.e. until
   return -l;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 }       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 /*********** Maximum Likelihood Estimation ***************/       for the memory).
        Model is determined by parameters x and covariates have to be 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       included manually here. 
 {  
   int i,j, iter;       */
   double **xi,*delti;  
   double fret;    int i, j, d, h, k;
   xi=matrix(1,npar,1,npar);    double **out, cov[NCOVMAX];
   for (i=1;i<=npar;i++)    double **newm;
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);    /* Hstepm could be zero and should return the unit matrix */
   printf("Powell\n");    for (i=1;i<=nlstate+ndeath;i++)
   powell(p,xi,npar,ftol,&iter,&fret,func);      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        po[i][j][0]=(i==j ? 1.0 : 0.0);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 /**** Computes Hessian and covariance matrix ***/        newm=savm;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        /* Covariates have to be included here again */
 {        cov[1]=1.;
   double  **a,**y,*x,pd;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double **hess;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int i, j,jk;        for (k=1; k<=cptcovage;k++)
   int *indx;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   double hessii(double p[], double delta, int theta, double delti[]);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   hess=matrix(1,npar,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\nCalculation of the hessian matrix. Wait...\n");        savm=oldm;
   for (i=1;i<=npar;i++){        oldm=newm;
     printf("%d",i);fflush(stdout);      }
     hess[i][i]=hessii(p,ftolhess,i,delti);      for(i=1; i<=nlstate+ndeath; i++)
     /*printf(" %f ",p[i]);*/        for(j=1;j<=nlstate+ndeath;j++) {
     /*printf(" %lf ",hess[i][i]);*/          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]);
             */
   for (i=1;i<=npar;i++) {        }
     for (j=1;j<=npar;j++)  {    } /* end h */
       if (j>i) {    return po;
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  /*************** log-likelihood *************/
       }  double func( double *x)
     }  {
   }    int i, ii, j, k, mi, d, kk;
   printf("\n");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   a=matrix(1,npar,1,npar);    int s1, s2;
   y=matrix(1,npar,1,npar);    double bbh, survp;
   x=vector(1,npar);    long ipmx;
   indx=ivector(1,npar);    /*extern weight */
   for (i=1;i<=npar;i++)    /* We are differentiating ll according to initial status */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   ludcmp(a,npar,indx,&pd);    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   for (j=1;j<=npar;j++) {    */
     for (i=1;i<=npar;i++) x[i]=0;    cov[1]=1.;
     x[j]=1;  
     lubksb(a,npar,indx,x);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];    if(mle==1){
     }      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++){
   printf("\n#Hessian matrix#\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       printf("%.3e ",hess[i][j]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     printf("\n");          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Recompute Inverse */            for (kk=1; kk<=cptcovage;kk++) {
   for (i=1;i<=npar;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            }
   ludcmp(a,npar,indx,&pd);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  printf("\n#Hessian matrix recomputed#\n");            savm=oldm;
             oldm=newm;
   for (j=1;j<=npar;j++) {          } /* end mult */
     for (i=1;i<=npar;i++) x[i]=0;        
     x[j]=1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     lubksb(a,npar,indx,x);          /* But now since version 0.9 we anticipate for bias and large stepm.
     for (i=1;i<=npar;i++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       y[i][j]=x[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
       printf("%.3e ",y[i][j]);           * the nearest (and in case of equal distance, to the lowest) interval but now
     }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     printf("\n");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
   */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   free_matrix(a,1,npar,1,npar);           * For stepm=1 the results are the same as for previous versions of Imach.
   free_matrix(y,1,npar,1,npar);           * For stepm > 1 the results are less biased than in previous versions. 
   free_vector(x,1,npar);           */
   free_ivector(indx,1,npar);          s1=s[mw[mi][i]][i];
   free_matrix(hess,1,npar,1,npar);          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
            */
 /*************** hessian matrix ****************/          /* 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 hessii( double x[], double delta, int theta, double delti[])          if( s2 > nlstate){ 
 {            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   int i;               to the likelihood is the probability to die between last step unit time and current 
   int l=1, lmax=20;               step unit time, which is also the differences between probability to die before dh 
   double k1,k2;               and probability to die before dh-stepm . 
   double p2[NPARMAX+1];               In version up to 0.92 likelihood was computed
   double res;          as if date of death was unknown. Death was treated as any other
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          health state: the date of the interview describes the actual state
   double fx;          and not the date of a change in health state. The former idea was
   int k=0,kmax=10;          to consider that at each interview the state was recorded
   double l1;          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   fx=func(x);          the contribution of an exact death to the likelihood. This new
   for (i=1;i<=npar;i++) p2[i]=x[i];          contribution is smaller and very dependent of the step unit
   for(l=0 ; l <=lmax; l++){          stepm. It is no more the probability to die between last interview
     l1=pow(10,l);          and month of death but the probability to survive from last
     delts=delt;          interview up to one month before death multiplied by the
     for(k=1 ; k <kmax; k=k+1){          probability to die within a month. Thanks to Chris
       delt = delta*(l1*k);          Jackson for correcting this bug.  Former versions increased
       p2[theta]=x[theta] +delt;          mortality artificially. The bad side is that we add another loop
       k1=func(p2)-fx;          which slows down the processing. The difference can be up to 10%
       p2[theta]=x[theta]-delt;          lower mortality.
       k2=func(p2)-fx;            */
       /*res= (k1-2.0*fx+k2)/delt/delt; */            lli=log(out[s1][s2] - savm[s1][s2]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          }else{
                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 #ifdef DEBUG            /*  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 */
       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);          } 
 #endif          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*if(lli ==000.0)*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*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); */
         k=kmax;          ipmx +=1;
       }          sw += weight[i];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         k=kmax; l=lmax*10.;        } /* end of wave */
       }      } /* end of individual */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    }  else if(mle==2){
         delts=delt;      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++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   delti[theta]=delts;            for (j=1;j<=nlstate+ndeath;j++){
   return res;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<=dh[mi][i]; d++){
 double hessij( double x[], double delti[], int thetai,int thetaj)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i;            for (kk=1; kk<=cptcovage;kk++) {
   int l=1, l1, lmax=20;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double k1,k2,k3,k4,res,fx;            }
   double p2[NPARMAX+1];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   fx=func(x);            oldm=newm;
   for (k=1; k<=2; k++) {          } /* end mult */
     for (i=1;i<=npar;i++) p2[i]=x[i];        
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     k1=func(p2)-fx;           * 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 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     k2=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
     p2[thetai]=x[thetai]-delti[thetai]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * -stepm/2 to stepm/2 .
     k3=func(p2)-fx;           * 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. 
     p2[thetai]=x[thetai]-delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          s1=s[mw[mi][i]][i];
     k4=func(p2)-fx;          s2=s[mw[mi+1][i]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          bbh=(double)bh[mi][i]/(double)stepm; 
 #ifdef DEBUG          /* bias is positive if real duration
     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);           * is higher than the multiple of stepm and negative otherwise.
 #endif           */
   }          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 */
   return res;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 }          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 /************** Inverse of matrix **************/          /*if(lli ==000.0)*/
 void ludcmp(double **a, int n, int *indx, double *d)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 {          ipmx +=1;
   int i,imax,j,k;          sw += weight[i];
   double big,dum,sum,temp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *vv;        } /* end of wave */
        } /* end of individual */
   vv=vector(1,n);    }  else if(mle==3){  /* exponential inter-extrapolation */
   *d=1.0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     big=0.0;        for(mi=1; mi<= wav[i]-1; mi++){
     for (j=1;j<=n;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       if ((temp=fabs(a[i][j])) > big) big=temp;            for (j=1;j<=nlstate+ndeath;j++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     vv[i]=1.0/big;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   for (j=1;j<=n;j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1;i<j;i++) {            newm=savm;
       sum=a[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            for (kk=1; kk<=cptcovage;kk++) {
       a[i][j]=sum;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     big=0.0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=j;i<=n;i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       sum=a[i][j];            savm=oldm;
       for (k=1;k<j;k++)            oldm=newm;
         sum -= a[i][k]*a[k][j];          } /* end mult */
       a[i][j]=sum;        
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         big=dum;          /* But now since version 0.9 we anticipate for bias and large stepm.
         imax=i;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (j != imax) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for (k=1;k<=n;k++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         dum=a[imax][k];           * probability in order to take into account the bias as a fraction of the way
         a[imax][k]=a[j][k];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         a[j][k]=dum;           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
       *d = -(*d);           * For stepm > 1 the results are less biased than in previous versions. 
       vv[imax]=vv[j];           */
     }          s1=s[mw[mi][i]][i];
     indx[j]=imax;          s2=s[mw[mi+1][i]][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;          bbh=(double)bh[mi][i]/(double)stepm; 
     if (j != n) {          /* bias is positive if real duration
       dum=1.0/(a[j][j]);           * is higher than the multiple of stepm and negative otherwise.
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           */
     }          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   free_vector(vv,1,n);  /* Doesn't work */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 ;          /*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); */
           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 */
      }else{  /* ml=4 no inter-extrapolation */
   for (i=1;i<=n;i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     ip=indx[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     sum=b[ip];        for(mi=1; mi<= wav[i]-1; mi++){
     b[ip]=b[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (ii)            for (j=1;j<=nlstate+ndeath;j++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     else if (sum) ii=i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum;            }
   }          for(d=0; d<dh[mi][i]; d++){
   for (i=n;i>=1;i--) {            newm=savm;
     sum=b[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            for (kk=1; kk<=cptcovage;kk++) {
     b[i]=sum/a[i][i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************ Frequencies ********************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 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)            savm=oldm;
 {  /* Some frequencies */            oldm=newm;
            } /* end mult */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        
   double ***freq; /* Frequencies */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double *pp;          ipmx +=1;
   double pos, k2, dateintsum=0,k2cpt=0;          sw += weight[i];
   FILE *ficresp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileresp[FILENAMELENGTH];        } /* end of wave */
        } /* end of individual */
   pp=vector(1,nlstate);    } /* End of if */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   strcpy(fileresp,"p");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   strcat(fileresp,fileres);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    return -l;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  }
     exit(0);  
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*********** Maximum Likelihood Estimation ***************/
   j1=0;  
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   j=cptcoveff;  {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    int i,j, iter;
      double **xi;
   for(k1=1; k1<=j;k1++){    double fret;
     for(i1=1; i1<=ncodemax[k1];i1++){    char filerespow[FILENAMELENGTH];
       j1++;    xi=matrix(1,npar,1,npar);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for (i=1;i<=npar;i++)
         scanf("%d", i);*/      for (j=1;j<=npar;j++)
       for (i=-1; i<=nlstate+ndeath; i++)          xi[i][j]=(i==j ? 1.0 : 0.0);
         for (jk=-1; jk<=nlstate+ndeath; jk++)      printf("Powell\n");  fprintf(ficlog,"Powell\n");
           for(m=agemin; m <= agemax+3; m++)    strcpy(filerespow,"pow"); 
             freq[i][jk][m]=0;    strcat(filerespow,fileres);
          if((ficrespow=fopen(filerespow,"w"))==NULL) {
       dateintsum=0;      printf("Problem with resultfile: %s\n", filerespow);
       k2cpt=0;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       for (i=1; i<=imx; i++) {    }
         bool=1;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         if  (cptcovn>0) {    for (i=1;i<=nlstate;i++)
           for (z1=1; z1<=cptcoveff; z1++)      for(j=1;j<=nlstate+ndeath;j++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
               bool=0;    fprintf(ficrespow,"\n");
         }    powell(p,xi,npar,ftol,&iter,&fret,func);
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){    fclose(ficrespow);
             k2=anint[m][i]+(mint[m][i]/12.);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if(agev[m][i]==0) agev[m][i]=agemax+1;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {  }
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /**** Computes Hessian and covariance matrix ***/
               }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                {
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double  **a,**y,*x,pd;
                 dateintsum=dateintsum+k2;    double **hess;
                 k2cpt++;    int i, j,jk;
               }    int *indx;
             }  
           }    double hessii(double p[], double delta, int theta, double delti[]);
         }    double hessij(double p[], double delti[], int i, int j);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
            void ludcmp(double **a, int npar, int *indx, double *d) ;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
     hess=matrix(1,npar,1,npar);
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");    printf("\nCalculation of the hessian matrix. Wait...\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         fprintf(ficresp, "**********\n#");    for (i=1;i<=npar;i++){
       }      printf("%d",i);fflush(stdout);
       for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      hess[i][i]=hessii(p,ftolhess,i,delti);
       fprintf(ficresp, "\n");      /*printf(" %f ",p[i]);*/
            /*printf(" %lf ",hess[i][i]);*/
       for(i=(int)agemin; i <= (int)agemax+3; i++){    }
         if(i==(int)agemax+3)    
           printf("Total");    for (i=1;i<=npar;i++) {
         else      for (j=1;j<=npar;j++)  {
           printf("Age %d", i);        if (j>i) { 
         for(jk=1; jk <=nlstate ; jk++){          printf(".%d%d",i,j);fflush(stdout);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
             pp[jk] += freq[jk][m][i];          hess[i][j]=hessij(p,delti,i,j);
         }          hess[j][i]=hess[i][j];    
         for(jk=1; jk <=nlstate ; jk++){          /*printf(" %lf ",hess[i][j]);*/
           for(m=-1, pos=0; m <=0 ; m++)        }
             pos += freq[jk][m][i];      }
           if(pp[jk]>=1.e-10)    }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    printf("\n");
           else    fprintf(ficlog,"\n");
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(jk=1; jk <=nlstate ; jk++){    
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    a=matrix(1,npar,1,npar);
             pp[jk] += freq[jk][m][i];    y=matrix(1,npar,1,npar);
         }    x=vector(1,npar);
     indx=ivector(1,npar);
         for(jk=1,pos=0; jk <=nlstate ; jk++)    for (i=1;i<=npar;i++)
           pos += pp[jk];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         for(jk=1; jk <=nlstate ; jk++){    ludcmp(a,npar,indx,&pd);
           if(pos>=1.e-5)  
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for (j=1;j<=npar;j++) {
           else      for (i=1;i<=npar;i++) x[i]=0;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      x[j]=1;
           if( i <= (int) agemax){      lubksb(a,npar,indx,x);
             if(pos>=1.e-5){      for (i=1;i<=npar;i++){ 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        matcov[i][j]=x[i];
               probs[i][jk][j1]= pp[jk]/pos;      }
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    }
             }  
             else    printf("\n#Hessian matrix#\n");
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    fprintf(ficlog,"\n#Hessian matrix#\n");
           }    for (i=1;i<=npar;i++) { 
         }      for (j=1;j<=npar;j++) { 
                printf("%.3e ",hess[i][j]);
         for(jk=-1; jk <=nlstate+ndeath; jk++)        fprintf(ficlog,"%.3e ",hess[i][j]);
           for(m=-1; m <=nlstate+ndeath; m++)      }
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      printf("\n");
         if(i <= (int) agemax)      fprintf(ficlog,"\n");
           fprintf(ficresp,"\n");    }
         printf("\n");  
       }    /* Recompute Inverse */
     }    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   dateintmean=dateintsum/k2cpt;    ludcmp(a,npar,indx,&pd);
    
   fclose(ficresp);    /*  printf("\n#Hessian matrix recomputed#\n");
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   /* End of Freq */      x[j]=1;
 }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 /************ Prevalence ********************/        y[i][j]=x[i];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        printf("%.3e ",y[i][j]);
 {  /* Some frequencies */        fprintf(ficlog,"%.3e ",y[i][j]);
        }
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      printf("\n");
   double ***freq; /* Frequencies */      fprintf(ficlog,"\n");
   double *pp;    }
   double pos, k2;    */
   
   pp=vector(1,nlstate);    free_matrix(a,1,npar,1,npar);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(y,1,npar,1,npar);
      free_vector(x,1,npar);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    free_ivector(indx,1,npar);
   j1=0;    free_matrix(hess,1,npar,1,npar);
    
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
    
   for(k1=1; k1<=j;k1++){  /*************** hessian matrix ****************/
     for(i1=1; i1<=ncodemax[k1];i1++){  double hessii( double x[], double delta, int theta, double delti[])
       j1++;  {
          int i;
       for (i=-1; i<=nlstate+ndeath; i++)      int l=1, lmax=20;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double k1,k2;
           for(m=agemin; m <= agemax+3; m++)    double p2[NPARMAX+1];
             freq[i][jk][m]=0;    double res;
          double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for (i=1; i<=imx; i++) {    double fx;
         bool=1;    int k=0,kmax=10;
         if  (cptcovn>0) {    double l1;
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    fx=func(x);
               bool=0;    for (i=1;i<=npar;i++) p2[i]=x[i];
         }    for(l=0 ; l <=lmax; l++){
         if (bool==1) {      l1=pow(10,l);
           for(m=firstpass; m<=lastpass; m++){      delts=delt;
             k2=anint[m][i]+(mint[m][i]/12.);      for(k=1 ; k <kmax; k=k+1){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        delt = delta*(l1*k);
               if(agev[m][i]==0) agev[m][i]=agemax+1;        p2[theta]=x[theta] +delt;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        k1=func(p2)-fx;
               if (m<lastpass) {        p2[theta]=x[theta]-delt;
                 if (calagedate>0)        k2=func(p2)-fx;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        /*res= (k1-2.0*fx+k2)/delt/delt; */
                 else        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  #ifdef DEBUG
               }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           }  #endif
         }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(i=(int)agemin; i <= (int)agemax+3; i++){          k=kmax;
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             pp[jk] += freq[jk][m][i];          k=kmax; l=lmax*10.;
         }        }
         for(jk=1; jk <=nlstate ; jk++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           for(m=-1, pos=0; m <=0 ; m++)          delts=delt;
             pos += freq[jk][m][i];        }
         }      }
            }
         for(jk=1; jk <=nlstate ; jk++){    delti[theta]=delts;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    return res; 
             pp[jk] += freq[jk][m][i];    
         }  }
          
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  double hessij( double x[], double delti[], int thetai,int thetaj)
          {
         for(jk=1; jk <=nlstate ; jk++){        int i;
           if( i <= (int) agemax){    int l=1, l1, lmax=20;
             if(pos>=1.e-5){    double k1,k2,k3,k4,res,fx;
               probs[i][jk][j1]= pp[jk]/pos;    double p2[NPARMAX+1];
             }    int k;
           }  
         }    fx=func(x);
            for (k=1; k<=2; k++) {
       }      for (i=1;i<=npar;i++) p2[i]=x[i];
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
      
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      p2[thetai]=x[thetai]+delti[thetai]/k;
   free_vector(pp,1,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
 }  /* End of Freq */    
       p2[thetai]=x[thetai]-delti[thetai]/k;
 /************* Waves Concatenation ***************/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    
 {      p2[thetai]=x[thetai]-delti[thetai]/k;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      Death is a valid wave (if date is known).      k4=func(p2)-fx;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  #ifdef DEBUG
      and mw[mi+1][i]. dh depends on stepm.      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      */      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
   int i, mi, m;    }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    return res;
      double sum=0., jmean=0.;*/  }
   
   int j, k=0,jk, ju, jl;  /************** Inverse of matrix **************/
   double sum=0.;  void ludcmp(double **a, int n, int *indx, double *d) 
   jmin=1e+5;  { 
   jmax=-1;    int i,imax,j,k; 
   jmean=0.;    double big,dum,sum,temp; 
   for(i=1; i<=imx; i++){    double *vv; 
     mi=0;   
     m=firstpass;    vv=vector(1,n); 
     while(s[m][i] <= nlstate){    *d=1.0; 
       if(s[m][i]>=1)    for (i=1;i<=n;i++) { 
         mw[++mi][i]=m;      big=0.0; 
       if(m >=lastpass)      for (j=1;j<=n;j++) 
         break;        if ((temp=fabs(a[i][j])) > big) big=temp; 
       else      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         m++;      vv[i]=1.0/big; 
     }/* end while */    } 
     if (s[m][i] > nlstate){    for (j=1;j<=n;j++) { 
       mi++;     /* Death is another wave */      for (i=1;i<j;i++) { 
       /* if(mi==0)  never been interviewed correctly before death */        sum=a[i][j]; 
          /* Only death is a correct wave */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       mw[mi][i]=m;        a[i][j]=sum; 
     }      } 
       big=0.0; 
     wav[i]=mi;      for (i=j;i<=n;i++) { 
     if(mi==0)        sum=a[i][j]; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        for (k=1;k<j;k++) 
   }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   for(i=1; i<=imx; i++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(mi=1; mi<wav[i];mi++){          big=dum; 
       if (stepm <=0)          imax=i; 
         dh[mi][i]=1;        } 
       else{      } 
         if (s[mw[mi+1][i]][i] > nlstate) {      if (j != imax) { 
           if (agedc[i] < 2*AGESUP) {        for (k=1;k<=n;k++) { 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          dum=a[imax][k]; 
           if(j==0) j=1;  /* Survives at least one month after exam */          a[imax][k]=a[j][k]; 
           k=k+1;          a[j][k]=dum; 
           if (j >= jmax) jmax=j;        } 
           if (j <= jmin) jmin=j;        *d = -(*d); 
           sum=sum+j;        vv[imax]=vv[j]; 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      } 
           }      indx[j]=imax; 
         }      if (a[j][j] == 0.0) a[j][j]=TINY; 
         else{      if (j != n) { 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        dum=1.0/(a[j][j]); 
           k=k+1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           if (j >= jmax) jmax=j;      } 
           else if (j <= jmin)jmin=j;    } 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    free_vector(vv,1,n);  /* Doesn't work */
           sum=sum+j;  ;
         }  } 
         jk= j/stepm;  
         jl= j -jk*stepm;  void lubksb(double **a, int n, int *indx, double b[]) 
         ju= j -(jk+1)*stepm;  { 
         if(jl <= -ju)    int i,ii=0,ip,j; 
           dh[mi][i]=jk;    double sum; 
         else   
           dh[mi][i]=jk+1;    for (i=1;i<=n;i++) { 
         if(dh[mi][i]==0)      ip=indx[i]; 
           dh[mi][i]=1; /* At least one step */      sum=b[ip]; 
       }      b[ip]=b[i]; 
     }      if (ii) 
   }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   jmean=sum/k;      else if (sum) ii=i; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      b[i]=sum; 
  }    } 
 /*********** Tricode ****************************/    for (i=n;i>=1;i--) { 
 void tricode(int *Tvar, int **nbcode, int imx)      sum=b[i]; 
 {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   int Ndum[20],ij=1, k, j, i;      b[i]=sum/a[i][i]; 
   int cptcode=0;    } 
   cptcoveff=0;  } 
    
   for (k=0; k<19; k++) Ndum[k]=0;  /************ Frequencies ********************/
   for (k=1; k<=7; k++) ncodemax[k]=0;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
   {  /* Some frequencies */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    
     for (i=1; i<=imx; i++) {    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       ij=(int)(covar[Tvar[j]][i]);    int first;
       Ndum[ij]++;    double ***freq; /* Frequencies */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    double *pp, **prop;
       if (ij > cptcode) cptcode=ij;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     }    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
     for (i=0; i<=cptcode; i++) {    
       if(Ndum[i]!=0) ncodemax[j]++;    pp=vector(1,nlstate);
     }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     ij=1;    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
     for (i=1; i<=ncodemax[j]; i++) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
       for (k=0; k<=19; k++) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         if (Ndum[k] != 0) {      exit(0);
           nbcode[Tvar[j]][ij]=k;    }
              freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
           ij++;    j1=0;
         }    
         if (ij > ncodemax[j]) break;    j=cptcoveff;
       }      if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }  
   }      first=1;
   
  for (k=0; k<19; k++) Ndum[k]=0;    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
  for (i=1; i<=ncovmodel-2; i++) {        j1++;
       ij=Tvar[i];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       Ndum[ij]++;          scanf("%d", i);*/
     }        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
  ij=1;            for(m=iagemin; m <= iagemax+3; m++)
  for (i=1; i<=10; i++) {              freq[i][jk][m]=0;
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;      for (i=1; i<=nlstate; i++)  
      ij++;        for(m=iagemin; m <= iagemax+3; m++)
    }          prop[i][m]=0;
  }        
          dateintsum=0;
     cptcoveff=ij-1;        k2cpt=0;
 }        for (i=1; i<=imx; i++) {
           bool=1;
 /*********** Health Expectancies ****************/          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 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 (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
 {          }
   /* Health expectancies */          if (bool==1){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;            for(m=firstpass; m<=lastpass; m++){
   double age, agelim, hf;              k2=anint[m][i]+(mint[m][i]/12.);
   double ***p3mat,***varhe;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
   double **dnewm,**doldm;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double *xp;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double **gp, **gm;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double ***gradg, ***trgradg;                if (m<lastpass) {
   int theta;                  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];
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);                }
   xp=vector(1,npar);                
   dnewm=matrix(1,nlstate*2,1,npar);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   doldm=matrix(1,nlstate*2,1,nlstate*2);                  dateintsum=dateintsum+k2;
                    k2cpt++;
   fprintf(ficreseij,"# Health expectancies\n");                }
   fprintf(ficreseij,"# Age");              }
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        }
   fprintf(ficreseij,"\n");         
         fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);        if  (cptcovn>0) {
   }          fprintf(ficresp, "\n#********** Variable "); 
   else  hstepm=estepm;            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* We compute the life expectancy from trapezoids spaced every estepm months          fprintf(ficresp, "**********\n#");
    * This is mainly to measure the difference between two models: for example        }
    * if stepm=24 months pijx are given only every 2 years and by summing them        for(i=1; i<=nlstate;i++) 
    * we are calculating an estimate of the Life Expectancy assuming a linear          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
    * progression inbetween and thus overestimating or underestimating according        fprintf(ficresp, "\n");
    * to the curvature of the survival function. If, for the same date, we        
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        for(i=iagemin; i <= iagemax+3; i++){
    * to compare the new estimate of Life expectancy with the same linear          if(i==iagemax+3){
    * hypothesis. A more precise result, taking into account a more precise            fprintf(ficlog,"Total");
    * curvature will be obtained if estepm is as small as stepm. */          }else{
             if(first==1){
   /* For example we decided to compute the life expectancy with the smallest unit */              first=0;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              printf("See log file for details...\n");
      nhstepm is the number of hstepm from age to agelim            }
      nstepm is the number of stepm from age to agelin.            fprintf(ficlog,"Age %d", i);
      Look at hpijx to understand the reason of that which relies in memory size          }
      and note for a fixed period like estepm months */          for(jk=1; jk <=nlstate ; jk++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      survival function given by stepm (the optimization length). Unfortunately it              pp[jk] += freq[jk][m][i]; 
      means that if the survival funtion is printed only each two years of age and if          }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          for(jk=1; jk <=nlstate ; jk++){
      results. So we changed our mind and took the option of the best precision.            for(m=-1, pos=0; m <=0 ; m++)
   */              pos += freq[jk][m][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            if(pp[jk]>=1.e-10){
               if(first==1){
   agelim=AGESUP;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              }
     /* nhstepm age range expressed in number of stepm */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            }else{
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */              if(first==1)
     /* if (stepm >= YEARM) hstepm=1;*/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          }
     gp=matrix(0,nhstepm,1,nlstate*2);  
     gm=matrix(0,nhstepm,1,nlstate*2);          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              pp[jk] += freq[jk][m][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          }       
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
             posprop += prop[jk][i];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          }
           for(jk=1; jk <=nlstate ; jk++){
     /* Computing Variances of health expectancies */            if(pos>=1.e-5){
               if(first==1)
      for(theta=1; theta <=npar; theta++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(i=1; i<=npar; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }else{
       }              if(first==1)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       cptj=0;            }
       for(j=1; j<= nlstate; j++){            if( i <= iagemax){
         for(i=1; i<=nlstate; i++){              if(pos>=1.e-5){
           cptj=cptj+1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){                probs[i][jk][j1]= pp[jk]/pos;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           }              }
         }              else
       }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                  }
                }
       for(i=1; i<=npar; i++)          
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for(m=-1; m <=nlstate+ndeath; m++)
                    if(freq[jk][m][i] !=0 ) {
       cptj=0;              if(first==1)
       for(j=1; j<= nlstate; j++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(i=1;i<=nlstate;i++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           cptj=cptj+1;              }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          if(i <= iagemax)
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            fprintf(ficresp,"\n");
           }          if(first==1)
         }            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
       for(j=1; j<= nlstate*2; j++)        }
         for(h=0; h<=nhstepm-1; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    }
         }    dateintmean=dateintsum/k2cpt; 
      }   
        fclose(ficresp);
 /* End theta */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
      for(h=0; h<=nhstepm-1; h++)  }
       for(j=1; j<=nlstate*2;j++)  
         for(theta=1; theta <=npar; theta++)  /************ Prevalence ********************/
           trgradg[h][j][theta]=gradg[h][theta][j];  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
        {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      for(i=1;i<=nlstate*2;i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
       for(j=1;j<=nlstate*2;j++)       We still use firstpass and lastpass as another selection.
         varhe[i][j][(int)age] =0.;    */
    
      printf("%d|",(int)age);fflush(stdout);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
      for(h=0;h<=nhstepm-1;h++){    double ***freq; /* Frequencies */
       for(k=0;k<=nhstepm-1;k++){    double *pp, **prop;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    double pos,posprop; 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    double  y2; /* in fractional years */
         for(i=1;i<=nlstate*2;i++)    int iagemin, iagemax;
           for(j=1;j<=nlstate*2;j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
     /* Computing expectancies */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     for(i=1; i<=nlstate;i++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for(j=1; j<=nlstate;j++)    j1=0;
         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;    j=cptcoveff;
              if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    
     for(k1=1; k1<=j;k1++){
         }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
     fprintf(ficreseij,"%3.0f",age );        
     cptj=0;        for (i=1; i<=nlstate; i++)  
     for(i=1; i<=nlstate;i++)          for(m=iagemin; m <= iagemax+3; m++)
       for(j=1; j<=nlstate;j++){            prop[i][m]=0.0;
         cptj++;       
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        for (i=1; i<=imx; i++) { /* Each individual */
       }          bool=1;
     fprintf(ficreseij,"\n");          if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
     free_matrix(gm,0,nhstepm,1,nlstate*2);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     free_matrix(gp,0,nhstepm,1,nlstate*2);                bool=0;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          if (bool==1) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   printf("\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   free_vector(xp,1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   free_matrix(dnewm,1,nlstate*2,1,npar);                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); 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
 }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
 /************ Variance ******************/                } 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)              }
 {            } /* end selection of waves */
   /* Variance of health expectancies */          }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }
   double **newm;        for(i=iagemin; i <= iagemax+3; i++){  
   double **dnewm,**doldm;          
   int i, j, nhstepm, hstepm, h, nstepm ;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   int k, cptcode;            posprop += prop[jk][i]; 
   double *xp;          } 
   double **gp, **gm;  
   double ***gradg, ***trgradg;          for(jk=1; jk <=nlstate ; jk++){     
   double ***p3mat;            if( i <=  iagemax){ 
   double age,agelim, hf;              if(posprop>=1.e-5){ 
   int theta;                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
   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");          }/* end jk */ 
   for(i=1; i<=nlstate;i++)        }/* end i */ 
     for(j=1; j<=nlstate;j++)      } /* end i1 */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    } /* end k1 */
   fprintf(ficresvij,"\n");    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   xp=vector(1,npar);    /*free_vector(pp,1,nlstate);*/
   dnewm=matrix(1,nlstate,1,npar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   doldm=matrix(1,nlstate,1,nlstate);  }  /* End of prevalence */
    
   if(estepm < stepm){  /************* Waves Concatenation ***************/
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  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)
   else  hstepm=estepm;    {
   /* For example we decided to compute the life expectancy with the smallest unit */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.       Death is a valid wave (if date is known).
      nhstepm is the number of hstepm from age to agelim       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      nstepm is the number of stepm from age to agelin.       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      Look at hpijx to understand the reason of that which relies in memory size       and mw[mi+1][i]. dh depends on stepm.
      and note for a fixed period like k years */       */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it    int i, mi, m;
      means that if the survival funtion is printed only each two years of age and if    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       double sum=0., jmean=0.;*/
      results. So we changed our mind and took the option of the best precision.    int first;
   */    int j, k=0,jk, ju, jl;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double sum=0.;
   agelim = AGESUP;    first=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    jmin=1e+5;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    jmax=-1;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    jmean=0.;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=imx; i++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      mi=0;
     gp=matrix(0,nhstepm,1,nlstate);      m=firstpass;
     gm=matrix(0,nhstepm,1,nlstate);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
     for(theta=1; theta <=npar; theta++){          mw[++mi][i]=m;
       for(i=1; i<=npar; i++){ /* Computes gradient */        if(m >=lastpass)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          break;
       }        else
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            m++;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }/* end while */
       if (s[m][i] > nlstate){
       if (popbased==1) {        mi++;     /* Death is another wave */
         for(i=1; i<=nlstate;i++)        /* if(mi==0)  never been interviewed correctly before death */
           prlim[i][i]=probs[(int)age][i][ij];           /* Only death is a correct wave */
       }        mw[mi][i]=m;
        }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){      wav[i]=mi;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      if(mi==0){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        if(first==0){
         }          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
       }          first=1;
            }
       for(i=1; i<=npar; i++) /* Computes gradient */        if(first==1){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } /* end mi==0 */
      } /* End individuals */
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    for(i=1; i<=imx; i++){
           prlim[i][i]=probs[(int)age][i][ij];      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
           dh[mi][i]=1;
       for(j=1; j<= nlstate; j++){        else{
         for(h=0; h<=nhstepm; h++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            if (agedc[i] < 2*AGESUP) {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         }            if(j==0) j=1;  /* Survives at least one month after exam */
       }            k=k+1;
             if (j >= jmax) jmax=j;
       for(j=1; j<= nlstate; j++)            if (j <= jmin) jmin=j;
         for(h=0; h<=nhstepm; h++){            sum=sum+j;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            /*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);*/
     } /* End theta */            if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          }
           else{
     for(h=0; h<=nhstepm; h++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       for(j=1; j<=nlstate;j++)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for(theta=1; theta <=npar; theta++)            k=k+1;
           trgradg[h][j][theta]=gradg[h][theta][j];            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for(i=1;i<=nlstate;i++)            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       for(j=1;j<=nlstate;j++)            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         vareij[i][j][(int)age] =0.;            sum=sum+j;
           }
     for(h=0;h<=nhstepm;h++){          jk= j/stepm;
       for(k=0;k<=nhstepm;k++){          jl= j -jk*stepm;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          ju= j -(jk+1)*stepm;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          if(mle <=1){ 
         for(i=1;i<=nlstate;i++)            if(jl==0){
           for(j=1;j<=nlstate;j++)              dh[mi][i]=jk;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              bh[mi][i]=0;
       }            }else{ /* We want a negative bias in order to only have interpolation ie
     }                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
     fprintf(ficresvij,"%.0f ",age );              bh[mi][i]=ju;
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          }else{
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            if(jl <= -ju){
       }              dh[mi][i]=jk;
     fprintf(ficresvij,"\n");              bh[mi][i]=jl;       /* bias is positive if real duration
     free_matrix(gp,0,nhstepm,1,nlstate);                                   * is higher than the multiple of stepm and negative otherwise.
     free_matrix(gm,0,nhstepm,1,nlstate);                                   */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            else{
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              dh[mi][i]=jk+1;
   } /* End age */              bh[mi][i]=ju;
              }
   free_vector(xp,1,npar);            if(dh[mi][i]==0){
   free_matrix(doldm,1,nlstate,1,npar);              dh[mi][i]=1; /* At least one step */
   free_matrix(dnewm,1,nlstate,1,nlstate);              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
 }            }
           }
 /************ Variance of prevlim ******************/        } /* end if mle */
 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)      } /* end wave */
 {    }
   /* Variance of prevalence limit */    jmean=sum/k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double **newm;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   double **dnewm,**doldm;   }
   int i, j, nhstepm, hstepm;  
   int k, cptcode;  /*********** Tricode ****************************/
   double *xp;  void tricode(int *Tvar, int **nbcode, int imx)
   double *gp, *gm;  {
   double **gradg, **trgradg;    
   double age,agelim;    int Ndum[20],ij=1, k, j, i, maxncov=19;
   int theta;    int cptcode=0;
        cptcoveff=0; 
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");   
   fprintf(ficresvpl,"# Age");    for (k=0; k<maxncov; k++) Ndum[k]=0;
   for(i=1; i<=nlstate;i++)    for (k=1; k<=7; k++) ncodemax[k]=0;
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   xp=vector(1,npar);                                 modality*/ 
   dnewm=matrix(1,nlstate,1,npar);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   doldm=matrix(1,nlstate,1,nlstate);        Ndum[ij]++; /*store the modality */
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   hstepm=1*YEARM; /* Every year of age */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                                         Tvar[j]. If V=sex and male is 0 and 
   agelim = AGESUP;                                         female is 1, then  cptcode=1.*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;      for (i=0; i<=cptcode; i++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        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 */
     gradg=matrix(1,npar,1,nlstate);      }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
     for(theta=1; theta <=npar; theta++){        for (k=0; k<= maxncov; k++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */          if (Ndum[k] != 0) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            nbcode[Tvar[j]][ij]=k; 
       }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            
       for(i=1;i<=nlstate;i++)            ij++;
         gp[i] = prlim[i][i];          }
              if (ij > ncodemax[j]) break; 
       for(i=1; i<=npar; i++) /* Computes gradient */        }  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }  
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
       for(i=1;i<=nlstate;i++)   for (i=1; i<=ncovmodel-2; i++) { 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     } /* End theta */     ij=Tvar[i];
      Ndum[ij]++;
     trgradg =matrix(1,nlstate,1,npar);   }
   
     for(j=1; j<=nlstate;j++)   ij=1;
       for(theta=1; theta <=npar; theta++)   for (i=1; i<= maxncov; i++) {
         trgradg[j][theta]=gradg[theta][j];     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
     for(i=1;i<=nlstate;i++)       ij++;
       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++)   cptcoveff=ij-1; /*Number of simple covariates*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  }
   
     fprintf(ficresvpl,"%.0f ",age );  /*********** Health Expectancies ****************/
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);  {
     free_vector(gm,1,nlstate);    /* Health expectancies */
     free_matrix(gradg,1,npar,1,nlstate);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     free_matrix(trgradg,1,nlstate,1,npar);    double age, agelim, hf;
   } /* End age */    double ***p3mat,***varhe;
     double **dnewm,**doldm;
   free_vector(xp,1,npar);    double *xp;
   free_matrix(doldm,1,nlstate,1,npar);    double **gp, **gm;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double ***gradg, ***trgradg;
     int theta;
 }  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 /************ Variance of one-step probabilities  ******************/    xp=vector(1,npar);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    dnewm=matrix(1,nlstate*nlstate,1,npar);
 {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   int i, j,  i1, k1, l1;    
   int k2, l2, j1,  z1;    fprintf(ficreseij,"# Health expectancies\n");
   int k=0,l, cptcode;    fprintf(ficreseij,"# Age");
   int first=1;    for(i=1; i<=nlstate;i++)
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      for(j=1; j<=nlstate;j++)
   double **dnewm,**doldm;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   double *xp;    fprintf(ficreseij,"\n");
   double *gp, *gm;  
   double **gradg, **trgradg;    if(estepm < stepm){
   double **mu;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double age,agelim, cov[NCOVMAX];    }
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    else  hstepm=estepm;   
   int theta;    /* We compute the life expectancy from trapezoids spaced every estepm months
   char fileresprob[FILENAMELENGTH];     * This is mainly to measure the difference between two models: for example
   char fileresprobcov[FILENAMELENGTH];     * if stepm=24 months pijx are given only every 2 years and by summing them
   char fileresprobcor[FILENAMELENGTH];     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   double ***varpij;     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   strcpy(fileresprob,"prob");     * to compare the new estimate of Life expectancy with the same linear 
   strcat(fileresprob,fileres);     * hypothesis. A more precise result, taking into account a more precise
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {     * curvature will be obtained if estepm is as small as stepm. */
     printf("Problem with resultfile: %s\n", fileresprob);  
   }    /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(fileresprobcov,"probcov");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(fileresprobcov,fileres);       nhstepm is the number of hstepm from age to agelim 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with resultfile: %s\n", fileresprobcov);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
   strcpy(fileresprobcor,"probcor");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   strcat(fileresprobcor,fileres);       survival function given by stepm (the optimization length). Unfortunately it
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {       means that if the survival funtion is printed only each two years of age and if
     printf("Problem with resultfile: %s\n", fileresprobcor);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
   printf("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);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  
      agelim=AGESUP;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresprob,"# Age");      /* nhstepm age range expressed in number of stepm */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fprintf(ficresprobcov,"# Age");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      /* if (stepm >= YEARM) hstepm=1;*/
   fprintf(ficresprobcov,"# Age");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   for(i=1; i<=nlstate;i++)      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     for(j=1; j<=(nlstate+ndeath);j++){      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(ficresprobcor," p%1d-%1d ",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");   
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      /* Computing Variances of health expectancies */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);       for(theta=1; theta <=npar; theta++){
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);        for(i=1; i<=npar; i++){ 
   first=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        }
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     exit(0);    
   }        cptj=0;
   else{        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"\n# Routine varprob");          for(i=1; i<=nlstate; i++){
   }            cptj=cptj+1;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     printf("Problem with html file: %s\n", optionfilehtm);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     exit(0);            }
   }          }
   else{        }
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");       
     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");       
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");        for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   cov[1]=1;        
   j=cptcoveff;        cptj=0;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(j=1; j<= nlstate; j++){
   j1=0;          for(i=1;i<=nlstate;i++){
   for(k1=1; k1<=1;k1++){            cptj=cptj+1;
     for(i1=1; i1<=ncodemax[k1];i1++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     j1++;  
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     if  (cptcovn>0) {            }
       fprintf(ficresprob, "\n#********** Variable ");          }
       fprintf(ficresprobcov, "\n#********** Variable ");        }
       fprintf(ficgp, "\n#********** Variable ");        for(j=1; j<= nlstate*nlstate; j++)
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");          for(h=0; h<=nhstepm-1; h++){
       fprintf(ficresprobcor, "\n#********** Variable ");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
       fprintf(ficresprob, "**********\n#");       } 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);     
       fprintf(ficresprobcov, "**********\n#");  /* End theta */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficgp, "**********\n#");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficgp, "**********\n#");       for(h=0; h<=nhstepm-1; h++)
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(j=1; j<=nlstate*nlstate;j++)
       fprintf(fichtm, "**********\n#");          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
           
       for (age=bage; age<=fage; age ++){  
         cov[2]=age;       for(i=1;i<=nlstate*nlstate;i++)
         for (k=1; k<=cptcovn;k++) {        for(j=1;j<=nlstate*nlstate;j++)
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          varhe[i][j][(int)age] =0.;
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       printf("%d|",(int)age);fflush(stdout);
         for (k=1; k<=cptcovprod;k++)       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       for(h=0;h<=nhstepm-1;h++){
                for(k=0;k<=nhstepm-1;k++){
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         gp=vector(1,(nlstate)*(nlstate+ndeath));          for(i=1;i<=nlstate*nlstate;i++)
         gm=vector(1,(nlstate)*(nlstate+ndeath));            for(j=1;j<=nlstate*nlstate;j++)
                  varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         for(theta=1; theta <=npar; theta++){        }
           for(i=1; i<=npar; i++)      }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      /* Computing expectancies */
                for(i=1; i<=nlstate;i++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(j=1; j<=nlstate;j++)
                    for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           k=0;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           for(i=1; i<= (nlstate); i++){            
             for(j=1; j<=(nlstate+ndeath);j++){  /* 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=k+1;  
               gp[k]=pmmij[i][j];          }
             }  
           }      fprintf(ficreseij,"%3.0f",age );
                cptj=0;
           for(i=1; i<=npar; i++)      for(i=1; i<=nlstate;i++)
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(j=1; j<=nlstate;j++){
              cptj++;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           k=0;        }
           for(i=1; i<=(nlstate); i++){      fprintf(ficreseij,"\n");
             for(j=1; j<=(nlstate+ndeath);j++){     
               k=k+1;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               gm[k]=pmmij[i][j];      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      printf("\n");
         }    fprintf(ficlog,"\n");
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    free_vector(xp,1,npar);
           for(theta=1; theta <=npar; theta++)    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             trgradg[j][theta]=gradg[theta][j];    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
            free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  }
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
          /************ Variance ******************/
         pmij(pmmij,cov,ncovmodel,x,nlstate);  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)
          {
         k=0;    /* Variance of health expectancies */
         for(i=1; i<=(nlstate); i++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           for(j=1; j<=(nlstate+ndeath);j++){    /* double **newm;*/
             k=k+1;    double **dnewm,**doldm;
             mu[k][(int) age]=pmmij[i][j];    double **dnewmp,**doldmp;
           }    int i, j, nhstepm, hstepm, h, nstepm ;
         }    int k, cptcode;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    double *xp;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    double **gp, **gm;  /* for var eij */
             varpij[i][j][(int)age] = doldm[i][j];    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
         /*printf("\n%d ",(int)age);    double *gpp, *gmp; /* for var p point j */
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double ***p3mat;
      }*/    double age,agelim, hf;
     double ***mobaverage;
         fprintf(ficresprob,"\n%d ",(int)age);    int theta;
         fprintf(ficresprobcov,"\n%d ",(int)age);    char digit[4];
         fprintf(ficresprobcor,"\n%d ",(int)age);    char digitp[25];
   
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    char fileresprobmorprev[FILENAMELENGTH];
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    if(popbased==1){
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      if(mobilav!=0)
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        strcpy(digitp,"-populbased-mobilav-");
         }      else strcpy(digitp,"-populbased-nomobil-");
         i=0;    }
         for (k=1; k<=(nlstate);k++){    else 
           for (l=1; l<=(nlstate+ndeath);l++){      strcpy(digitp,"-stablbased-");
             i=i++;  
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    if (mobilav!=0) {
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             for (j=1; j<=i;j++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             }      }
           }    }
         }/* end of loop for state */  
       } /* end of loop for age */    strcpy(fileresprobmorprev,"prmorprev"); 
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    sprintf(digit,"%-d",ij);
       for (k1=1; k1<=(nlstate);k1++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         for (l1=1; l1<=(nlstate+ndeath);l1++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           if(l1==k1) continue;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           i=(k1-1)*(nlstate+ndeath)+l1;    strcat(fileresprobmorprev,fileres);
           for (k2=1; k2<=(nlstate);k2++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             for (l2=1; l2<=(nlstate+ndeath);l2++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
               if(l2==k2) continue;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               j=(k2-1)*(nlstate+ndeath)+l2;    }
               if(j<=i) continue;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               for (age=bage; age<=fage; age ++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                 if ((int)age %5==0){    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);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      fprintf(ficresprobmorprev," p.%-d SE",j);
                   mu1=mu[i][(int) age]/stepm*YEARM ;      for(i=1; i<=nlstate;i++)
                   mu2=mu[j][(int) age]/stepm*YEARM;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   /* Computing eigen value of matrix of covariance */    }  
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    fprintf(ficresprobmorprev,"\n");
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
                   /* Eigen vectors */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));      exit(0);
                   v21=sqrt(1.-v11*v11);    }
                   v12=-v21;    else{
                   v22=v11;      fprintf(ficgp,"\n# Routine varevsij");
                   /*printf(fignu*/    }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      printf("Problem with html file: %s\n", optionfilehtm);
                   if(first==1){      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
                     first=0;      exit(0);
                     fprintf(ficgp,"\nset parametric;set nolabel");    }
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);    else{
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      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>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);    }
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    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(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)) t \"%d\"",\    fprintf(ficresvij,"# Age");
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    for(i=1; i<=nlstate;i++)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      for(j=1; j<=nlstate;j++)
                   }else{        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                     first=0;    fprintf(ficresvij,"\n");
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    xp=vector(1,npar);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    dnewm=matrix(1,nlstate,1,npar);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    doldm=matrix(1,nlstate,1,nlstate);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   }/* if first */    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                 } /* age mod 5 */  
               } /* end loop age */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);    gpp=vector(nlstate+1,nlstate+ndeath);
               first=1;    gmp=vector(nlstate+1,nlstate+ndeath);
             } /*l12 */    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           } /* k12 */    
         } /*l1 */    if(estepm < stepm){
       }/* k1 */      printf ("Problem %d lower than %d\n",estepm, stepm);
     } /* loop covariates */    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    else  hstepm=estepm;   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    /* For example we decided to compute the life expectancy with the smallest unit */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);       nhstepm is the number of hstepm from age to agelim 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       nstepm is the number of stepm from age to agelin. 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like k years */
   free_vector(xp,1,npar);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficresprob);       survival function given by stepm (the optimization length). Unfortunately it
   fclose(ficresprobcov);       means that if the survival funtion is printed every two years of age and if
   fclose(ficresprobcor);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fclose(ficgp);       results. So we changed our mind and took the option of the best precision.
   fclose(fichtm);    */
 }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 /******************* Printing html file ***********/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   int lastpass, int stepm, int weightopt, char model[],\      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   int popforecast, int estepm ,\      gp=matrix(0,nhstepm,1,nlstate);
                   double jprev1, double mprev1,double anprev1, \      gm=matrix(0,nhstepm,1,nlstate);
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;  
   /*char optionfilehtm[FILENAMELENGTH];*/      for(theta=1; theta <=npar; theta++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     printf("Problem with %s \n",optionfilehtm), exit(0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  - 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        if (popbased==1) {
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          if(mobilav ==0){
  - Life expectancies by age and initial health status (estepm=%2d months):            for(i=1; i<=nlstate;i++)
    <a href=\"e%s\">e%s</a> <br>\n</li>", \              prlim[i][i]=probs[(int)age][i][ij];
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n              prlim[i][i]=mobaverage[(int)age][i][ij];
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n          }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        }
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        for(j=1; j<= nlstate; j++){
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n          for(h=0; h<=nhstepm; h++){
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
  - 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);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
  if(popforecast==1) fprintf(fichtm,"\n        }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        /* This for computing probability of death (h=1 means
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n           computed over hstepm matrices product = hstepm*stepm months) 
         <br>",fileres,fileres,fileres,fileres);           as a weighted average of prlim.
  else        */
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 fprintf(fichtm," <li>Graphs</li><p>");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
  m=cptcoveff;        }    
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        /* end probability of death */
   
  jj1=0;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
  for(k1=1; k1<=m;k1++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    for(i1=1; i1<=ncodemax[k1];i1++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      jj1++;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      if (cptcovn > 0) {   
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        if (popbased==1) {
        for (cpt=1; cpt<=cptcoveff;cpt++)          if(mobilav ==0){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            for(i=1; i<=nlstate;i++)
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              prlim[i][i]=probs[(int)age][i][ij];
      }          }else{ /* mobilav */ 
      /* Pij */            for(i=1; i<=nlstate;i++)
      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>              prlim[i][i]=mobaverage[(int)age][i][ij];
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
      /* Quasi-incidences */        }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        for(j=1; j<= nlstate; j++){
        /* Stable prevalence in each health state */          for(h=0; h<=nhstepm; h++){
        for(cpt=1; cpt<nlstate;cpt++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
        }        }
     for(cpt=1; cpt<=nlstate;cpt++) {        /* This for computing probability of death (h=1 means
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident           computed over hstepm matrices product = hstepm*stepm months) 
 interval) in state (%d): v%s%d%d.png <br>           as a weighted average of prlim.
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          */
      }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      for(cpt=1; cpt<=nlstate;cpt++) {          for(i=1,gmp[j]=0.; i<= nlstate; i++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }    
      }        /* end probability of death */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>        for(j=1; j<= nlstate; j++) /* vareij */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(h=0; h<=nhstepm; h++){
    }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  }          }
 fclose(fichtm);  
 }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 /******************* Gnuplot file **************/        }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
       } /* End theta */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);      for(h=0; h<=nhstepm; h++) /* veij */
   }        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
 #ifdef windows            trgradg[h][j][theta]=gradg[h][theta][j];
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 m=pow(2,cptcoveff);        for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
  /* 1eme*/    
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
 #ifdef windows        for(j=1;j<=nlstate;j++)
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          vareij[i][j][(int)age] =0.;
      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);  
 #endif      for(h=0;h<=nhstepm;h++){
 #ifdef unix        for(k=0;k<=nhstepm;k++){
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 #endif          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
 for (i=1; i<= nlstate ; i ++) {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }    
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* pptj */
     for (i=1; i<= nlstate ; i ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          varppt[j][i]=doldmp[j][i];
      for (i=1; i<= nlstate ; i ++) {      /* end ppptj */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /*  x centered again */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 }        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));   
 #ifdef unix      if (popbased==1) {
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        if(mobilav ==0){
 #endif          for(i=1; i<=nlstate;i++)
    }            prlim[i][i]=probs[(int)age][i][ij];
   }        }else{ /* mobilav */ 
   /*2 eme*/          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
   for (k1=1; k1<= m ; k1 ++) {        }
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);               
          /* This for computing probability of death (h=1 means
     for (i=1; i<= nlstate+1 ; i ++) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       k=2*i;         as a weighted average of prlim.
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      */
       for (j=1; j<= nlstate+1 ; j ++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
 }        }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      /* end probability of death */
       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);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for (j=1; j<= nlstate+1 ; j ++) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=nlstate;i++){
 }            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      } 
       for (j=1; j<= nlstate+1 ; j ++) {      fprintf(ficresprobmorprev,"\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficresvij,"%.0f ",age );
 }        for(i=1; i<=nlstate;i++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(j=1; j<=nlstate;j++){
       else fprintf(ficgp,"\" t\"\" w l 0,");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     }        }
   }      fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
   /*3eme*/      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=2+nlstate*(2*cpt-2);    } /* End age */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for (i=1; i< nlstate ; i ++) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
   }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
    */
   /* CV preval stat */    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    free_vector(xp,1,npar);
       k=3;    free_matrix(doldm,1,nlstate,1,nlstate);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    free_matrix(dnewm,1,nlstate,1,npar);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       for (i=1; i< nlstate ; i ++)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,"+$%d",k+i+1);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    fclose(ficresprobmorprev);
          fclose(ficgp);
       l=3+(nlstate+ndeath)*cpt;    fclose(fichtm);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  }  
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;  /************ Variance of prevlim ******************/
         fprintf(ficgp,"+$%d",l+i+1);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
       }  {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* Variance of prevalence limit */
     }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   }      double **newm;
      double **dnewm,**doldm;
   /* proba elementaires */    int i, j, nhstepm, hstepm;
    for(i=1,jk=1; i <=nlstate; i++){    int k, cptcode;
     for(k=1; k <=(nlstate+ndeath); k++){    double *xp;
       if (k != i) {    double *gp, *gm;
         for(j=1; j <=ncovmodel; j++){    double **gradg, **trgradg;
            double age,agelim;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    int theta;
           jk++;     
           fprintf(ficgp,"\n");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         }    fprintf(ficresvpl,"# Age");
       }    for(i=1; i<=nlstate;i++)
     }        fprintf(ficresvpl," %1d-%1d",i,i);
    }    fprintf(ficresvpl,"\n");
   
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    xp=vector(1,npar);
      for(jk=1; jk <=m; jk++) {    dnewm=matrix(1,nlstate,1,npar);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    doldm=matrix(1,nlstate,1,nlstate);
        if (ng==2)    
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    hstepm=1*YEARM; /* Every year of age */
        else    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          fprintf(ficgp,"\nset title \"Probability\"\n");    agelim = AGESUP;
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        i=1;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        for(k2=1; k2<=nlstate; k2++) {      if (stepm >= YEARM) hstepm=1;
          k3=i;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
          for(k=1; k<=(nlstate+ndeath); k++) {      gradg=matrix(1,npar,1,nlstate);
            if (k != k2){      gp=vector(1,nlstate);
              if(ng==2)      gm=vector(1,nlstate);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);  
              else      for(theta=1; theta <=npar; theta++){
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(i=1; i<=npar; i++){ /* Computes gradient */
              ij=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              for(j=3; j <=ncovmodel; j++) {        }
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=1;i<=nlstate;i++)
                  ij++;          gp[i] = prlim[i][i];
                }      
                else        for(i=1; i<=npar; i++) /* Computes gradient */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
              }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              fprintf(ficgp,")/(1");        for(i=1;i<=nlstate;i++)
                        gm[i] = prlim[i][i];
              for(k1=1; k1 <=nlstate; k1++){    
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for(i=1;i<=nlstate;i++)
                ij=1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                for(j=3; j <=ncovmodel; j++){      } /* End theta */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      trgradg =matrix(1,nlstate,1,npar);
                    ij++;  
                  }      for(j=1; j<=nlstate;j++)
                  else        for(theta=1; theta <=npar; theta++)
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          trgradg[j][theta]=gradg[theta][j];
                }  
                fprintf(ficgp,")");      for(i=1;i<=nlstate;i++)
              }        varpl[i][(int)age] =0.;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
              i=i+ncovmodel;      for(i=1;i<=nlstate;i++)
            }        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]));
    fclose(ficgp);      fprintf(ficresvpl,"\n");
 }  /* end gnuplot */      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
 /*************** Moving average **************/      free_matrix(trgradg,1,nlstate,1,npar);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    } /* End age */
   
   int i, cpt, cptcod;    free_vector(xp,1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    free_matrix(doldm,1,nlstate,1,npar);
       for (i=1; i<=nlstate;i++)    free_matrix(dnewm,1,nlstate,1,nlstate);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;  }
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  /************ Variance of one-step probabilities  ******************/
       for (i=1; i<=nlstate;i++){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  {
           for (cpt=0;cpt<=4;cpt++){    int i, j=0,  i1, k1, l1, t, tj;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int k2, l2, j1,  z1;
           }    int k=0,l, cptcode;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int first=1, first1;
         }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       }    double **dnewm,**doldm;
     }    double *xp;
        double *gp, *gm;
 }    double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
 /************** Forecasting ******************/    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 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){    int theta;
      char fileresprob[FILENAMELENGTH];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    char fileresprobcov[FILENAMELENGTH];
   int *popage;    char fileresprobcor[FILENAMELENGTH];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;    double ***varpij;
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
  agelim=AGESUP;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    }
      strcpy(fileresprobcov,"probcov"); 
      strcat(fileresprobcov,fileres);
   strcpy(fileresf,"f");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   strcat(fileresf,fileres);      printf("Problem with resultfile: %s\n", fileresprobcov);
   if((ficresf=fopen(fileresf,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     printf("Problem with forecast resultfile: %s\n", fileresf);    }
   }    strcpy(fileresprobcor,"probcor"); 
   printf("Computing forecasting: result on file '%s' \n", fileresf);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   if (mobilav==1) {    }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   if (stepm<=12) stepsize=1;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      
   agelim=AGESUP;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   hstepm=1;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   hstepm=hstepm/stepm;    fprintf(ficresprobcov,"# Age");
   yp1=modf(dateintmean,&yp);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   anprojmean=yp;    fprintf(ficresprobcov,"# Age");
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);    for(i=1; i<=nlstate;i++)
   jprojmean=yp;      for(j=1; j<=(nlstate+ndeath);j++){
   if(jprojmean==0) jprojmean=1;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   if(mprojmean==0) jprojmean=1;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      }  
     /* fprintf(ficresprob,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresprobcov,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresprobcor,"\n");
       k=k+1;   */
       fprintf(ficresf,"\n#******");   xp=vector(1,npar);
       for(j=1;j<=cptcoveff;j++) {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       fprintf(ficresf,"******\n");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fprintf(ficresf,"# StartingAge FinalAge");    first=1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
            printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
            fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      exit(0);
         fprintf(ficresf,"\n");    }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      else{
       fprintf(ficgp,"\n# Routine varprob");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           nhstepm = nhstepm/hstepm;      printf("Problem with html file: %s\n", optionfilehtm);
                fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      exit(0);
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      else{
              fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           for (h=0; h<=nhstepm; h++){      fprintf(fichtm,"\n");
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
             }      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
             for(j=1; j<=nlstate+ndeath;j++) {      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");
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  }
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    cov[1]=1;
                 else {    tj=cptcoveff;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                 }    j1=0;
                    for(t=1; t<=tj;t++){
               }      for(i1=1; i1<=ncodemax[t];i1++){ 
               if (h==(int)(calagedate+12*cpt)){        j1++;
                 fprintf(ficresf," %.3f", kk1);        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 "); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprobcov, "**********\n#\n");
       }          
     }          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficgp, "**********\n#\n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
           
   fclose(ficresf);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 /************** Forecasting ******************/          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 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){          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int *popage;          fprintf(ficresprobcor, "**********\n#");    
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        }
   double *popeffectif,*popcount;        
   double ***p3mat,***tabpop,***tabpopprev;        for (age=bage; age<=fage; age ++){ 
   char filerespop[FILENAMELENGTH];          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   agelim=AGESUP;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          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]]];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   strcpy(filerespop,"pop");          gp=vector(1,(nlstate)*(nlstate+ndeath));
   strcat(filerespop,fileres);          gm=vector(1,(nlstate)*(nlstate+ndeath));
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      
     printf("Problem with forecast resultfile: %s\n", filerespop);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
   if (mobilav==1) {            k=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1; i<= (nlstate); i++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
                 gp[k]=pmmij[i][j];
   stepsize=(int) (stepm+YEARM-1)/YEARM;              }
   if (stepm<=12) stepsize=1;            }
              
   agelim=AGESUP;            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   hstepm=1;      
   hstepm=hstepm/stepm;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              k=0;
   if (popforecast==1) {            for(i=1; i<=(nlstate); i++){
     if((ficpop=fopen(popfile,"r"))==NULL) {              for(j=1; j<=(nlstate+ndeath);j++){
       printf("Problem with population file : %s\n",popfile);exit(0);                k=k+1;
     }                gm[k]=pmmij[i][j];
     popage=ivector(0,AGESUP);              }
     popeffectif=vector(0,AGESUP);            }
     popcount=vector(0,AGESUP);       
                for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     i=1;                gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          }
      
     imx=i;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            for(theta=1; theta <=npar; theta++)
   }              trgradg[j][theta]=gradg[theta][j];
           
   for(cptcov=1;cptcov<=i2;cptcov++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       k=k+1;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficrespop,"\n#******");          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       for(j=1;j<=cptcoveff;j++) {          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       }  
       fprintf(ficrespop,"******\n");          pmij(pmmij,cov,ncovmodel,x,nlstate);
       fprintf(ficrespop,"# Age");          
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          k=0;
       if (popforecast==1)  fprintf(ficrespop," [Population]");          for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
       for (cpt=0; cpt<=0;cpt++) {              k=k+1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                mu[k][(int) age]=pmmij[i][j];
                    }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           nhstepm = nhstepm/hstepm;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                        varpij[i][j][(int)age] = doldm[i][j];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;          /*printf("\n%d ",(int)age);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                    printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           for (h=0; h<=nhstepm; h++){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             if (h==(int) (calagedate+YEARM*cpt)) {            }*/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }          fprintf(ficresprob,"\n%d ",(int)age);
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficresprobcov,"\n%d ",(int)age);
               kk1=0.;kk2=0;          fprintf(ficresprobcor,"\n%d ",(int)age);
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                 else {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                 }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
               }          }
               if (h==(int)(calagedate+12*cpt)){          i=0;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          for (k=1; k<=(nlstate);k++){
                   /*fprintf(ficrespop," %.3f", kk1);            for (l=1; l<=(nlstate+ndeath);l++){ 
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/              i=i++;
               }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
             }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             for(i=1; i<=nlstate;i++){              for (j=1; j<=i;j++){
               kk1=0.;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 for(j=1; j<=nlstate;j++){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   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)];          }/* end of loop for state */
             }        } /* end of loop for age */
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        /* Confidence intervalle of pij  */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        /*
           }          fprintf(ficgp,"\nset noparametric;unset label");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
         }          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);
            fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   /******/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        first1=1;
           nhstepm = nhstepm/hstepm;        for (k2=1; k2<=(nlstate);k2++){
                    for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(l2==k2) continue;
           oldm=oldms;savm=savms;            j=(k2-1)*(nlstate+ndeath)+l2;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (k1=1; k1<=(nlstate);k1++){
           for (h=0; h<=nhstepm; h++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
             if (h==(int) (calagedate+YEARM*cpt)) {                if(l1==k1) continue;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                i=(k1-1)*(nlstate+ndeath)+l1;
             }                if(i<=j) continue;
             for(j=1; j<=nlstate+ndeath;j++) {                for (age=bage; age<=fage; age ++){ 
               kk1=0.;kk2=0;                  if ((int)age %5==0){
               for(i=1; i<=nlstate;i++) {                                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                        v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
               }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                    mu1=mu[i][(int) age]/stepm*YEARM ;
             }                    mu2=mu[j][(int) age]/stepm*YEARM;
           }                    c12=cv12/sqrt(v1*v2);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    /* Computing eigen value of matrix of covariance */
         }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
    }                    /* Eigen vectors */
   }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                      /*v21=sqrt(1.-v11*v11); *//* error */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
   if (popforecast==1) {                    v22=v11;
     free_ivector(popage,0,AGESUP);                    tnalp=v21/v11;
     free_vector(popeffectif,0,AGESUP);                    if(first1==1){
     free_vector(popcount,0,AGESUP);                      first1=0;
   }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    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);
   fclose(ficrespop);                    /*printf(fignu*/
 }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
 /***********************************************/                    if(first==1){
 /**************** Main Program *****************/                      first=0;
 /***********************************************/                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
 int main(int argc, char *argv[])                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 {                      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);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   double agedeb, agefin,hf;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double fret;                      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",\
   double **xi,tmp,delta;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double dum; /* Dummy variable */                    }else{
   double ***p3mat;                      first=0;
   int *indx;                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   char line[MAXLINE], linepar[MAXLINE];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   int firstobs=1, lastobs=10;                      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",\
   int sdeb, sfin; /* Status at beginning and end */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   int c,  h , cpt,l;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   int ju,jl, mi;                    }/* if first */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                  } /* age mod 5 */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                } /* end loop age */
   int mobilav=0,popforecast=0;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   int hstepm, nhstepm;                first=1;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;              } /*l12 */
             } /* k12 */
   double bage, fage, age, agelim, agebase;          } /*l1 */
   double ftolpl=FTOL;        }/* k1 */
   double **prlim;      } /* loop covariates */
   double *severity;    }
   double ***param; /* Matrix of parameters */    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   double  *p;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   double **matcov; /* Matrix of covariance */    free_vector(xp,1,npar);
   double ***delti3; /* Scale */    fclose(ficresprob);
   double *delti; /* Scale */    fclose(ficresprobcov);
   double ***eij, ***vareij;    fclose(ficresprobcor);
   double **varpl; /* Variances of prevalence limits by age */    fclose(ficgp);
   double *epj, vepp;    fclose(fichtm);
   double kk1, kk2;  }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
    
   /******************* Printing html file ***********/
   char *alph[]={"a","a","b","c","d","e"}, str[4];  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   char z[1]="c", occ;                    int popforecast, int estepm ,\
 #include <sys/time.h>                    double jprev1, double mprev1,double anprev1, \
 #include <time.h>                    double jprev2, double mprev2,double anprev2){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int jj1, k1, i1, cpt;
      /*char optionfilehtm[FILENAMELENGTH];*/
   /* long total_usecs;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   struct timeval start_time, end_time;      printf("Problem with %s \n",optionfilehtm), exit(0);
        fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    }
   getcwd(pathcd, size);  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   printf("\n%s",version);   - 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
   if(argc <=1){   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
     printf("\nEnter the parameter file name: ");   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
     scanf("%s",pathtot);   - Life expectancies by age and initial health status (estepm=%2d months): 
   }     <a href=\"e%s\">e%s</a> <br>\n</li>", \
   else{    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
     strcpy(pathtot,argv[1]);  
   }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);   m=cptcoveff;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /* cutv(path,optionfile,pathtot,'\\');*/  
    jj1=0;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);   for(k1=1; k1<=m;k1++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);     for(i1=1; i1<=ncodemax[k1];i1++){
   chdir(path);       jj1++;
   replace(pathc,path);       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 /*-------- arguments in the command line --------*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   strcpy(fileres,"r");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcat(fileres, optionfilefiname);       }
   strcat(fileres,".txt");    /* Other files have txt extension */       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
   /*---------arguments file --------*/  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       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>
     printf("Problem with optionfile %s\n",optionfile);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
     goto end;         /* Stable prevalence in each health state */
   }         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
   strcpy(filereso,"o");  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
   strcat(filereso,fileres);         }
   if((ficparo=fopen(filereso,"w"))==NULL) {       for(cpt=1; cpt<=nlstate;cpt++) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          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);
        }
   /* Reads comments: lines beginning with '#' */       fprintf(fichtm,"\n<br>- Total life expectancy by age and
   while((c=getc(ficpar))=='#' && c!= EOF){  health expectancies in states (1) and (2): e%s%d.png<br>
     ungetc(c,ficpar);  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     fgets(line, MAXLINE, ficpar);     } /* end i1 */
     puts(line);   }/* End k1 */
     fputs(line,ficparo);   fprintf(fichtm,"</ul>");
   }  
   ungetc(c,ficpar);  
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
   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);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
   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);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
   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);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
 while((c=getc(ficpar))=='#' && c!= EOF){   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
     ungetc(c,ficpar);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
     fgets(line, MAXLINE, ficpar);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
     puts(line);   - 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);
     fputs(line,ficparo);  
   }  /*  if(popforecast==1) fprintf(fichtm,"\n */
   ungetc(c,ficpar);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
      /*      <br>",fileres,fileres,fileres,fileres); */
   covar=matrix(0,NCOVMAX,1,n);  /*  else  */
   cptcovn=0;  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
   ncovmodel=2+cptcovn;   m=cptcoveff;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   /* Read guess parameters */   jj1=0;
   /* Reads comments: lines beginning with '#' */   for(k1=1; k1<=m;k1++){
   while((c=getc(ficpar))=='#' && c!= EOF){     for(i1=1; i1<=ncodemax[k1];i1++){
     ungetc(c,ficpar);       jj1++;
     fgets(line, MAXLINE, ficpar);       if (cptcovn > 0) {
     puts(line);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fputs(line,ficparo);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   ungetc(c,ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       for(cpt=1; cpt<=nlstate;cpt++) {
     for(i=1; i <=nlstate; i++)         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
     for(j=1; j <=nlstate+ndeath-1; j++){  interval) in state (%d): v%s%d%d.png <br>
       fscanf(ficpar,"%1d%1d",&i1,&j1);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
       fprintf(ficparo,"%1d%1d",i1,j1);       }
       printf("%1d%1d",i,j);     } /* end i1 */
       for(k=1; k<=ncovmodel;k++){   }/* End k1 */
         fscanf(ficpar," %lf",&param[i][j][k]);   fprintf(fichtm,"</ul>");
         printf(" %lf",param[i][j][k]);  fclose(fichtm);
         fprintf(ficparo," %lf",param[i][j][k]);  }
       }  
       fscanf(ficpar,"\n");  /******************* Gnuplot file **************/
       printf("\n");  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       fprintf(ficparo,"\n");  
     }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      int ng;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
   p=param[1][1];      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
      }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    /*#ifdef windows */
     ungetc(c,ficpar);      fprintf(ficgp,"cd \"%s\" \n",pathc);
     fgets(line, MAXLINE, ficpar);      /*#endif */
     puts(line);  m=pow(2,cptcoveff);
     fputs(line,ficparo);    
   }   /* 1eme*/
   ungetc(c,ficpar);    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       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 <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){       for (i=1; i<= nlstate ; i ++) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       printf("%1d%1d",i,j);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficparo,"%1d%1d",i1,j1);       }
       for(k=1; k<=ncovmodel;k++){       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
         fscanf(ficpar,"%le",&delti3[i][j][k]);       for (i=1; i<= nlstate ; i ++) {
         printf(" %le",delti3[i][j][k]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficparo," %le",delti3[i][j][k]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       } 
       fscanf(ficpar,"\n");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
       printf("\n");       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficparo,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       }  
   delti=delti3[1][1];       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       }
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    /*2 eme*/
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    for (k1=1; k1<= m ; k1 ++) { 
     puts(line);      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
     fputs(line,ficparo);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   }      
   ungetc(c,ficpar);      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   matcov=matrix(1,npar,1,npar);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
   for(i=1; i <=npar; i++){        for (j=1; j<= nlstate+1 ; j ++) {
     fscanf(ficpar,"%s",&str);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     printf("%s",str);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fprintf(ficparo,"%s",str);        }   
     for(j=1; j <=i; j++){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       fscanf(ficpar," %le",&matcov[i][j]);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       printf(" %.5le",matcov[i][j]);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
       fprintf(ficparo," %.5le",matcov[i][j]);        for (j=1; j<= nlstate+1 ; j ++) {
     }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fscanf(ficpar,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("\n");        }   
     fprintf(ficparo,"\n");        fprintf(ficgp,"\" t\"\" w l 0,");
   }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
   for(i=1; i <=npar; i++)        for (j=1; j<= nlstate+1 ; j ++) {
     for(j=i+1;j<=npar;j++)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       matcov[i][j]=matcov[j][i];          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
   printf("\n");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     /*-------- Rewriting paramater file ----------*/    }
      strcpy(rfileres,"r");    /* "Rparameterfile */    
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    /*3eme*/
      strcat(rfileres,".");    /* */    
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    for (k1=1; k1<= m ; k1 ++) { 
     if((ficres =fopen(rfileres,"w"))==NULL) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        k=2+nlstate*(2*cpt-2);
     }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     fprintf(ficres,"#%s\n",version);        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
            /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     /*-------- data file ----------*/          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     if((fic=fopen(datafile,"r"))==NULL)    {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       printf("Problem with datafile: %s\n", datafile);goto end;          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     n= lastobs;          
     severity = vector(1,maxwav);        */
     outcome=imatrix(1,maxwav+1,1,n);        for (i=1; i< nlstate ; i ++) {
     num=ivector(1,n);          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);
     moisnais=vector(1,n);          
     annais=vector(1,n);        } 
     moisdc=vector(1,n);      }
     andc=vector(1,n);    }
     agedc=vector(1,n);    
     cod=ivector(1,n);    /* CV preval stable (period) */
     weight=vector(1,n);    for (k1=1; k1<= m ; k1 ++) { 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for (cpt=1; cpt<=nlstate ; cpt ++) {
     mint=matrix(1,maxwav,1,n);        k=3;
     anint=matrix(1,maxwav,1,n);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     s=imatrix(1,maxwav+1,1,n);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
     adl=imatrix(1,maxwav+1,1,n);            
     tab=ivector(1,NCOVMAX);        for (i=1; i<= nlstate ; i ++)
     ncodemax=ivector(1,8);          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     i=1;        
     while (fgets(line, MAXLINE, fic) != NULL)    {        l=3+(nlstate+ndeath)*cpt;
       if ((i >= firstobs) && (i <=lastobs)) {        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
                for (i=1; i< nlstate ; i ++) {
         for (j=maxwav;j>=1;j--){          l=3+(nlstate+ndeath)*cpt;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          fprintf(ficgp,"+$%d",l+i+1);
           strcpy(line,stra);        }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
           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);    /* proba elementaires */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        if (k != i) {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            jk++; 
         for (j=ncovcol;j>=1;j--){            fprintf(ficgp,"\n");
           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;}*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
         i=i+1;         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
       }         if (ng==2)
     }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     /* printf("ii=%d", ij);         else
        scanf("%d",i);*/           fprintf(ficgp,"\nset title \"Probability\"\n");
   imx=i-1; /* Number of individuals */         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
   /* for (i=1; i<=imx; i++){         for(k2=1; k2<=nlstate; k2++) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;           k3=i;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;           for(k=1; k<=(nlstate+ndeath); k++) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;             if (k != k2){
     }*/               if(ng==2)
    /*  for (i=1; i<=imx; i++){                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
      if (s[4][i]==9)  s[4][i]=-1;               else
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
                 for(j=3; j <=ncovmodel; j++) {
   /* Calculation of the number of parameter from char model*/                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   Tvar=ivector(1,15);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   Tprod=ivector(1,15);                   ij++;
   Tvaraff=ivector(1,15);                 }
   Tvard=imatrix(1,15,1,2);                 else
   Tage=ivector(1,15);                         fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   }
   if (strlen(model) >1){               fprintf(ficgp,")/(1");
     j=0, j1=0, k1=1, k2=1;               
     j=nbocc(model,'+');               for(k1=1; k1 <=nlstate; k1++){   
     j1=nbocc(model,'*');                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     cptcovn=j+1;                 ij=1;
     cptcovprod=j1;                 for(j=3; j <=ncovmodel; j++){
                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     strcpy(modelsav,model);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                     ij++;
       printf("Error. Non available option model=%s ",model);                   }
       goto end;                   else
     }                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                     }
     for(i=(j+1); i>=1;i--){                 fprintf(ficgp,")");
       cutv(stra,strb,modelsav,'+');               }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
       /*scanf("%d",i);*/               i=i+ncovmodel;
       if (strchr(strb,'*')) {             }
         cutv(strd,strc,strb,'*');           } /* end k */
         if (strcmp(strc,"age")==0) {         } /* end k2 */
           cptcovprod--;       } /* end jk */
           cutv(strb,stre,strd,'V');     } /* end ng */
           Tvar[i]=atoi(stre);     fclose(ficgp); 
           cptcovage++;  }  /* end gnuplot */
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  
         }  /*************** Moving average **************/
         else if (strcmp(strd,"age")==0) {  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    int i, cpt, cptcod;
           Tvar[i]=atoi(stre);    int modcovmax =1;
           cptcovage++;    int mobilavrange, mob;
           Tage[cptcovage]=i;    double age;
         }  
         else {    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           cutv(strb,stre,strc,'V');                             a covariate has 2 modalities */
           Tvar[i]=ncovcol+k1;    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
           Tvard[k1][1]=atoi(strc);      if(mobilav==1) mobilavrange=5; /* default */
           Tvard[k1][2]=atoi(stre);      else mobilavrange=mobilav;
           Tvar[cptcovn+k2]=Tvard[k1][1];      for (age=bage; age<=fage; age++)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for (i=1; i<=nlstate;i++)
           for (k=1; k<=lastobs;k++)          for (cptcod=1;cptcod<=modcovmax;cptcod++)
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
           k1++;      /* We keep the original values on the extreme ages bage, fage and for 
           k2=k2+2;         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. 
       }      */ 
       else {      for (mob=3;mob <=mobilavrange;mob=mob+2){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
        /*  scanf("%d",i);*/          for (i=1; i<=nlstate;i++){
       cutv(strd,strc,strb,'V');            for (cptcod=1;cptcod<=modcovmax;cptcod++){
       Tvar[i]=atoi(strc);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
       }                for (cpt=1;cpt<=(mob-1)/2;cpt++){
       strcpy(modelsav,stra);                    mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
         scanf("%d",i);*/                }
     }              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
 }            }
            }
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        }/* end age */
   printf("cptcovprod=%d ", cptcovprod);      }/* end mob */
   scanf("%d ",i);*/    }else return -1;
     fclose(fic);    return 0;
   }/* End movingaverage */
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;  /************** Forecasting ******************/
     }  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){
     /*-calculation of age at interview from date of interview and age at death -*/    /* proj1, year, month, day of starting projection 
     agev=matrix(1,maxwav,1,imx);       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
     for (i=1; i<=imx; i++) {       anproj2 year of en of projection (same day and month as proj1).
       for(m=2; (m<= maxwav); m++) {    */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
          anint[m][i]=9999;    int *popage;
          s[m][i]=-1;    double agec; /* generic age */
        }    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double *popeffectif,*popcount;
       }    double ***p3mat;
     }    double ***mobaverage;
     char fileresf[FILENAMELENGTH];
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    agelim=AGESUP;
       for(m=1; (m<= maxwav); m++){    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
         if(s[m][i] >0){   
           if (s[m][i] >= nlstate+1) {    strcpy(fileresf,"f"); 
             if(agedc[i]>0)    strcat(fileresf,fileres);
               if(moisdc[i]!=99 && andc[i]!=9999)    if((ficresf=fopen(fileresf,"w"))==NULL) {
                 agev[m][i]=agedc[i];      printf("Problem with forecast resultfile: %s\n", fileresf);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
            else {    }
               if (andc[i]!=9999){    printf("Computing forecasting: result on file '%s' \n", fileresf);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
               agev[m][i]=-1;  
               }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             }  
           }    if (mobilav!=0) {
           else if(s[m][i] !=9){ /* Should no more exist */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             if(mint[m][i]==99 || anint[m][i]==9999)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               agev[m][i]=1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             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);*/  
             }    stepsize=(int) (stepm+YEARM-1)/YEARM;
             else if(agev[m][i] >agemax){    if (stepm<=12) stepsize=1;
               agemax=agev[m][i];    if(estepm < stepm){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    else  hstepm=estepm;   
             /*   agev[m][i] = age[i]+2*m;*/  
           }    hstepm=hstepm/stepm; 
           else { /* =9 */    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
             agev[m][i]=1;                                 fractional in yp1 */
             s[m][i]=-1;    anprojmean=yp;
           }    yp2=modf((yp1*12),&yp);
         }    mprojmean=yp;
         else /*= 0 Unknown */    yp1=modf((yp2*30.5),&yp);
           agev[m][i]=1;    jprojmean=yp;
       }    if(jprojmean==0) jprojmean=1;
        if(mprojmean==0) jprojmean=1;
     }  
     for (i=1; i<=imx; i++)  {    i1=cptcoveff;
       for(m=1; (m<= maxwav); m++){    if (cptcovn < 1){i1=1;}
         if (s[m][i] > (nlstate+ndeath)) {    
           printf("Error: Wrong value in nlstate or ndeath\n");      fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
           goto end;    
         }    fprintf(ficresf,"#****** Routine prevforecast **\n");
       }  
     }  /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
     free_vector(severity,1,maxwav);        fprintf(ficresf,"\n#******");
     free_imatrix(outcome,1,maxwav+1,1,n);        for(j=1;j<=cptcoveff;j++) {
     free_vector(moisnais,1,n);          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]]);
     free_vector(annais,1,n);        }
     /* free_matrix(mint,1,maxwav,1,n);        fprintf(ficresf,"******\n");
        free_matrix(anint,1,maxwav,1,n);*/        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
     free_vector(moisdc,1,n);        for(j=1; j<=nlstate+ndeath;j++){ 
     free_vector(andc,1,n);          for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
              fprintf(ficresf," p.%d",j);
     wav=ivector(1,imx);        }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficresf,"\n");
              fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
       Tcode=ivector(1,100);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            oldm=oldms;savm=savms;
       ncodemax[1]=1;            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          
                  for (h=0; h<=nhstepm; h++){
    codtab=imatrix(1,100,1,10);              if (h*hstepm/YEARM*stepm ==yearp) {
    h=0;                fprintf(ficresf,"\n");
    m=pow(2,cptcoveff);                for(j=1;j<=cptcoveff;j++) 
                    fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
    for(k=1;k<=cptcoveff; k++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
      for(i=1; i <=(m/pow(2,k));i++){              } 
        for(j=1; j <= ncodemax[k]; j++){              for(j=1; j<=nlstate+ndeath;j++) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                ppij=0.;
            h++;                for(i=1; i<=nlstate;i++) {
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                  if (mobilav==1) 
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
          }                  else {
        }                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
      }                  }
    }                  if (h*hstepm/YEARM*stepm== yearp) {
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       codtab[1][2]=1;codtab[2][2]=2; */                  }
    /* for(i=1; i <=m ;i++){                } /* end i */
       for(k=1; k <=cptcovn; k++){                if (h*hstepm/YEARM*stepm==yearp) {
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                  fprintf(ficresf," %.3f", ppij);
       }                }
       printf("\n");              }/* end j */
       }            } /* end h */
       scanf("%d",i);*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              } /* end agec */
    /* Calculates basic frequencies. Computes observed prevalence at single age        } /* end yearp */
        and prints on file fileres'p'. */      } /* end cptcod */
     } /* end  cptcov */
             
        if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresf);
     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 */  /************** Forecasting *****not tested NB*************/
        populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     /* For 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] */    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    int *popage;
     double calagedatem, agelim, kk1, kk2;
     if(mle==1){    double *popeffectif,*popcount;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    double ***p3mat,***tabpop,***tabpopprev;
     }    double ***mobaverage;
        char filerespop[FILENAMELENGTH];
     /*--------- 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);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
    jk=1;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    for(i=1,jk=1; i <=nlstate; i++){    
      for(k=1; k <=(nlstate+ndeath); k++){    
        if (k != i)    strcpy(filerespop,"pop"); 
          {    strcat(filerespop,fileres);
            printf("%d%d ",i,k);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
            fprintf(ficres,"%1d%1d ",i,k);      printf("Problem with forecast resultfile: %s\n", filerespop);
            for(j=1; j <=ncovmodel; j++){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
              printf("%f ",p[jk]);    }
              fprintf(ficres,"%f ",p[jk]);    printf("Computing forecasting: result on file '%s' \n", filerespop);
              jk++;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
            }  
            printf("\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
            fprintf(ficres,"\n");  
          }    if (mobilav!=0) {
      }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
  if(mle==1){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     /* Computing hessian and covariance matrix */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     ftolhess=ftol; /* Usually correct */      }
     hesscov(matcov, p, npar, delti, ftolhess, func);    }
  }  
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    stepsize=(int) (stepm+YEARM-1)/YEARM;
     printf("# Scales (for hessian or gradient estimation)\n");    if (stepm<=12) stepsize=1;
      for(i=1,jk=1; i <=nlstate; i++){    
       for(j=1; j <=nlstate+ndeath; j++){    agelim=AGESUP;
         if (j!=i) {    
           fprintf(ficres,"%1d%1d",i,j);    hstepm=1;
           printf("%1d%1d",i,j);    hstepm=hstepm/stepm; 
           for(k=1; k<=ncovmodel;k++){    
             printf(" %.5e",delti[jk]);    if (popforecast==1) {
             fprintf(ficres," %.5e",delti[jk]);      if((ficpop=fopen(popfile,"r"))==NULL) {
             jk++;        printf("Problem with population file : %s\n",popfile);exit(0);
           }        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
           printf("\n");      } 
           fprintf(ficres,"\n");      popage=ivector(0,AGESUP);
         }      popeffectif=vector(0,AGESUP);
       }      popcount=vector(0,AGESUP);
      }      
          i=1;   
     k=1;      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+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");     
     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");      imx=i;
     for(i=1;i<=npar;i++){      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
       /*  if (k>nlstate) k=1;    }
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fprintf(ficres,"%3d",i);        k=k+1;
       printf("%3d",i);        fprintf(ficrespop,"\n#******");
       for(j=1; j<=i;j++){        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficres," %.5e",matcov[i][j]);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         printf(" %.5e",matcov[i][j]);        }
       }        fprintf(ficrespop,"******\n");
       fprintf(ficres,"\n");        fprintf(ficrespop,"# Age");
       printf("\n");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       k++;        if (popforecast==1)  fprintf(ficrespop," [Population]");
     }        
            for (cpt=0; cpt<=0;cpt++) { 
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       ungetc(c,ficpar);          
       fgets(line, MAXLINE, ficpar);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
       puts(line);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       fputs(line,ficparo);            nhstepm = nhstepm/hstepm; 
     }            
     ungetc(c,ficpar);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     estepm=0;            oldm=oldms;savm=savms;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     if (estepm==0 || estepm < stepm) estepm=stepm;          
     if (fage <= 2) {            for (h=0; h<=nhstepm; h++){
       bage = ageminpar;              if (h==(int) (calagedatem+YEARM*cpt)) {
       fage = agemaxpar;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
     }              } 
                  for(j=1; j<=nlstate+ndeath;j++) {
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                kk1=0.;kk2=0;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                for(i=1; i<=nlstate;i++) {              
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                  if (mobilav==1) 
                      kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     while((c=getc(ficpar))=='#' && c!= EOF){                  else {
     ungetc(c,ficpar);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
     fgets(line, MAXLINE, ficpar);                  }
     puts(line);                }
     fputs(line,ficparo);                if (h==(int)(calagedatem+12*cpt)){
   }                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   ungetc(c,ficpar);                    /*fprintf(ficrespop," %.3f", kk1);
                        if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              for(i=1; i<=nlstate;i++){
                      kk1=0.;
   while((c=getc(ficpar))=='#' && c!= EOF){                  for(j=1; j<=nlstate;j++){
     ungetc(c,ficpar);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     fgets(line, MAXLINE, ficpar);                  }
     puts(line);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
     fputs(line,ficparo);              }
   }  
   ungetc(c,ficpar);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                  fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          }
         }
   fscanf(ficpar,"pop_based=%d\n",&popbased);   
   fprintf(ficparo,"pop_based=%d\n",popbased);      /******/
   fprintf(ficres,"pop_based=%d\n",popbased);    
          for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     ungetc(c,ficpar);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     fgets(line, MAXLINE, ficpar);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     puts(line);            nhstepm = nhstepm/hstepm; 
     fputs(line,ficparo);            
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   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);            for (h=0; h<=nhstepm; h++){
 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);              if (h==(int) (calagedatem+YEARM*cpt)) {
 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);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
 while((c=getc(ficpar))=='#' && c!= EOF){                kk1=0.;kk2=0;
     ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {              
     fgets(line, MAXLINE, ficpar);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     puts(line);                }
     fputs(line,ficparo);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   }              }
   ungetc(c,ficpar);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          }
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     } 
     }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /*------------ gnuplot -------------*/  
   strcpy(optionfilegnuplot,optionfilefiname);    if (popforecast==1) {
   strcat(optionfilegnuplot,".gp");      free_ivector(popage,0,AGESUP);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      free_vector(popeffectif,0,AGESUP);
     printf("Problem with file %s",optionfilegnuplot);      free_vector(popcount,0,AGESUP);
   }    }
   fclose(ficgp);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /*--------- index.htm --------*/    fclose(ficrespop);
   }
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");  /***********************************************/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  /**************** Main Program *****************/
     printf("Problem with %s \n",optionfilehtm), exit(0);  /***********************************************/
   }  
   int main(int argc, char *argv[])
   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    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
 \n    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
 Total number of observations=%d <br>\n    double agedeb, agefin,hf;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Parameter files<br>\n    double fret;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    double **xi,tmp,delta;
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);  
   fclose(fichtm);    double dum; /* Dummy variable */
     double ***p3mat;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    double ***mobaverage;
      int *indx;
 /*------------ free_vector  -------------*/    char line[MAXLINE], linepar[MAXLINE];
  chdir(path);    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
      int firstobs=1, lastobs=10;
  free_ivector(wav,1,imx);    int sdeb, sfin; /* Status at beginning and end */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int c,  h , cpt,l;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      int ju,jl, mi;
  free_ivector(num,1,n);    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
  free_vector(agedc,1,n);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
  fclose(ficparo);    int mobilav=0,popforecast=0;
  fclose(ficres);    int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   /*--------------- Prevalence limit --------------*/  
      double bage, fage, age, agelim, agebase;
   strcpy(filerespl,"pl");    double ftolpl=FTOL;
   strcat(filerespl,fileres);    double **prlim;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double *severity;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double ***param; /* Matrix of parameters */
   }    double  *p;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **matcov; /* Matrix of covariance */
   fprintf(ficrespl,"#Prevalence limit\n");    double ***delti3; /* Scale */
   fprintf(ficrespl,"#Age ");    double *delti; /* Scale */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double ***eij, ***vareij;
   fprintf(ficrespl,"\n");    double **varpl; /* Variances of prevalence limits by age */
      double *epj, vepp;
   prlim=matrix(1,nlstate,1,nlstate);    double kk1, kk2;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char *alph[]={"a","a","b","c","d","e"}, str[4];
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    char z[1]="c", occ;
   agebase=ageminpar;  #include <sys/time.h>
   agelim=agemaxpar;  #include <time.h>
   ftolpl=1.e-10;    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   i1=cptcoveff;   
   if (cptcovn < 1){i1=1;}    /* long total_usecs;
        struct timeval start_time, end_time;
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         k=k+1;    getcwd(pathcd, size);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    printf("\n%s\n%s",version,fullversion);
         for(j=1;j<=cptcoveff;j++)    if(argc <=1){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("\nEnter the parameter file name: ");
         fprintf(ficrespl,"******\n");      scanf("%s",pathtot);
            }
         for (age=agebase; age<=agelim; age++){    else{
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      strcpy(pathtot,argv[1]);
           fprintf(ficrespl,"%.0f",age );    }
           for(i=1; i<=nlstate;i++)    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
           fprintf(ficrespl," %.5f", prlim[i][i]);    /*cygwin_split_path(pathtot,path,optionfile);
           fprintf(ficrespl,"\n");      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
         }    /* cutv(path,optionfile,pathtot,'\\');*/
       }  
     }    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   fclose(ficrespl);    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
   /*------------- h Pij x at various ages ------------*/    replace(pathc,path);
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /*-------- arguments in the command line --------*/
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* Log file */
   }    strcat(filelog, optionfilefiname);
   printf("Computing pij: result on file '%s' \n", filerespij);    strcat(filelog,".log");    /* */
      if((ficlog=fopen(filelog,"w"))==NULL)    {
   stepsize=(int) (stepm+YEARM-1)/YEARM;      printf("Problem with logfile %s\n",filelog);
   /*if (stepm<=24) stepsize=2;*/      goto end;
     }
   agelim=AGESUP;    fprintf(ficlog,"Log filename:%s\n",filelog);
   hstepm=stepsize*YEARM; /* Every year of age */    fprintf(ficlog,"\n%s",version);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    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);
   k=0;    fflush(ficlog);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* */
       k=k+1;    strcpy(fileres,"r");
         fprintf(ficrespij,"\n#****** ");    strcat(fileres, optionfilefiname);
         for(j=1;j<=cptcoveff;j++)    strcat(fileres,".txt");    /* Other files have txt extension */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    /*---------arguments file --------*/
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if((ficpar=fopen(optionfile,"r"))==NULL)    {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("Problem with optionfile %s\n",optionfile);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      goto end;
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    strcpy(filereso,"o");
           for(i=1; i<=nlstate;i++)    strcat(filereso,fileres);
             for(j=1; j<=nlstate+ndeath;j++)    if((ficparo=fopen(filereso,"w"))==NULL) {
               fprintf(ficrespij," %1d-%1d",i,j);      printf("Problem with Output resultfile: %s\n", filereso);
           fprintf(ficrespij,"\n");      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
            for (h=0; h<=nhstepm; h++){      goto end;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    }
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)    /* Reads comments: lines beginning with '#' */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    while((c=getc(ficpar))=='#' && c!= EOF){
             fprintf(ficrespij,"\n");      ungetc(c,ficpar);
              }      fgets(line, MAXLINE, ficpar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      puts(line);
           fprintf(ficrespij,"\n");      fputs(line,ficparo);
         }    }
     }    ungetc(c,ficpar);
   }  
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   fclose(ficrespij);    while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
   /*---------- Forecasting ------------------*/      puts(line);
   if((stepm == 1) && (strcmp(model,".")==0)){      fputs(line,ficparo);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    ungetc(c,ficpar);
   }    
   else{     
     erreur=108;    covar=matrix(0,NCOVMAX,1,n); 
     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);    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
   }    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
    
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   /*---------- Health expectancies and variances ------------*/    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
   strcpy(filerest,"t");    /* Read guess parameters */
   strcat(filerest,fileres);    /* Reads comments: lines beginning with '#' */
   if((ficrest=fopen(filerest,"w"))==NULL) {    while((c=getc(ficpar))=='#' && c!= EOF){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      ungetc(c,ficpar);
   }      fgets(line, MAXLINE, ficpar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      puts(line);
       fputs(line,ficparo);
     }
   strcpy(filerese,"e");    ungetc(c,ficpar);
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    for(i=1; i <=nlstate; i++)
   }      for(j=1; j <=nlstate+ndeath-1; j++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        fscanf(ficpar,"%1d%1d",&i1,&j1);
         fprintf(ficparo,"%1d%1d",i1,j1);
  strcpy(fileresv,"v");        if(mle==1)
   strcat(fileresv,fileres);          printf("%1d%1d",i,j);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficlog,"%1d%1d",i,j);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        for(k=1; k<=ncovmodel;k++){
   }          fscanf(ficpar," %lf",&param[i][j][k]);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          if(mle==1){
   calagedate=-1;            printf(" %lf",param[i][j][k]);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            fprintf(ficlog," %lf",param[i][j][k]);
           }
   k=0;          else
   for(cptcov=1;cptcov<=i1;cptcov++){            fprintf(ficlog," %lf",param[i][j][k]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficparo," %lf",param[i][j][k]);
       k=k+1;        }
       fprintf(ficrest,"\n#****** ");        fscanf(ficpar,"\n");
       for(j=1;j<=cptcoveff;j++)        if(mle==1)
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf("\n");
       fprintf(ficrest,"******\n");        fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       fprintf(ficreseij,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
       fprintf(ficreseij,"******\n");  
     p=param[1][1];
       fprintf(ficresvij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    /* Reads comments: lines beginning with '#' */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    while((c=getc(ficpar))=='#' && c!= EOF){
       fprintf(ficresvij,"******\n");      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      puts(line);
       oldm=oldms;savm=savms;      fputs(line,ficparo);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      }
      ungetc(c,ficpar);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    /* 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);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        printf("%1d%1d",i,j);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        fprintf(ficparo,"%1d%1d",i1,j1);
       fprintf(ficrest,"\n");        for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
       epj=vector(1,nlstate+1);          printf(" %le",delti3[i][j][k]);
       for(age=bage; age <=fage ;age++){          fprintf(ficparo," %le",delti3[i][j][k]);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        }
         if (popbased==1) {        fscanf(ficpar,"\n");
           for(i=1; i<=nlstate;i++)        printf("\n");
             prlim[i][i]=probs[(int)age][i][k];        fprintf(ficparo,"\n");
         }      }
            }
         fprintf(ficrest," %4.0f",age);    delti=delti3[1][1];
         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];    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    
           }    /* Reads comments: lines beginning with '#' */
           epj[nlstate+1] +=epj[j];    while((c=getc(ficpar))=='#' && c!= EOF){
         }      ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
         for(i=1, vepp=0.;i <=nlstate;i++)      puts(line);
           for(j=1;j <=nlstate;j++)      fputs(line,ficparo);
             vepp += vareij[i][j][(int)age];    }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    ungetc(c,ficpar);
         for(j=1;j <=nlstate;j++){    
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    matcov=matrix(1,npar,1,npar);
         }    for(i=1; i <=npar; i++){
         fprintf(ficrest,"\n");      fscanf(ficpar,"%s",&str);
       }      if(mle==1)
     }        printf("%s",str);
   }      fprintf(ficlog,"%s",str);
 free_matrix(mint,1,maxwav,1,n);      fprintf(ficparo,"%s",str);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      for(j=1; j <=i; j++){
     free_vector(weight,1,n);        fscanf(ficpar," %le",&matcov[i][j]);
   fclose(ficreseij);        if(mle==1){
   fclose(ficresvij);          printf(" %.5le",matcov[i][j]);
   fclose(ficrest);          fprintf(ficlog," %.5le",matcov[i][j]);
   fclose(ficpar);        }
   free_vector(epj,1,nlstate+1);        else
            fprintf(ficlog," %.5le",matcov[i][j]);
   /*------- Variance limit prevalence------*/          fprintf(ficparo," %.5le",matcov[i][j]);
       }
   strcpy(fileresvpl,"vpl");      fscanf(ficpar,"\n");
   strcat(fileresvpl,fileres);      if(mle==1)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        printf("\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficlog,"\n");
     exit(0);      fprintf(ficparo,"\n");
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
   k=0;        matcov[i][j]=matcov[j][i];
   for(cptcov=1;cptcov<=i1;cptcov++){     
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if(mle==1)
       k=k+1;      printf("\n");
       fprintf(ficresvpl,"\n#****** ");    fprintf(ficlog,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");    /*-------- Rewriting paramater file ----------*/
          strcpy(rfileres,"r");    /* "Rparameterfile */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       oldm=oldms;savm=savms;    strcat(rfileres,".");    /* */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    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;
   fclose(ficresvpl);    }
     fprintf(ficres,"#%s\n",version);
   /*---------- End : free ----------------*/      
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /*-------- data file ----------*/
      if((fic=fopen(datafile,"r"))==NULL)    {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      printf("Problem with datafile: %s\n", datafile);goto end;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
      }
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    n= lastobs;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    severity = vector(1,maxwav);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    outcome=imatrix(1,maxwav+1,1,n);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    num=ivector(1,n);
      moisnais=vector(1,n);
   free_matrix(matcov,1,npar,1,npar);    annais=vector(1,n);
   free_vector(delti,1,npar);    moisdc=vector(1,n);
   free_matrix(agev,1,maxwav,1,imx);    andc=vector(1,n);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    agedc=vector(1,n);
     cod=ivector(1,n);
   fprintf(fichtm,"\n</body>");    weight=vector(1,n);
   fclose(fichtm);    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   fclose(ficgp);    mint=matrix(1,maxwav,1,n);
      anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
   if(erreur >0)    tab=ivector(1,NCOVMAX);
     printf("End of Imach with error or warning %d\n",erreur);    ncodemax=ivector(1,8);
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    i=1;
      while (fgets(line, MAXLINE, fic) != NULL)    {
   /* 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);*/      if ((i >= firstobs) && (i <=lastobs)) {
   /*printf("Total time was %d uSec.\n", total_usecs);*/          
   /*------ End -----------*/        for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
  end:          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 #ifdef windows          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   /* chdir(pathcd);*/        }
 #endif          
  /*system("wgnuplot graph.plt");*/        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
  strcpy(plotcmd,GNUPLOTPROGRAM);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
  system(plotcmd);        for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 #ifdef windows        } 
   while (z[0] != 'q') {        num[i]=atol(stra);
     /* chdir(path); */          
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
     scanf("%s",z);          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;}*/
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);        i=i+1;
     else if (z[0] == 'g') system(plotcmd);      }
     else if (z[0] == 'q') exit(0);    }
   }    /* printf("ii=%d", ij);
 #endif       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.1.48  
changed lines
  Added in v.1.82


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