Diff for /imach/src/imach.c between versions 1.51 and 1.82

version 1.51, 2002/07/19 12:22:25 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
 #define ODIRSEPARATOR '/'    variance of p varprob
 #else    forecasting if prevfcast==1 prevforecast call prevalence()
 #define DIRSEPARATOR '/'    health expectancies
 #define ODIRSEPARATOR '\\'    Variance-covariance of DFLE
 #endif    prevalence()
      movingaverage()
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    varevsij() 
 int erreur; /* Error number */    if popbased==1 varevsij(,popbased)
 int nvar;    total life expectancies
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    Variance of stable prevalence
 int npar=NPARMAX;   end
 int nlstate=2; /* Number of live states */  */
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  
    
 int *wav; /* Number of waves for this individuual 0 is possible */  #include <math.h>
 int maxwav; /* Maxim number of waves */  #include <stdio.h>
 int jmin, jmax; /* min, max spacing between 2 waves */  #include <stdlib.h>
 int mle, weightopt;  #include <unistd.h>
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define MAXLINE 256
 double jmean; /* Mean space between 2 waves */  #define GNUPLOTPROGRAM "gnuplot"
 double **oldm, **newm, **savm; /* Working pointers to matrices */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define FILENAMELENGTH 80
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*#define DEBUG*/
 FILE *ficlog;  #define windows
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 FILE *ficresprobmorprev;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 char filerese[FILENAMELENGTH];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];  #define NINTERVMAX 8
 FILE  *ficresvpl;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 char fileresvpl[FILENAMELENGTH];  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 char title[MAXLINE];  #define NCOVMAX 8 /* Maximum number of covariates */
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #define MAXN 20000
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  #define AGEBASE 40
 char filelog[FILENAMELENGTH]; /* Log file */  #ifdef windows
 char filerest[FILENAMELENGTH];  #define DIRSEPARATOR '\\'
 char fileregp[FILENAMELENGTH];  #define ODIRSEPARATOR '/'
 char popfile[FILENAMELENGTH];  #else
   #define DIRSEPARATOR '/'
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  #define ODIRSEPARATOR '\\'
   #endif
 #define NR_END 1  
 #define FREE_ARG char*  /* $Id$ */
 #define FTOL 1.0e-10  /* $State$ */
   
 #define NRANSI  char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 #define ITMAX 200  char fullversion[]="$Revision$ $Date$"; 
   int erreur; /* Error number */
 #define TOL 2.0e-4  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define CGOLD 0.3819660  int npar=NPARMAX;
 #define ZEPS 1.0e-10  int nlstate=2; /* Number of live states */
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define GOLD 1.618034  int popbased=0;
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 static double maxarg1,maxarg2;  int jmin, jmax; /* min, max spacing between 2 waves */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int mle, weightopt;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #define rint(a) floor(a+0.5)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 static double sqrarg;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 int imx;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 int stepm;  FILE *ficresprobmorprev;
 /* Stepm, step in month: minimum step interpolation*/  FILE *fichtm; /* Html File */
   FILE *ficreseij;
 int estepm;  char filerese[FILENAMELENGTH];
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 int m,nb;  FILE  *ficresvpl;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  char fileresvpl[FILENAMELENGTH];
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  char title[MAXLINE];
 double **pmmij, ***probs, ***mobaverage;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 double dateintmean=0;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 double *weight;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 int **s; /* Status */  char filelog[FILENAMELENGTH]; /* Log file */
 double *agedc, **covar, idx;  char filerest[FILENAMELENGTH];
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
 /**************** split *************************/  #define NR_END 1
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  #define NRANSI 
   #define ITMAX 200 
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define TOL 2.0e-4 
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */  #define CGOLD 0.3819660 
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  #define ZEPS 1.0e-10 
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  #define GOLD 1.618034 
   #define GLIMIT 100.0 
       if ( getwd( dirc ) == NULL ) {  #define TINY 1.0e-20 
 #else  
       extern char       *getcwd( );  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #endif    
          return( GLOCK_ERROR_GETCWD );  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       }  #define rint(a) floor(a+0.5)
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  static double sqrarg;
       s++;                              /* after this, the filename */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       l2 = strlen( s );                 /* length of filename */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  int imx; 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int stepm;
       dirc[l1-l2] = 0;                  /* add zero */  /* Stepm, step in month: minimum step interpolation*/
    }  
    l1 = strlen( dirc );                 /* length of directory */  int estepm;
 #ifdef windows  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  int m,nb;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 #endif  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    s = strrchr( name, '.' );            /* find last / */  double **pmmij, ***probs;
    s++;  double dateintmean=0;
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  double *weight;
    l2= strlen( s)+1;  int **s; /* Status */
    strncpy( finame, name, l1-l2);  double *agedc, **covar, idx;
    finame[l1-l2]= 0;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    return( 0 );                         /* we're done */  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   
 /******************************************/  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void replace(char *s, char*t)  {
 {    char  *ss;                            /* pointer */
   int i;    int   l1, l2;                         /* length counters */
   int lg=20;  
   i=0;    l1 = strlen(path );                   /* length of path */
   lg=strlen(t);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(i=0; i<= lg; i++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     (s[i] = t[i]);    if ( ss == NULL ) {                   /* no directory, so use current */
     if (t[i]== '\\') s[i]='/';      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 int nbocc(char *s, char occ)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   int i,j=0;      }
   int lg=20;      strcpy( name, path );               /* we've got it */
   i=0;    } else {                              /* strip direcotry from path */
   lg=strlen(s);      ss++;                               /* after this, the filename */
   for(i=0; i<= lg; i++) {      l2 = strlen( ss );                  /* length of filename */
   if  (s[i] == occ ) j++;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   }      strcpy( name, ss );         /* save file name */
   return j;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
     }
 void cutv(char *u,char *v, char*t, char occ)    l1 = strlen( dirc );                  /* length of directory */
 {  #ifdef windows
   /* cuts string t into u and v where u is ended by char occ excluding it    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  #else
      gives u="abcedf" and v="ghi2j" */    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   int i,lg,j,p=0;  #endif
   i=0;    ss = strrchr( name, '.' );            /* find last / */
   for(j=0; j<=strlen(t)-1; j++) {    ss++;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    strcpy(ext,ss);                       /* save extension */
   }    l1= strlen( name);
     l2= strlen(ss)+1;
   lg=strlen(t);    strncpy( finame, name, l1-l2);
   for(j=0; j<p; j++) {    finame[l1-l2]= 0;
     (u[j] = t[j]);    return( 0 );                          /* we're done */
   }  }
      u[p]='\0';  
   
    for(j=0; j<= lg; j++) {  /******************************************/
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  void replace(char *s, char*t)
 }  {
     int i;
 /********************** nrerror ********************/    int lg=20;
     i=0;
 void nrerror(char error_text[])    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   fprintf(stderr,"ERREUR ...\n");      (s[i] = t[i]);
   fprintf(stderr,"%s\n",error_text);      if (t[i]== '\\') s[i]='/';
   exit(1);    }
 }  }
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  int nbocc(char *s, char occ)
 {  {
   double *v;    int i,j=0;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    int lg=20;
   if (!v) nrerror("allocation failure in vector");    i=0;
   return v-nl+NR_END;    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /************************ free vector ******************/    }
 void free_vector(double*v, int nl, int nh)    return j;
 {  }
   free((FREE_ARG)(v+nl-NR_END));  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /************************ivector *******************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 int *ivector(long nl,long nh)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   int *v;    int i,lg,j,p=0;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    i=0;
   if (!v) nrerror("allocation failure in ivector");    for(j=0; j<=strlen(t)-1; j++) {
   return v-nl+NR_END;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /******************free ivector **************************/    lg=strlen(t);
 void free_ivector(int *v, long nl, long nh)    for(j=0; j<p; j++) {
 {      (u[j] = t[j]);
   free((FREE_ARG)(v+nl-NR_END));    }
 }       u[p]='\0';
   
 /******************* imatrix *******************************/     for(j=0; j<= lg; j++) {
 int **imatrix(long nrl, long nrh, long ncl, long nch)      if (j>=(p+1))(v[j-p-1] = t[j]);
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    }
 {  }
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  /********************** nrerror ********************/
    
   /* allocate pointers to rows */  void nrerror(char error_text[])
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    fprintf(stderr,"ERREUR ...\n");
   m += NR_END;    fprintf(stderr,"%s\n",error_text);
   m -= nrl;    exit(EXIT_FAILURE);
    }
    /*********************** vector *******************/
   /* allocate rows and set pointers to them */  double *vector(int nl, int nh)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    double *v;
   m[nrl] += NR_END;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   m[nrl] -= ncl;    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  }
    
   /* return pointer to array of pointers to rows */  /************************ free vector ******************/
   return m;  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /****************** free_imatrix *************************/  }
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /************************ivector *******************************/
       long nch,ncl,nrh,nrl;  char *cvector(long nl,long nh)
      /* free an int matrix allocated by imatrix() */  {
 {    char *v;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
   free((FREE_ARG) (m+nrl-NR_END));    if (!v) nrerror("allocation failure in cvector");
 }    return v-nl+NR_END;
   }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /******************free ivector **************************/
 {  void free_cvector(char *v, long nl, long nh)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  {
   double **m;    free((FREE_ARG)(v+nl-NR_END));
   }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /************************ivector *******************************/
   m += NR_END;  int *ivector(long nl,long nh)
   m -= nrl;  {
     int *v;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in ivector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /******************free ivector **************************/
   return m;  void free_ivector(int *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*************************free matrix ************************/  }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  /******************* imatrix *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   free((FREE_ARG)(m+nrl-NR_END));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 }  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 /******************* ma3x *******************************/    int **m; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    
 {    /* allocate pointers to rows */ 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double ***m;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    m -= nrl; 
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    
   m -= nrl;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    m[nrl] += NR_END; 
   m[nrl] += NR_END;    m[nrl] -= ncl; 
   m[nrl] -= ncl;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
     /* return pointer to array of pointers to rows */ 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    return m; 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  } 
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /****************** free_imatrix *************************/
   for (j=ncl+1; j<=nch; j++)  void free_imatrix(m,nrl,nrh,ncl,nch)
     m[nrl][j]=m[nrl][j-1]+nlay;        int **m;
          long nch,ncl,nrh,nrl; 
   for (i=nrl+1; i<=nrh; i++) {       /* free an int matrix allocated by imatrix() */ 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  { 
     for (j=ncl+1; j<=nch; j++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       m[i][j]=m[i][j-1]+nlay;    free((FREE_ARG) (m+nrl-NR_END)); 
   }  } 
   return m;  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 {    double **m;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /***************** f1dim *************************/  
 extern int ncom;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 extern double (*nrfunc)(double []);    m[nrl] += NR_END;
      m[nrl] -= ncl;
 double f1dim(double x)  
 {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int j;    return m;
   double f;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   double *xt;     */
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /*************************free matrix ************************/
   f=(*nrfunc)(xt);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   free_vector(xt,1,ncom);  {
   return f;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /******************* ma3x *******************************/
 {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   int iter;  {
   double a,b,d,etemp;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double fu,fv,fw,fx;    double ***m;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double e=0.0;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
   a=(ax < cx ? ax : cx);    m -= nrl;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   fw=fv=fx=(*f)(x);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] += NR_END;
     xm=0.5*(a+b);    m[nrl] -= ncl;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     printf(".");fflush(stdout);  
     fprintf(ficlog,".");fflush(ficlog);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     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);    m[nrl][ncl] += NR_END;
     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);    m[nrl][ncl] -= nll;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    for (j=ncl+1; j<=nch; j++) 
 #endif      m[nrl][j]=m[nrl][j-1]+nlay;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    
       *xmin=x;    for (i=nrl+1; i<=nrh; i++) {
       return fx;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
     ftemp=fu;        m[i][j]=m[i][j-1]+nlay;
     if (fabs(e) > tol1) {    }
       r=(x-w)*(fx-fv);    return m; 
       q=(x-v)*(fx-fw);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       p=(x-v)*q-(x-w)*r;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       q=2.0*(q-r);    */
       if (q > 0.0) p = -p;  }
       q=fabs(q);  
       etemp=e;  /*************************free ma3x ************************/
       e=d;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       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));    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       else {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         d=p/q;    free((FREE_ARG)(m+nrl-NR_END));
         u=x+d;  }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /***************** f1dim *************************/
       }  extern int ncom; 
     } else {  extern double *pcom,*xicom;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern double (*nrfunc)(double []); 
     }   
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  double f1dim(double x) 
     fu=(*f)(u);  { 
     if (fu <= fx) {    int j; 
       if (u >= x) a=x; else b=x;    double f;
       SHFT(v,w,x,u)    double *xt; 
         SHFT(fv,fw,fx,fu)   
         } else {    xt=vector(1,ncom); 
           if (u < x) a=u; else b=u;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
           if (fu <= fw || w == x) {    f=(*nrfunc)(xt); 
             v=w;    free_vector(xt,1,ncom); 
             w=u;    return f; 
             fv=fw;  } 
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  /*****************brent *************************/
             v=u;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
             fv=fu;  { 
           }    int iter; 
         }    double a,b,d,etemp;
   }    double fu,fv,fw,fx;
   nrerror("Too many iterations in brent");    double ftemp;
   *xmin=x;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   return fx;    double e=0.0; 
 }   
     a=(ax < cx ? ax : cx); 
 /****************** mnbrak ***********************/    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    fw=fv=fx=(*f)(x); 
             double (*func)(double))    for (iter=1;iter<=ITMAX;iter++) { 
 {      xm=0.5*(a+b); 
   double ulim,u,r,q, dum;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double fu;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        printf(".");fflush(stdout);
   *fa=(*func)(*ax);      fprintf(ficlog,".");fflush(ficlog);
   *fb=(*func)(*bx);  #ifdef DEBUG
   if (*fb > *fa) {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     SHFT(dum,*ax,*bx,dum)      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);
       SHFT(dum,*fb,*fa,dum)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       }  #endif
   *cx=(*bx)+GOLD*(*bx-*ax);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   *fc=(*func)(*cx);        *xmin=x; 
   while (*fb > *fc) {        return fx; 
     r=(*bx-*ax)*(*fb-*fc);      } 
     q=(*bx-*cx)*(*fb-*fa);      ftemp=fu;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      if (fabs(e) > tol1) { 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        r=(x-w)*(fx-fv); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        q=(x-v)*(fx-fw); 
     if ((*bx-u)*(u-*cx) > 0.0) {        p=(x-v)*q-(x-w)*r; 
       fu=(*func)(u);        q=2.0*(q-r); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {        if (q > 0.0) p = -p; 
       fu=(*func)(u);        q=fabs(q); 
       if (fu < *fc) {        etemp=e; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        e=d; 
           SHFT(*fb,*fc,fu,(*func)(u))        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 if ((u-ulim)*(ulim-*cx) >= 0.0) {        else { 
       u=ulim;          d=p/q; 
       fu=(*func)(u);          u=x+d; 
     } else {          if (u-a < tol2 || b-u < tol2) 
       u=(*cx)+GOLD*(*cx-*bx);            d=SIGN(tol1,xm-x); 
       fu=(*func)(u);        } 
     }      } else { 
     SHFT(*ax,*bx,*cx,u)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       SHFT(*fa,*fb,*fc,fu)      } 
       }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 }      fu=(*f)(u); 
       if (fu <= fx) { 
 /*************** linmin ************************/        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 int ncom;          SHFT(fv,fw,fx,fu) 
 double *pcom,*xicom;          } else { 
 double (*nrfunc)(double []);            if (u < x) a=u; else b=u; 
              if (fu <= fw || w == x) { 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))              v=w; 
 {              w=u; 
   double brent(double ax, double bx, double cx,              fv=fw; 
                double (*f)(double), double tol, double *xmin);              fw=fu; 
   double f1dim(double x);            } else if (fu <= fv || v == x || v == w) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,              v=u; 
               double *fc, double (*func)(double));              fv=fu; 
   int j;            } 
   double xx,xmin,bx,ax;          } 
   double fx,fb,fa;    } 
      nrerror("Too many iterations in brent"); 
   ncom=n;    *xmin=x; 
   pcom=vector(1,n);    return fx; 
   xicom=vector(1,n);  } 
   nrfunc=func;  
   for (j=1;j<=n;j++) {  /****************** mnbrak ***********************/
     pcom[j]=p[j];  
     xicom[j]=xi[j];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   }              double (*func)(double)) 
   ax=0.0;  { 
   xx=1.0;    double ulim,u,r,q, dum;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double fu; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);   
 #ifdef DEBUG    *fa=(*func)(*ax); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    *fb=(*func)(*bx); 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if (*fb > *fa) { 
 #endif      SHFT(dum,*ax,*bx,dum) 
   for (j=1;j<=n;j++) {        SHFT(dum,*fb,*fa,dum) 
     xi[j] *= xmin;        } 
     p[j] += xi[j];    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   free_vector(xicom,1,n);    while (*fb > *fc) { 
   free_vector(pcom,1,n);      r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 /*************** powell ************************/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      ulim=(*bx)+GLIMIT*(*cx-*bx); 
             double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   void linmin(double p[], double xi[], int n, double *fret,      } else if ((*cx-u)*(u-ulim) > 0.0) { 
               double (*func)(double []));        fu=(*func)(u); 
   int i,ibig,j;        if (fu < *fc) { 
   double del,t,*pt,*ptt,*xit;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double fp,fptt;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double *xits;            } 
   pt=vector(1,n);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   ptt=vector(1,n);        u=ulim; 
   xit=vector(1,n);        fu=(*func)(u); 
   xits=vector(1,n);      } else { 
   *fret=(*func)(p);        u=(*cx)+GOLD*(*cx-*bx); 
   for (j=1;j<=n;j++) pt[j]=p[j];        fu=(*func)(u); 
   for (*iter=1;;++(*iter)) {      } 
     fp=(*fret);      SHFT(*ax,*bx,*cx,u) 
     ibig=0;        SHFT(*fa,*fb,*fc,fu) 
     del=0.0;        } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  } 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /*************** linmin ************************/
       printf(" %d %.12f",i, p[i]);  
     fprintf(ficlog," %d %.12f",i, p[i]);  int ncom; 
     printf("\n");  double *pcom,*xicom;
     fprintf(ficlog,"\n");  double (*nrfunc)(double []); 
     for (i=1;i<=n;i++) {   
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       fptt=(*fret);  { 
 #ifdef DEBUG    double brent(double ax, double bx, double cx, 
       printf("fret=%lf \n",*fret);                 double (*f)(double), double tol, double *xmin); 
       fprintf(ficlog,"fret=%lf \n",*fret);    double f1dim(double x); 
 #endif    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("%d",i);fflush(stdout);                double *fc, double (*func)(double)); 
       fprintf(ficlog,"%d",i);fflush(ficlog);    int j; 
       linmin(p,xit,n,fret,func);    double xx,xmin,bx,ax; 
       if (fabs(fptt-(*fret)) > del) {    double fx,fb,fa;
         del=fabs(fptt-(*fret));   
         ibig=i;    ncom=n; 
       }    pcom=vector(1,n); 
 #ifdef DEBUG    xicom=vector(1,n); 
       printf("%d %.12e",i,(*fret));    nrfunc=func; 
       fprintf(ficlog,"%d %.12e",i,(*fret));    for (j=1;j<=n;j++) { 
       for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      xicom[j]=xi[j]; 
         printf(" x(%d)=%.12e",j,xit[j]);    } 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    ax=0.0; 
       }    xx=1.0; 
       for(j=1;j<=n;j++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         printf(" p=%.12e",p[j]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         fprintf(ficlog," p=%.12e",p[j]);  #ifdef DEBUG
       }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       printf("\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       fprintf(ficlog,"\n");  #endif
 #endif    for (j=1;j<=n;j++) { 
     }      xi[j] *= xmin; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      p[j] += xi[j]; 
 #ifdef DEBUG    } 
       int k[2],l;    free_vector(xicom,1,n); 
       k[0]=1;    free_vector(pcom,1,n); 
       k[1]=-1;  } 
       printf("Max: %.12e",(*func)(p));  
       fprintf(ficlog,"Max: %.12e",(*func)(p));  /*************** powell ************************/
       for (j=1;j<=n;j++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         printf(" %.12e",p[j]);              double (*func)(double [])) 
         fprintf(ficlog," %.12e",p[j]);  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
       printf("\n");                double (*func)(double [])); 
       fprintf(ficlog,"\n");    int i,ibig,j; 
       for(l=0;l<=1;l++) {    double del,t,*pt,*ptt,*xit;
         for (j=1;j<=n;j++) {    double fp,fptt;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double *xits;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    pt=vector(1,n); 
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    ptt=vector(1,n); 
         }    xit=vector(1,n); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    xits=vector(1,n); 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
 #endif    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
       ibig=0; 
       free_vector(xit,1,n);      del=0.0; 
       free_vector(xits,1,n);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       free_vector(ptt,1,n);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       free_vector(pt,1,n);      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       return;      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        fprintf(ficlog," %d %.12lf",i, p[i]);
     for (j=1;j<=n;j++) {        fprintf(ficrespow," %.12lf", p[i]);
       ptt[j]=2.0*p[j]-pt[j];      }
       xit[j]=p[j]-pt[j];      printf("\n");
       pt[j]=p[j];      fprintf(ficlog,"\n");
     }      fprintf(ficrespow,"\n");
     fptt=(*func)(ptt);      for (i=1;i<=n;i++) { 
     if (fptt < fp) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        fptt=(*fret); 
       if (t < 0.0) {  #ifdef DEBUG
         linmin(p,xit,n,fret,func);        printf("fret=%lf \n",*fret);
         for (j=1;j<=n;j++) {        fprintf(ficlog,"fret=%lf \n",*fret);
           xi[j][ibig]=xi[j][n];  #endif
           xi[j][n]=xit[j];        printf("%d",i);fflush(stdout);
         }        fprintf(ficlog,"%d",i);fflush(ficlog);
 #ifdef DEBUG        linmin(p,xit,n,fret,func); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        if (fabs(fptt-(*fret)) > del) { 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          del=fabs(fptt-(*fret)); 
         for(j=1;j<=n;j++){          ibig=i; 
           printf(" %.12e",xit[j]);        } 
           fprintf(ficlog," %.12e",xit[j]);  #ifdef DEBUG
         }        printf("%d %.12e",i,(*fret));
         printf("\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
         fprintf(ficlog,"\n");        for (j=1;j<=n;j++) {
 #endif          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
 /**** Prevalence limit ****************/          fprintf(ficlog," p=%.12e",p[j]);
         }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        printf("\n");
 {        fprintf(ficlog,"\n");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #endif
      matrix by transitions matrix until convergence is reached */      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int i, ii,j,k;  #ifdef DEBUG
   double min, max, maxmin, maxmax,sumnew=0.;        int k[2],l;
   double **matprod2();        k[0]=1;
   double **out, cov[NCOVMAX], **pmij();        k[1]=-1;
   double **newm;        printf("Max: %.12e",(*func)(p));
   double agefin, delaymax=50 ; /* Max number of years to converge */        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   for (ii=1;ii<=nlstate+ndeath;ii++)          printf(" %.12e",p[j]);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog," %.12e",p[j]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
     }        printf("\n");
         fprintf(ficlog,"\n");
    cov[1]=1.;        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     newm=savm;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     /* Covariates have to be included here again */          }
      cov[2]=agefin;          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)));
       for (k=1; k<=cptcovn;k++) {        }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #endif
         /*      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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        free_vector(xit,1,n); 
       for (k=1; k<=cptcovprod;k++)        free_vector(xits,1,n); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        return; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      } 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
     savm=oldm;        xit[j]=p[j]-pt[j]; 
     oldm=newm;        pt[j]=p[j]; 
     maxmax=0.;      } 
     for(j=1;j<=nlstate;j++){      fptt=(*func)(ptt); 
       min=1.;      if (fptt < fp) { 
       max=0.;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       for(i=1; i<=nlstate; i++) {        if (t < 0.0) { 
         sumnew=0;          linmin(p,xit,n,fret,func); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          for (j=1;j<=n;j++) { 
         prlim[i][j]= newm[i][j]/(1-sumnew);            xi[j][ibig]=xi[j][n]; 
         max=FMAX(max,prlim[i][j]);            xi[j][n]=xit[j]; 
         min=FMIN(min,prlim[i][j]);          }
       }  #ifdef DEBUG
       maxmin=max-min;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       maxmax=FMAX(maxmax,maxmin);          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++){
     if(maxmax < ftolpl){            printf(" %.12e",xit[j]);
       return prlim;            fprintf(ficlog," %.12e",xit[j]);
     }          }
   }          printf("\n");
 }          fprintf(ficlog,"\n");
   #endif
 /*************** transition probabilities ***************/        }
       } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    } 
 {  } 
   double s1, s2;  
   /*double t34;*/  /**** Prevalence limit (stable prevalence)  ****************/
   int i,j,j1, nc, ii, jj;  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(i=1; i<= nlstate; i++){  {
     for(j=1; j<i;j++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       matrix by transitions matrix until convergence is reached */
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int i, ii,j,k;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    double min, max, maxmin, maxmax,sumnew=0.;
       }    double **matprod2();
       ps[i][j]=s2;    double **out, cov[NCOVMAX], **pmij();
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for (ii=1;ii<=nlstate+ndeath;ii++)
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      for (j=1;j<=nlstate+ndeath;j++){
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }      }
       ps[i][j]=s2;  
     }     cov[1]=1.;
   }   
     /*ps[3][2]=1;*/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(i=1; i<= nlstate; i++){      newm=savm;
      s1=0;      /* Covariates have to be included here again */
     for(j=1; j<i; j++)       cov[2]=agefin;
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)        for (k=1; k<=cptcovn;k++) {
       s1+=exp(ps[i][j]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     ps[i][i]=1./(s1+1.);          /*      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<i; j++)        }
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(j=i+1; j<=nlstate+ndeath; j++)        for (k=1; k<=cptcovprod;k++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for(jj=1; jj<= nlstate+ndeath; jj++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       ps[ii][jj]=0;  
       ps[ii][ii]=1;      savm=oldm;
     }      oldm=newm;
   }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
         min=1.;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        max=0.;
     for(jj=1; jj<= nlstate+ndeath; jj++){        for(i=1; i<=nlstate; i++) {
      printf("%lf ",ps[ii][jj]);          sumnew=0;
    }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     printf("\n ");          prlim[i][j]= newm[i][j]/(1-sumnew);
     }          max=FMAX(max,prlim[i][j]);
     printf("\n ");printf("%lf ",cov[2]);*/          min=FMIN(min,prlim[i][j]);
 /*        }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        maxmin=max-min;
   goto end;*/        maxmax=FMAX(maxmax,maxmin);
     return ps;      }
 }      if(maxmax < ftolpl){
         return prlim;
 /**************** Product of 2 matrices ******************/      }
     }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*************** transition probabilities ***************/ 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      before: only the contents of out is modified. The function returns  {
      a pointer to pointers identical to out */    double s1, s2;
   long i, j, k;    /*double t34;*/
   for(i=nrl; i<= nrh; i++)    int i,j,j1, nc, ii, jj;
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      for(i=1; i<= nlstate; i++){
         out[i][k] +=in[i][j]*b[j][k];      for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   return out;          /*s2 += param[i][j][nc]*cov[nc];*/
 }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
 /************* Higher Matrix Product ***************/        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      }
 {      for(j=i+1; j<=nlstate+ndeath;j++){
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      duration (i.e. until          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
      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).        ps[i][j]=s2;
      Model is determined by parameters x and covariates have to be      }
      included manually here.    }
       /*ps[3][2]=1;*/
      */  
     for(i=1; i<= nlstate; i++){
   int i, j, d, h, k;       s1=0;
   double **out, cov[NCOVMAX];      for(j=1; j<i; j++)
   double **newm;        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
   /* Hstepm could be zero and should return the unit matrix */        s1+=exp(ps[i][j]);
   for (i=1;i<=nlstate+ndeath;i++)      ps[i][i]=1./(s1+1.);
     for (j=1;j<=nlstate+ndeath;j++){      for(j=1; j<i; j++)
       oldm[i][j]=(i==j ? 1.0 : 0.0);        ps[i][j]= exp(ps[i][j])*ps[i][i];
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for(j=i+1; j<=nlstate+ndeath; j++)
     }        ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for(h=1; h <=nhstepm; h++){    } /* end i */
     for(d=1; d <=hstepm; d++){  
       newm=savm;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       /* Covariates have to be included here again */      for(jj=1; jj<= nlstate+ndeath; jj++){
       cov[1]=1.;        ps[ii][jj]=0;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        ps[ii][ii]=1;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      }
       for (k=1; k<=cptcovage;k++)    }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/     }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      printf("\n ");
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      printf("\n ");printf("%lf ",cov[2]);*/
       savm=oldm;  /*
       oldm=newm;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     }    goto end;*/
     for(i=1; i<=nlstate+ndeath; i++)      return ps;
       for(j=1;j<=nlstate+ndeath;j++) {  }
         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]);  /**************** Product of 2 matrices ******************/
          */  
       }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   } /* end h */  {
   return po;    /* 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(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
 /*************** log-likelihood *************/       a pointer to pointers identical to out */
 double func( double *x)    long i, j, k;
 {    for(i=nrl; i<= nrh; i++)
   int i, ii, j, k, mi, d, kk;      for(k=ncolol; k<=ncoloh; k++)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double **out;          out[i][k] +=in[i][j]*b[j][k];
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    return out;
   long ipmx;  }
   /*extern weight */  
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /************* Higher Matrix Product ***************/
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   */  {
   cov[1]=1.;    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
   for(k=1; k<=nlstate; k++) ll[k]=0.;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){       nhstepm*hstepm matrices. 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for(mi=1; mi<= wav[i]-1; mi++){       (typically every 2 years instead of every month which is too big 
       for (ii=1;ii<=nlstate+ndeath;ii++)       for the memory).
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       Model is determined by parameters x and covariates have to be 
       for(d=0; d<dh[mi][i]; d++){       included manually here. 
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       */
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    int i, j, d, h, k;
         }    double **out, cov[NCOVMAX];
            double **newm;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    /* Hstepm could be zero and should return the unit matrix */
         savm=oldm;    for (i=1;i<=nlstate+ndeath;i++)
         oldm=newm;      for (j=1;j<=nlstate+ndeath;j++){
                oldm[i][j]=(i==j ? 1.0 : 0.0);
                po[i][j][0]=(i==j ? 1.0 : 0.0);
       } /* end mult */      }
          /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    for(h=1; h <=nhstepm; h++){
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      for(d=1; d <=hstepm; d++){
       ipmx +=1;        newm=savm;
       sw += weight[i];        /* Covariates have to be included here again */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        cov[1]=1.;
     } /* end of wave */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   } /* end of individual */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        for (k=1; k<=cptcovprod;k++)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   return -l;  
 }  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 /*********** Maximum Likelihood Estimation ***************/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        savm=oldm;
 {        oldm=newm;
   int i,j, iter;      }
   double **xi,*delti;      for(i=1; i<=nlstate+ndeath; i++)
   double fret;        for(j=1;j<=nlstate+ndeath;j++) {
   xi=matrix(1,npar,1,npar);          po[i][j][h]=newm[i][j];
   for (i=1;i<=npar;i++)          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     for (j=1;j<=npar;j++)           */
       xi[i][j]=(i==j ? 1.0 : 0.0);        }
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    } /* end h */
   powell(p,xi,npar,ftol,&iter,&fret,func);    return po;
   }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /*************** log-likelihood *************/
   double func( double *x)
 }  {
     int i, ii, j, k, mi, d, kk;
 /**** Computes Hessian and covariance matrix ***/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    double **out;
 {    double sw; /* Sum of weights */
   double  **a,**y,*x,pd;    double lli; /* Individual log likelihood */
   double **hess;    int s1, s2;
   int i, j,jk;    double bbh, survp;
   int *indx;    long ipmx;
     /*extern weight */
   double hessii(double p[], double delta, int theta, double delti[]);    /* We are differentiating ll according to initial status */
   double hessij(double p[], double delti[], int i, int j);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /*for(i=1;i<imx;i++) 
   void ludcmp(double **a, int npar, int *indx, double *d) ;      printf(" %d\n",s[4][i]);
     */
   hess=matrix(1,npar,1,npar);    cov[1]=1.;
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){    if(mle==1){
     printf("%d",i);fflush(stdout);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficlog,"%d",i);fflush(ficlog);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     hess[i][i]=hessii(p,ftolhess,i,delti);        for(mi=1; mi<= wav[i]-1; mi++){
     /*printf(" %f ",p[i]);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
     /*printf(" %lf ",hess[i][i]);*/            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=npar;i++) {            }
     for (j=1;j<=npar;j++)  {          for(d=0; d<dh[mi][i]; d++){
       if (j>i) {            newm=savm;
         printf(".%d%d",i,j);fflush(stdout);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);            for (kk=1; kk<=cptcovage;kk++) {
         hess[i][j]=hessij(p,delti,i,j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         hess[j][i]=hess[i][j];                }
         /*printf(" %lf ",hess[i][j]);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   printf("\n");          } /* end mult */
   fprintf(ficlog,"\n");        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          /* But now since version 0.9 we anticipate for bias and large stepm.
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");           * 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 
   a=matrix(1,npar,1,npar);           * the nearest (and in case of equal distance, to the lowest) interval but now
   y=matrix(1,npar,1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   x=vector(1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   indx=ivector(1,npar);           * probability in order to take into account the bias as a fraction of the way
   for (i=1;i<=npar;i++)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];           * -stepm/2 to stepm/2 .
   ludcmp(a,npar,indx,&pd);           * 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. 
   for (j=1;j<=npar;j++) {           */
     for (i=1;i<=npar;i++) x[i]=0;          s1=s[mw[mi][i]][i];
     x[j]=1;          s2=s[mw[mi+1][i]][i];
     lubksb(a,npar,indx,x);          bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1;i<=npar;i++){          /* bias is positive if real duration
       matcov[i][j]=x[i];           * is higher than the multiple of stepm and negative otherwise.
     }           */
   }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   printf("\n#Hessian matrix#\n");            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   fprintf(ficlog,"\n#Hessian matrix#\n");               to the likelihood is the probability to die between last step unit time and current 
   for (i=1;i<=npar;i++) {               step unit time, which is also the differences between probability to die before dh 
     for (j=1;j<=npar;j++) {               and probability to die before dh-stepm . 
       printf("%.3e ",hess[i][j]);               In version up to 0.92 likelihood was computed
       fprintf(ficlog,"%.3e ",hess[i][j]);          as if date of death was unknown. Death was treated as any other
     }          health state: the date of the interview describes the actual state
     printf("\n");          and not the date of a change in health state. The former idea was
     fprintf(ficlog,"\n");          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   /* Recompute Inverse */          the contribution of an exact death to the likelihood. This new
   for (i=1;i<=npar;i++)          contribution is smaller and very dependent of the step unit
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          stepm. It is no more the probability to die between last interview
   ludcmp(a,npar,indx,&pd);          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
   /*  printf("\n#Hessian matrix recomputed#\n");          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
   for (j=1;j<=npar;j++) {          mortality artificially. The bad side is that we add another loop
     for (i=1;i<=npar;i++) x[i]=0;          which slows down the processing. The difference can be up to 10%
     x[j]=1;          lower mortality.
     lubksb(a,npar,indx,x);            */
     for (i=1;i<=npar;i++){            lli=log(out[s1][s2] - savm[s1][s2]);
       y[i][j]=x[i];          }else{
       printf("%.3e ",y[i][j]);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       fprintf(ficlog,"%.3e ",y[i][j]);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     }          } 
     printf("\n");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     fprintf(ficlog,"\n");          /*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;
           sw += weight[i];
   free_matrix(a,1,npar,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_matrix(y,1,npar,1,npar);        } /* end of wave */
   free_vector(x,1,npar);      } /* end of individual */
   free_ivector(indx,1,npar);    }  else if(mle==2){
   free_matrix(hess,1,npar,1,npar);      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++)
             for (j=1;j<=nlstate+ndeath;j++){
 /*************** hessian matrix ****************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double hessii( double x[], double delta, int theta, double delti[])              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   int i;          for(d=0; d<=dh[mi][i]; d++){
   int l=1, lmax=20;            newm=savm;
   double k1,k2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double p2[NPARMAX+1];            for (kk=1; kk<=cptcovage;kk++) {
   double res;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            }
   double fx;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k=0,kmax=10;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double l1;            savm=oldm;
             oldm=newm;
   fx=func(x);          } /* end mult */
   for (i=1;i<=npar;i++) p2[i]=x[i];        
   for(l=0 ; l <=lmax; l++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     l1=pow(10,l);          /* But now since version 0.9 we anticipate for bias and large stepm.
     delts=delt;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for(k=1 ; k <kmax; k=k+1){           * (in months) between two waves is not a multiple of stepm, we rounded to 
       delt = delta*(l1*k);           * the nearest (and in case of equal distance, to the lowest) interval but now
       p2[theta]=x[theta] +delt;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       k1=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       p2[theta]=x[theta]-delt;           * probability in order to take into account the bias as a fraction of the way
       k2=func(p2)-fx;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       /*res= (k1-2.0*fx+k2)/delt/delt; */           * -stepm/2 to stepm/2 .
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           * 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. 
 #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);          s1=s[mw[mi][i]][i];
       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);          s2=s[mw[mi+1][i]][i];
 #endif          bbh=(double)bh[mi][i]/(double)stepm; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /* bias is positive if real duration
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){           * is higher than the multiple of stepm and negative otherwise.
         k=kmax;           */
       }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         k=kmax; l=lmax*10.;          /*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]);*/
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          /*if(lli ==000.0)*/
         delts=delt;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       }          ipmx +=1;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   delti[theta]=delts;        } /* end of wave */
   return res;      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 double hessij( double x[], double delti[], int thetai,int thetaj)        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   int i;            for (j=1;j<=nlstate+ndeath;j++){
   int l=1, l1, lmax=20;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double k1,k2,k3,k4,res,fx;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double p2[NPARMAX+1];            }
   int k;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   fx=func(x);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (k=1; k<=2; k++) {            for (kk=1; kk<=cptcovage;kk++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetai]=x[thetai]+delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     k1=func(p2)-fx;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
     p2[thetai]=x[thetai]+delti[thetai]/k;            oldm=newm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          } /* end mult */
     k2=func(p2)-fx;        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetai]=x[thetai]-delti[thetai]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     k3=func(p2)-fx;           * (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
     p2[thetai]=x[thetai]-delti[thetai]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     k4=func(p2)-fx;           * probability in order to take into account the bias as a fraction of the way
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 #ifdef DEBUG           * -stepm/2 to stepm/2 .
     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);           * For stepm=1 the results are the same as for previous versions of Imach.
     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);           * For stepm > 1 the results are less biased than in previous versions. 
 #endif           */
   }          s1=s[mw[mi][i]][i];
   return res;          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 /************** Inverse of matrix **************/           * is higher than the multiple of stepm and negative otherwise.
 void ludcmp(double **a, int n, int *indx, double *d)           */
 {          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
   int i,imax,j,k;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double big,dum,sum,temp;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *vv;          /*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); */
   vv=vector(1,n);          ipmx +=1;
   *d=1.0;          sw += weight[i];
   for (i=1;i<=n;i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     big=0.0;        } /* end of wave */
     for (j=1;j<=n;j++)      } /* end of individual */
       if ((temp=fabs(a[i][j])) > big) big=temp;    }else{  /* ml=4 no inter-extrapolation */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     vv[i]=1.0/big;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   for (j=1;j<=n;j++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1;i<j;i++) {            for (j=1;j<=nlstate+ndeath;j++){
       sum=a[i][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;            }
     }          for(d=0; d<dh[mi][i]; d++){
     big=0.0;            newm=savm;
     for (i=j;i<=n;i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       sum=a[i][j];            for (kk=1; kk<=cptcovage;kk++) {
       for (k=1;k<j;k++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         sum -= a[i][k]*a[k][j];            }
       a[i][j]=sum;          
       if ( (dum=vv[i]*fabs(sum)) >= big) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         big=dum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         imax=i;            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
     if (j != imax) {        
       for (k=1;k<=n;k++) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         dum=a[imax][k];          ipmx +=1;
         a[imax][k]=a[j][k];          sw += weight[i];
         a[j][k]=dum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       *d = -(*d);      } /* end of individual */
       vv[imax]=vv[j];    } /* End of if */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     indx[j]=imax;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     if (a[j][j] == 0.0) a[j][j]=TINY;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if (j != n) {    return -l;
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  
   }  /*********** Maximum Likelihood Estimation ***************/
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 }  {
     int i,j, iter;
 void lubksb(double **a, int n, int *indx, double b[])    double **xi;
 {    double fret;
   int i,ii=0,ip,j;    char filerespow[FILENAMELENGTH];
   double sum;    xi=matrix(1,npar,1,npar);
      for (i=1;i<=npar;i++)
   for (i=1;i<=n;i++) {      for (j=1;j<=npar;j++)
     ip=indx[i];        xi[i][j]=(i==j ? 1.0 : 0.0);
     sum=b[ip];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     b[ip]=b[i];    strcpy(filerespow,"pow"); 
     if (ii)    strcat(filerespow,fileres);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     else if (sum) ii=i;      printf("Problem with resultfile: %s\n", filerespow);
     b[i]=sum;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
   for (i=n;i>=1;i--) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     sum=b[i];    for (i=1;i<=nlstate;i++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for(j=1;j<=nlstate+ndeath;j++)
     b[i]=sum/a[i][i];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   }    fprintf(ficrespow,"\n");
 }    powell(p,xi,npar,ftol,&iter,&fret,func);
   
 /************ Frequencies ********************/    fclose(ficrespow);
 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)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 {  /* Some frequencies */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   int first;  }
   double ***freq; /* Frequencies */  
   double *pp;  /**** Computes Hessian and covariance matrix ***/
   double pos, k2, dateintsum=0,k2cpt=0;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    double  **a,**y,*x,pd;
      double **hess;
   pp=vector(1,nlstate);    int i, j,jk;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int *indx;
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);    double hessii(double p[], double delta, int theta, double delti[]);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double hessij(double p[], double delti[], int i, int j);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     exit(0);  
   }    hess=matrix(1,npar,1,npar);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    printf("\nCalculation of the hessian matrix. Wait...\n");
      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   j=cptcoveff;    for (i=1;i<=npar;i++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   first=1;      hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
   for(k1=1; k1<=j;k1++){      /*printf(" %lf ",hess[i][i]);*/
     for(i1=1; i1<=ncodemax[k1];i1++){    }
       j1++;    
       /*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++)          if (j>i) { 
         for (jk=-1; jk<=nlstate+ndeath; jk++)            printf(".%d%d",i,j);fflush(stdout);
           for(m=agemin; m <= agemax+3; m++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
             freq[i][jk][m]=0;          hess[i][j]=hessij(p,delti,i,j);
                hess[j][i]=hess[i][j];    
       dateintsum=0;          /*printf(" %lf ",hess[i][j]);*/
       k2cpt=0;        }
       for (i=1; i<=imx; i++) {      }
         bool=1;    }
         if  (cptcovn>0) {    printf("\n");
           for (z1=1; z1<=cptcoveff; z1++)    fprintf(ficlog,"\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         if (bool==1) {    
           for(m=firstpass; m<=lastpass; m++){    a=matrix(1,npar,1,npar);
             k2=anint[m][i]+(mint[m][i]/12.);    y=matrix(1,npar,1,npar);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    x=vector(1,npar);
               if(agev[m][i]==0) agev[m][i]=agemax+1;    indx=ivector(1,npar);
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=npar;i++)
               if (m<lastpass) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    ludcmp(a,npar,indx,&pd);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
               }    for (j=1;j<=npar;j++) {
                    for (i=1;i<=npar;i++) x[i]=0;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      x[j]=1;
                 dateintsum=dateintsum+k2;      lubksb(a,npar,indx,x);
                 k2cpt++;      for (i=1;i<=npar;i++){ 
               }        matcov[i][j]=x[i];
             }      }
           }    }
         }  
       }    printf("\n#Hessian matrix#\n");
            fprintf(ficlog,"\n#Hessian matrix#\n");
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
       if  (cptcovn>0) {        printf("%.3e ",hess[i][j]);
         fprintf(ficresp, "\n#********** Variable ");        fprintf(ficlog,"%.3e ",hess[i][j]);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      }
         fprintf(ficresp, "**********\n#");      printf("\n");
       }      fprintf(ficlog,"\n");
       for(i=1; i<=nlstate;i++)    }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");    /* Recompute Inverse */
          for (i=1;i<=npar;i++)
       for(i=(int)agemin; i <= (int)agemax+3; i++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         if(i==(int)agemax+3){    ludcmp(a,npar,indx,&pd);
           fprintf(ficlog,"Total");  
         }else{    /*  printf("\n#Hessian matrix recomputed#\n");
           if(first==1){  
             first=0;    for (j=1;j<=npar;j++) {
             printf("See log file for details...\n");      for (i=1;i<=npar;i++) x[i]=0;
           }      x[j]=1;
           fprintf(ficlog,"Age %d", i);      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
         for(jk=1; jk <=nlstate ; jk++){        y[i][j]=x[i];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        printf("%.3e ",y[i][j]);
             pp[jk] += freq[jk][m][i];        fprintf(ficlog,"%.3e ",y[i][j]);
         }      }
         for(jk=1; jk <=nlstate ; jk++){      printf("\n");
           for(m=-1, pos=0; m <=0 ; m++)      fprintf(ficlog,"\n");
             pos += freq[jk][m][i];    }
           if(pp[jk]>=1.e-10){    */
             if(first==1){  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    free_matrix(a,1,npar,1,npar);
             }    free_matrix(y,1,npar,1,npar);
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    free_vector(x,1,npar);
           }else{    free_ivector(indx,1,npar);
             if(first==1)    free_matrix(hess,1,npar,1,npar);
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
           }  }
         }  
   /*************** hessian matrix ****************/
         for(jk=1; jk <=nlstate ; jk++){  double hessii( double x[], double delta, int theta, double delti[])
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  {
             pp[jk] += freq[jk][m][i];    int i;
         }    int l=1, lmax=20;
     double k1,k2;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double p2[NPARMAX+1];
           pos += pp[jk];    double res;
         for(jk=1; jk <=nlstate ; jk++){    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           if(pos>=1.e-5){    double fx;
             if(first==1)    int k=0,kmax=10;
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double l1;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           }else{    fx=func(x);
             if(first==1)    for (i=1;i<=npar;i++) p2[i]=x[i];
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for(l=0 ; l <=lmax; l++){
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      l1=pow(10,l);
           }      delts=delt;
           if( i <= (int) agemax){      for(k=1 ; k <kmax; k=k+1){
             if(pos>=1.e-5){        delt = delta*(l1*k);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        p2[theta]=x[theta] +delt;
               probs[i][jk][j1]= pp[jk]/pos;        k1=func(p2)-fx;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        p2[theta]=x[theta]-delt;
             }        k2=func(p2)-fx;
             else        /*res= (k1-2.0*fx+k2)/delt/delt; */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           }        
         }  #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);
         for(jk=-1; jk <=nlstate+ndeath; jk++)        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);
           for(m=-1; m <=nlstate+ndeath; m++)  #endif
             if(freq[jk][m][i] !=0 ) {        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             if(first==1)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          k=kmax;
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);        }
             }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         if(i <= (int) agemax)          k=kmax; l=lmax*10.;
           fprintf(ficresp,"\n");        }
         if(first==1)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           printf("Others in log...\n");          delts=delt;
         fprintf(ficlog,"\n");        }
       }      }
     }    }
   }    delti[theta]=delts;
   dateintmean=dateintsum/k2cpt;    return res; 
      
   fclose(ficresp);  }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  double hessij( double x[], double delti[], int thetai,int thetaj)
    {
   /* End of Freq */    int i;
 }    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
 /************ Prevalence ********************/    double p2[NPARMAX+1];
 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)    int k;
 {  /* Some frequencies */  
      fx=func(x);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for (k=1; k<=2; k++) {
   double ***freq; /* Frequencies */      for (i=1;i<=npar;i++) p2[i]=x[i];
   double *pp;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double pos, k2;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
   pp=vector(1,nlstate);    
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      k2=func(p2)-fx;
   j1=0;    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   j=cptcoveff;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      k3=func(p2)-fx;
      
   for(k1=1; k1<=j;k1++){      p2[thetai]=x[thetai]-delti[thetai]/k;
     for(i1=1; i1<=ncodemax[k1];i1++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       j1++;      k4=func(p2)-fx;
            res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for (i=-1; i<=nlstate+ndeath; i++)    #ifdef DEBUG
         for (jk=-1; jk<=nlstate+ndeath; jk++)        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
           for(m=agemin; m <= agemax+3; m++)      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);
             freq[i][jk][m]=0;  #endif
          }
       for (i=1; i<=imx; i++) {    return res;
         bool=1;  }
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /************** Inverse of matrix **************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  void ludcmp(double **a, int n, int *indx, double *d) 
               bool=0;  { 
         }    int i,imax,j,k; 
         if (bool==1) {    double big,dum,sum,temp; 
           for(m=firstpass; m<=lastpass; m++){    double *vv; 
             k2=anint[m][i]+(mint[m][i]/12.);   
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    vv=vector(1,n); 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    *d=1.0; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=n;i++) { 
               if (m<lastpass) {      big=0.0; 
                 if (calagedate>0)      for (j=1;j<=n;j++) 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        if ((temp=fabs(a[i][j])) > big) big=temp; 
                 else      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      vv[i]=1.0/big; 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    } 
               }    for (j=1;j<=n;j++) { 
             }      for (i=1;i<j;i++) { 
           }        sum=a[i][j]; 
         }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       }        a[i][j]=sum; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      } 
         for(jk=1; jk <=nlstate ; jk++){      big=0.0; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=j;i<=n;i++) { 
             pp[jk] += freq[jk][m][i];        sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
         for(jk=1; jk <=nlstate ; jk++){          sum -= a[i][k]*a[k][j]; 
           for(m=-1, pos=0; m <=0 ; m++)        a[i][j]=sum; 
             pos += freq[jk][m][i];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         }          big=dum; 
                  imax=i; 
         for(jk=1; jk <=nlstate ; jk++){        } 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } 
             pp[jk] += freq[jk][m][i];      if (j != imax) { 
         }        for (k=1;k<=n;k++) { 
                  dum=a[imax][k]; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          a[imax][k]=a[j][k]; 
                  a[j][k]=dum; 
         for(jk=1; jk <=nlstate ; jk++){            } 
           if( i <= (int) agemax){        *d = -(*d); 
             if(pos>=1.e-5){        vv[imax]=vv[j]; 
               probs[i][jk][j1]= pp[jk]/pos;      } 
             }      indx[j]=imax; 
           }      if (a[j][j] == 0.0) a[j][j]=TINY; 
         }/* end jk */      if (j != n) { 
       }/* end i */        dum=1.0/(a[j][j]); 
     } /* end i1 */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   } /* end k1 */      } 
     } 
      free_vector(vv,1,n);  /* Doesn't work */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  ;
   free_vector(pp,1,nlstate);  } 
    
 }  /* End of Freq */  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
 /************* Waves Concatenation ***************/    int i,ii=0,ip,j; 
     double sum; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)   
 {    for (i=1;i<=n;i++) { 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      ip=indx[i]; 
      Death is a valid wave (if date is known).      sum=b[ip]; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      b[ip]=b[i]; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      if (ii) 
      and mw[mi+1][i]. dh depends on stepm.        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      */      else if (sum) ii=i; 
       b[i]=sum; 
   int i, mi, m;    } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    for (i=n;i>=1;i--) { 
      double sum=0., jmean=0.;*/      sum=b[i]; 
   int first;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   int j, k=0,jk, ju, jl;      b[i]=sum/a[i][i]; 
   double sum=0.;    } 
   first=0;  } 
   jmin=1e+5;  
   jmax=-1;  /************ Frequencies ********************/
   jmean=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)
   for(i=1; i<=imx; i++){  {  /* Some frequencies */
     mi=0;    
     m=firstpass;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     while(s[m][i] <= nlstate){    int first;
       if(s[m][i]>=1)    double ***freq; /* Frequencies */
         mw[++mi][i]=m;    double *pp, **prop;
       if(m >=lastpass)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         break;    FILE *ficresp;
       else    char fileresp[FILENAMELENGTH];
         m++;    
     }/* end while */    pp=vector(1,nlstate);
     if (s[m][i] > nlstate){    prop=matrix(1,nlstate,iagemin,iagemax+3);
       mi++;     /* Death is another wave */    strcpy(fileresp,"p");
       /* if(mi==0)  never been interviewed correctly before death */    strcat(fileresp,fileres);
          /* Only death is a correct wave */    if((ficresp=fopen(fileresp,"w"))==NULL) {
       mw[mi][i]=m;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     wav[i]=mi;    }
     if(mi==0){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       if(first==0){    j1=0;
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);    
         first=1;    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       if(first==1){  
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);    first=1;
       }  
     } /* end mi==0 */    for(k1=1; k1<=j;k1++){
   }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   for(i=1; i<=imx; i++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for(mi=1; mi<wav[i];mi++){          scanf("%d", i);*/
       if (stepm <=0)        for (i=-1; i<=nlstate+ndeath; i++)  
         dh[mi][i]=1;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       else{            for(m=iagemin; m <= iagemax+3; m++)
         if (s[mw[mi+1][i]][i] > nlstate) {              freq[i][jk][m]=0;
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for (i=1; i<=nlstate; i++)  
           if(j==0) j=1;  /* Survives at least one month after exam */        for(m=iagemin; m <= iagemax+3; m++)
           k=k+1;          prop[i][m]=0;
           if (j >= jmax) jmax=j;        
           if (j <= jmin) jmin=j;        dateintsum=0;
           sum=sum+j;        k2cpt=0;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for (i=1; i<=imx; i++) {
           }          bool=1;
         }          if  (cptcovn>0) {
         else{            for (z1=1; z1<=cptcoveff; z1++) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           k=k+1;                bool=0;
           if (j >= jmax) jmax=j;          }
           else if (j <= jmin)jmin=j;          if (bool==1){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for(m=firstpass; m<=lastpass; m++){
           sum=sum+j;              k2=anint[m][i]+(mint[m][i]/12.);
         }              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         jk= j/stepm;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         jl= j -jk*stepm;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         ju= j -(jk+1)*stepm;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         if(jl <= -ju)                if (m<lastpass) {
           dh[mi][i]=jk;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         else                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           dh[mi][i]=jk+1;                }
         if(dh[mi][i]==0)                
           dh[mi][i]=1; /* At least one step */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       }                  dateintsum=dateintsum+k2;
     }                  k2cpt++;
   }                }
   jmean=sum/k;              }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            }
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          }
  }        }
          
 /*********** Tricode ****************************/        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 void tricode(int *Tvar, int **nbcode, int imx)  
 {        if  (cptcovn>0) {
   int Ndum[20],ij=1, k, j, i;          fprintf(ficresp, "\n#********** Variable "); 
   int cptcode=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   cptcoveff=0;          fprintf(ficresp, "**********\n#");
          }
   for (k=0; k<19; k++) Ndum[k]=0;        for(i=1; i<=nlstate;i++) 
   for (k=1; k<=7; k++) ncodemax[k]=0;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        
     for (i=1; i<=imx; i++) {        for(i=iagemin; i <= iagemax+3; i++){
       ij=(int)(covar[Tvar[j]][i]);          if(i==iagemax+3){
       Ndum[ij]++;            fprintf(ficlog,"Total");
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          }else{
       if (ij > cptcode) cptcode=ij;            if(first==1){
     }              first=0;
               printf("See log file for details...\n");
     for (i=0; i<=cptcode; i++) {            }
       if(Ndum[i]!=0) ncodemax[j]++;            fprintf(ficlog,"Age %d", i);
     }          }
     ij=1;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
     for (i=1; i<=ncodemax[j]; i++) {          }
       for (k=0; k<=19; k++) {          for(jk=1; jk <=nlstate ; jk++){
         if (Ndum[k] != 0) {            for(m=-1, pos=0; m <=0 ; m++)
           nbcode[Tvar[j]][ij]=k;              pos += freq[jk][m][i];
                      if(pp[jk]>=1.e-10){
           ij++;              if(first==1){
         }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         if (ij > ncodemax[j]) break;              }
       }                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }            }else{
   }                if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  for (k=0; k<19; k++) Ndum[k]=0;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
  for (i=1; i<=ncovmodel-2; i++) {          }
    ij=Tvar[i];  
    Ndum[ij]++;          for(jk=1; jk <=nlstate ; jk++){
  }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
  ij=1;          }       
  for (i=1; i<=10; i++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
    if((Ndum[i]!=0) && (i<=ncovcol)){            pos += pp[jk];
      Tvaraff[ij]=i;            posprop += prop[jk][i];
      ij++;          }
    }          for(jk=1; jk <=nlstate ; jk++){
  }            if(pos>=1.e-5){
                if(first==1)
  cptcoveff=ij-1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
 /*********** Health Expectancies ****************/              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 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(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 {            if( i <= iagemax){
   /* Health expectancies */              if(pos>=1.e-5){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double age, agelim, hf;                probs[i][jk][j1]= pp[jk]/pos;
   double ***p3mat,***varhe;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double **dnewm,**doldm;              }
   double *xp;              else
   double **gp, **gm;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double ***gradg, ***trgradg;            }
   int theta;          }
           
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   xp=vector(1,npar);            for(m=-1; m <=nlstate+ndeath; m++)
   dnewm=matrix(1,nlstate*2,1,npar);              if(freq[jk][m][i] !=0 ) {
   doldm=matrix(1,nlstate*2,1,nlstate*2);              if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficreseij,"# Health expectancies\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficreseij,"# Age");              }
   for(i=1; i<=nlstate;i++)          if(i <= iagemax)
     for(j=1; j<=nlstate;j++)            fprintf(ficresp,"\n");
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          if(first==1)
   fprintf(ficreseij,"\n");            printf("Others in log...\n");
           fprintf(ficlog,"\n");
   if(estepm < stepm){        }
     printf ("Problem %d lower than %d\n",estepm, stepm);      }
   }    }
   else  hstepm=estepm;      dateintmean=dateintsum/k2cpt; 
   /* We compute the life expectancy from trapezoids spaced every estepm months   
    * This is mainly to measure the difference between two models: for example    fclose(ficresp);
    * if stepm=24 months pijx are given only every 2 years and by summing them    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    * we are calculating an estimate of the Life Expectancy assuming a linear    free_vector(pp,1,nlstate);
    * progression inbetween and thus overestimating or underestimating according    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
    * to the curvature of the survival function. If, for the same date, we    /* End of Freq */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  }
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise  /************ Prevalence ********************/
    * curvature will be obtained if estepm is as small as stepm. */  void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
   /* For example we decided to compute the life expectancy with the smallest unit */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.       in each health status at the date of interview (if between dateprev1 and dateprev2).
      nhstepm is the number of hstepm from age to agelim       We still use firstpass and lastpass as another selection.
      nstepm is the number of stepm from age to agelin.    */
      Look at hpijx to understand the reason of that which relies in memory size   
      and note for a fixed period like estepm months */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double ***freq; /* Frequencies */
      survival function given by stepm (the optimization length). Unfortunately it    double *pp, **prop;
      means that if the survival funtion is printed only each two years of age and if    double pos,posprop; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double  y2; /* in fractional years */
      results. So we changed our mind and took the option of the best precision.    int iagemin, iagemax;
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    iagemin= (int) agemin;
     iagemax= (int) agemax;
   agelim=AGESUP;    /*pp=vector(1,nlstate);*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /* nhstepm age range expressed in number of stepm */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    j1=0;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    
     /* if (stepm >= YEARM) hstepm=1;*/    j=cptcoveff;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    for(k1=1; k1<=j;k1++){
     gp=matrix(0,nhstepm,1,nlstate*2);      for(i1=1; i1<=ncodemax[k1];i1++){
     gm=matrix(0,nhstepm,1,nlstate*2);        j1++;
         
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for (i=1; i<=nlstate; i++)  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(m=iagemin; m <= iagemax+3; m++)
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              prop[i][m]=0.0;
         
         for (i=1; i<=imx; i++) { /* Each individual */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          bool=1;
           if  (cptcovn>0) {
     /* Computing Variances of health expectancies */            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      for(theta=1; theta <=npar; theta++){                bool=0;
       for(i=1; i<=npar; i++){          } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          if (bool==1) { 
       }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       cptj=0;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(j=1; j<= nlstate; j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         for(i=1; i<=nlstate; i++){                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
           cptj=cptj+1;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){                  /*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]]);*/
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           }                  prop[s[m][i]][iagemax+3] += weight[i]; 
         }                } 
       }              }
                  } /* end selection of waves */
                }
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(i=iagemin; i <= iagemax+3; i++){  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            
                for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       cptj=0;            posprop += prop[jk][i]; 
       for(j=1; j<= nlstate; j++){          } 
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;          for(jk=1; jk <=nlstate ; jk++){     
           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.;              if(posprop>=1.e-5){ 
           }                probs[i][jk][j1]= prop[jk][i]/posprop;
         }              } 
       }            } 
       for(j=1; j<= nlstate*2; j++)          }/* end jk */ 
         for(h=0; h<=nhstepm-1; h++){        }/* end i */ 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      } /* end i1 */
         }    } /* end k1 */
      }    
        /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 /* End theta */    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  }  /* End of prevalence */
   
      for(h=0; h<=nhstepm-1; h++)  /************* Waves Concatenation ***************/
       for(j=1; j<=nlstate*2;j++)  
         for(theta=1; theta <=npar; theta++)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           trgradg[h][j][theta]=gradg[h][theta][j];  {
          /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
      for(i=1;i<=nlstate*2;i++)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for(j=1;j<=nlstate*2;j++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         varhe[i][j][(int)age] =0.;       and mw[mi+1][i]. dh depends on stepm.
        */
      printf("%d|",(int)age);fflush(stdout);  
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    int i, mi, m;
      for(h=0;h<=nhstepm-1;h++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for(k=0;k<=nhstepm-1;k++){       double sum=0., jmean=0.;*/
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    int first;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    int j, k=0,jk, ju, jl;
         for(i=1;i<=nlstate*2;i++)    double sum=0.;
           for(j=1;j<=nlstate*2;j++)    first=0;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    jmin=1e+5;
       }    jmax=-1;
     }    jmean=0.;
     /* Computing expectancies */    for(i=1; i<=imx; i++){
     for(i=1; i<=nlstate;i++)      mi=0;
       for(j=1; j<=nlstate;j++)      m=firstpass;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      while(s[m][i] <= nlstate){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        if(s[m][i]>=1)
                    mw[++mi][i]=m;
 /* 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]);*/        if(m >=lastpass)
           break;
         }        else
           m++;
     fprintf(ficreseij,"%3.0f",age );      }/* end while */
     cptj=0;      if (s[m][i] > nlstate){
     for(i=1; i<=nlstate;i++)        mi++;     /* Death is another wave */
       for(j=1; j<=nlstate;j++){        /* if(mi==0)  never been interviewed correctly before death */
         cptj++;           /* Only death is a correct wave */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        mw[mi][i]=m;
       }      }
     fprintf(ficreseij,"\n");  
          wav[i]=mi;
     free_matrix(gm,0,nhstepm,1,nlstate*2);      if(mi==0){
     free_matrix(gp,0,nhstepm,1,nlstate*2);        if(first==0){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          first=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   }        if(first==1){
   printf("\n");          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   fprintf(ficlog,"\n");        }
       } /* end mi==0 */
   free_vector(xp,1,npar);    } /* End individuals */
   free_matrix(dnewm,1,nlstate*2,1,npar);  
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    for(i=1; i<=imx; i++){
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      for(mi=1; mi<wav[i];mi++){
 }        if (stepm <=0)
           dh[mi][i]=1;
 /************ Variance ******************/        else{
 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)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 {            if (agedc[i] < 2*AGESUP) {
   /* Variance of health expectancies */            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            if(j==0) j=1;  /* Survives at least one month after exam */
   /* double **newm;*/            k=k+1;
   double **dnewm,**doldm;            if (j >= jmax) jmax=j;
   double **dnewmp,**doldmp;            if (j <= jmin) jmin=j;
   int i, j, nhstepm, hstepm, h, nstepm ;            sum=sum+j;
   int k, cptcode;            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   double *xp;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double **gp, **gm;  /* for var eij */            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]);
   double ***gradg, ***trgradg; /*for var eij */            }
   double **gradgp, **trgradgp; /* for var p point j */          }
   double *gpp, *gmp; /* for var p point j */          else{
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   double ***p3mat;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double age,agelim, hf;            k=k+1;
   int theta;            if (j >= jmax) jmax=j;
   char digit[4];            else if (j <= jmin)jmin=j;
   char digitp[16];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   char fileresprobmorprev[FILENAMELENGTH];            if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             sum=sum+j;
   if(popbased==1)          }
     strcpy(digitp,"-populbased-");          jk= j/stepm;
   else          jl= j -jk*stepm;
     strcpy(digitp,"-stablbased-");          ju= j -(jk+1)*stepm;
           if(mle <=1){ 
   strcpy(fileresprobmorprev,"prmorprev");            if(jl==0){
   sprintf(digit,"%-d",ij);              dh[mi][i]=jk;
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/              bh[mi][i]=0;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */            }else{ /* We want a negative bias in order to only have interpolation ie
   strcat(fileresprobmorprev,digitp); /* Popbased or not */                    * at the price of an extra matrix product in likelihood */
   strcat(fileresprobmorprev,fileres);              dh[mi][i]=jk+1;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);            }
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);          }else{
   }            if(jl <= -ju){
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              dh[mi][i]=jk;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              bh[mi][i]=jl;       /* bias is positive if real duration
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");                                   * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);                                   */
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){            }
     fprintf(ficresprobmorprev," p.%-d SE",j);            else{
     for(i=1; i<=nlstate;i++)              dh[mi][i]=jk+1;
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);              bh[mi][i]=ju;
   }              }
   fprintf(ficresprobmorprev,"\n");            if(dh[mi][i]==0){
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {              dh[mi][i]=1; /* At least one step */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              bh[mi][i]=ju; /* At least one step */
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);              /*  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);*/
     exit(0);            }
   }          }
   else{        } /* end if mle */
     fprintf(ficgp,"\n# Routine varevsij");      } /* end wave */
   }    }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    jmean=sum/k;
     printf("Problem with html file: %s\n", optionfilehtm);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     exit(0);   }
   }  
   else{  /*********** Tricode ****************************/
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  void tricode(int *Tvar, int **nbcode, int imx)
   }  {
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   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");    int cptcode=0;
   fprintf(ficresvij,"# Age");    cptcoveff=0; 
   for(i=1; i<=nlstate;i++)   
     for(j=1; j<=nlstate;j++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    for (k=1; k<=7; k++) ncodemax[k]=0;
   fprintf(ficresvij,"\n");  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   xp=vector(1,npar);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   dnewm=matrix(1,nlstate,1,npar);                                 modality*/ 
   doldm=matrix(1,nlstate,1,nlstate);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);        Ndum[ij]++; /*store the modality */
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);                                         Tvar[j]. If V=sex and male is 0 and 
   gpp=vector(nlstate+1,nlstate+ndeath);                                         female is 1, then  cptcode=1.*/
   gmp=vector(nlstate+1,nlstate+ndeath);      }
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
        for (i=0; i<=cptcode; i++) {
   if(estepm < stepm){        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 */
     printf ("Problem %d lower than %d\n",estepm, stepm);      }
   }  
   else  hstepm=estepm;        ij=1; 
   /* For example we decided to compute the life expectancy with the smallest unit */      for (i=1; i<=ncodemax[j]; i++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        for (k=0; k<= maxncov; k++) {
      nhstepm is the number of hstepm from age to agelim          if (Ndum[k] != 0) {
      nstepm is the number of stepm from age to agelin.            nbcode[Tvar[j]][ij]=k; 
      Look at hpijx to understand the reason of that which relies in memory size            /* 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; */
      and note for a fixed period like k years */            
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            ij++;
      survival function given by stepm (the optimization length). Unfortunately it          }
      means that if the survival funtion is printed only each two years of age and if          if (ij > ncodemax[j]) break; 
      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.      } 
   */    }  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
   agelim = AGESUP;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   for (i=1; i<=ncovmodel-2; i++) { 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     ij=Tvar[i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);     Ndum[ij]++;
     gp=matrix(0,nhstepm,1,nlstate);   }
     gm=matrix(0,nhstepm,1,nlstate);  
    ij=1;
    for (i=1; i<= maxncov; i++) {
     for(theta=1; theta <=npar; theta++){     if((Ndum[i]!=0) && (i<=ncovcol)){
       for(i=1; i<=npar; i++){ /* Computes gradient */       Tvaraff[ij]=i; /*For printing */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);       ij++;
       }     }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   
    cptcoveff=ij-1; /*Number of simple covariates*/
       if (popbased==1) {  }
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /*********** Health Expectancies ****************/
       }  
    void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    /* Health expectancies */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         }    double age, agelim, hf;
       }    double ***p3mat,***varhe;
       /* This for computing forces of mortality (h=1)as a weighted average */    double **dnewm,**doldm;
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    double *xp;
         for(i=1; i<= nlstate; i++)    double **gp, **gm;
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    double ***gradg, ***trgradg;
       }        int theta;
       /* end force of mortality */  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for(i=1; i<=npar; i++) /* Computes gradient */    xp=vector(1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
      fprintf(ficreseij,"# Health expectancies\n");
       if (popbased==1) {    fprintf(ficreseij,"# Age");
         for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
           prlim[i][i]=probs[(int)age][i][ij];      for(j=1; j<=nlstate;j++)
       }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    if(estepm < stepm){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      printf ("Problem %d lower than %d\n",estepm, stepm);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }    else  hstepm=estepm;   
       }    /* We compute the life expectancy from trapezoids spaced every estepm months
       /* This for computing force of mortality (h=1)as a weighted average */     * This is mainly to measure the difference between two models: for example
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){     * 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 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];     * progression in between and thus overestimating or underestimating according
       }         * to the curvature of the survival function. If, for the same date, we 
       /* end force of mortality */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
       for(j=1; j<= nlstate; j++) /* vareij */     * hypothesis. A more precise result, taking into account a more precise
         for(h=0; h<=nhstepm; h++){     * curvature will be obtained if estepm is as small as stepm. */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    /* For example we decided to compute the life expectancy with the smallest unit */
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];       nhstepm is the number of hstepm from age to agelim 
       }       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
     } /* End theta */       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
     for(h=0; h<=nhstepm; h++) /* veij */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for(j=1; j<=nlstate;j++)       results. So we changed our mind and took the option of the best precision.
         for(theta=1; theta <=npar; theta++)    */
           trgradg[h][j][theta]=gradg[h][theta][j];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    agelim=AGESUP;
       for(theta=1; theta <=npar; theta++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         trgradgp[j][theta]=gradgp[theta][j];      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     for(i=1;i<=nlstate;i++)      /* if (stepm >= YEARM) hstepm=1;*/
       for(j=1;j<=nlstate;j++)      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         vareij[i][j][(int)age] =0.;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     for(h=0;h<=nhstepm;h++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       for(k=0;k<=nhstepm;k++){      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         for(i=1;i<=nlstate;i++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           for(j=1;j<=nlstate;j++)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;   
       }  
     }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     /* pptj */      /* Computing Variances of health expectancies */
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);  
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);       for(theta=1; theta <=npar; theta++){
     for(j=nlstate+1;j<=nlstate+ndeath;j++)        for(i=1; i<=npar; i++){ 
       for(i=nlstate+1;i<=nlstate+ndeath;i++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         varppt[j][i]=doldmp[j][i];        }
     /* end ppptj */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        cptj=0;
          for(j=1; j<= nlstate; j++){
     if (popbased==1) {          for(i=1; i<=nlstate; i++){
       for(i=1; i<=nlstate;i++)            cptj=cptj+1;
         prlim[i][i]=probs[(int)age][i][ij];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                }
     /* This for computing force of mortality (h=1)as a weighted average */          }
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){        }
       for(i=1; i<= nlstate; i++)       
         gmp[j] += prlim[i][i]*p3mat[i][j][1];       
     }            for(i=1; i<=npar; i++) 
     /* end force of mortality */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);        
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){        cptj=0;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        for(j=1; j<= nlstate; j++){
       for(i=1; i<=nlstate;i++){          for(i=1;i<=nlstate;i++){
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);            cptj=cptj+1;
       }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     }  
     fprintf(ficresprobmorprev,"\n");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
     fprintf(ficresvij,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++){        for(j=1; j<= nlstate*nlstate; j++)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          for(h=0; h<=nhstepm-1; h++){
       }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);       } 
     free_matrix(gm,0,nhstepm,1,nlstate);     
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  /* End theta */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   } /* End age */  
   free_vector(gpp,nlstate+1,nlstate+ndeath);       for(h=0; h<=nhstepm-1; h++)
   free_vector(gmp,nlstate+1,nlstate+ndeath);        for(j=1; j<=nlstate*nlstate;j++)
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);          for(theta=1; theta <=npar; theta++)
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/            trgradg[h][j][theta]=gradg[h][theta][j];
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");       
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */  
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");       for(i=1;i<=nlstate*nlstate;i++)
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);        for(j=1;j<=nlstate*nlstate;j++)
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          varhe[i][j][(int)age] =0.;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);  
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);       printf("%d|",(int)age);fflush(stdout);
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
   free_vector(xp,1,npar);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   free_matrix(doldm,1,nlstate,1,nlstate);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   free_matrix(dnewm,1,nlstate,1,npar);          for(i=1;i<=nlstate*nlstate;i++)
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            for(j=1;j<=nlstate*nlstate;j++)
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        }
   fclose(ficresprobmorprev);      }
   fclose(ficgp);      /* Computing expectancies */
   fclose(fichtm);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
 }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 /************ Variance of prevlim ******************/            
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  /* 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]);*/
 {  
   /* Variance of prevalence limit */          }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;      fprintf(ficreseij,"%3.0f",age );
   double **dnewm,**doldm;      cptj=0;
   int i, j, nhstepm, hstepm;      for(i=1; i<=nlstate;i++)
   int k, cptcode;        for(j=1; j<=nlstate;j++){
   double *xp;          cptj++;
   double *gp, *gm;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   double **gradg, **trgradg;        }
   double age,agelim;      fprintf(ficreseij,"\n");
   int theta;     
          free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   fprintf(ficresvpl,"# Age");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   for(i=1; i<=nlstate;i++)      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficresvpl," %1d-%1d",i,i);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficresvpl,"\n");    }
     printf("\n");
   xp=vector(1,npar);    fprintf(ficlog,"\n");
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   hstepm=1*YEARM; /* Every year of age */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   agelim = AGESUP;  }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /************ Variance ******************/
     if (stepm >= YEARM) hstepm=1;  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     gradg=matrix(1,npar,1,nlstate);    /* Variance of health expectancies */
     gp=vector(1,nlstate);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     gm=vector(1,nlstate);    /* double **newm;*/
     double **dnewm,**doldm;
     for(theta=1; theta <=npar; theta++){    double **dnewmp,**doldmp;
       for(i=1; i<=npar; i++){ /* Computes gradient */    int i, j, nhstepm, hstepm, h, nstepm ;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int k, cptcode;
       }    double *xp;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double **gp, **gm;  /* for var eij */
       for(i=1;i<=nlstate;i++)    double ***gradg, ***trgradg; /*for var eij */
         gp[i] = prlim[i][i];    double **gradgp, **trgradgp; /* for var p point j */
        double *gpp, *gmp; /* for var p point j */
       for(i=1; i<=npar; i++) /* Computes gradient */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double ***p3mat;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double age,agelim, hf;
       for(i=1;i<=nlstate;i++)    double ***mobaverage;
         gm[i] = prlim[i][i];    int theta;
     char digit[4];
       for(i=1;i<=nlstate;i++)    char digitp[25];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */    char fileresprobmorprev[FILENAMELENGTH];
   
     trgradg =matrix(1,nlstate,1,npar);    if(popbased==1){
       if(mobilav!=0)
     for(j=1; j<=nlstate;j++)        strcpy(digitp,"-populbased-mobilav-");
       for(theta=1; theta <=npar; theta++)      else strcpy(digitp,"-populbased-nomobil-");
         trgradg[j][theta]=gradg[theta][j];    }
     else 
     for(i=1;i<=nlstate;i++)      strcpy(digitp,"-stablbased-");
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    if (mobilav!=0) {
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(i=1;i<=nlstate;i++)      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
     fprintf(ficresvpl,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    strcpy(fileresprobmorprev,"prmorprev"); 
     free_vector(gp,1,nlstate);    sprintf(digit,"%-d",ij);
     free_vector(gm,1,nlstate);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     free_matrix(gradg,1,npar,1,nlstate);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     free_matrix(trgradg,1,nlstate,1,npar);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   } /* End age */    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   free_vector(xp,1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   free_matrix(doldm,1,nlstate,1,npar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
 /************ Variance of one-step probabilities  ******************/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 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(j=nlstate+1; j<=(nlstate+ndeath);j++){
 {      fprintf(ficresprobmorprev," p.%-d SE",j);
   int i, j=0,  i1, k1, l1, t, tj;      for(i=1; i<=nlstate;i++)
   int k2, l2, j1,  z1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int k=0,l, cptcode;    }  
   int first=1, first1;    fprintf(ficresprobmorprev,"\n");
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double **dnewm,**doldm;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double *xp;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   double *gp, *gm;      exit(0);
   double **gradg, **trgradg;    }
   double **mu;    else{
   double age,agelim, cov[NCOVMAX];      fprintf(ficgp,"\n# Routine varevsij");
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    }
   int theta;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   char fileresprob[FILENAMELENGTH];      printf("Problem with html file: %s\n", optionfilehtm);
   char fileresprobcov[FILENAMELENGTH];      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   char fileresprobcor[FILENAMELENGTH];      exit(0);
     }
   double ***varpij;    else{
       fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   strcpy(fileresprob,"prob");      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   strcat(fileresprob,fileres);    }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("Problem with resultfile: %s\n", fileresprob);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    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");
   strcpy(fileresprobcov,"probcov");    for(i=1; i<=nlstate;i++)
   strcat(fileresprobcov,fileres);      for(j=1; j<=nlstate;j++)
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     printf("Problem with resultfile: %s\n", fileresprobcov);    fprintf(ficresvij,"\n");
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  
   }    xp=vector(1,npar);
   strcpy(fileresprobcor,"probcor");    dnewm=matrix(1,nlstate,1,npar);
   strcat(fileresprobcor,fileres);    doldm=matrix(1,nlstate,1,nlstate);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     printf("Problem with resultfile: %s\n", fileresprobcor);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  
   }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    gpp=vector(nlstate+1,nlstate+ndeath);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    gmp=vector(nlstate+1,nlstate+ndeath);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    if(estepm < stepm){
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    else  hstepm=estepm;   
   fprintf(ficresprob,"# Age");    /* For example we decided to compute the life expectancy with the smallest unit */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   fprintf(ficresprobcov,"# Age");       nhstepm is the number of hstepm from age to agelim 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");       nstepm is the number of stepm from age to agelin. 
   fprintf(ficresprobcov,"# Age");       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for(i=1; i<=nlstate;i++)       survival function given by stepm (the optimization length). Unfortunately it
     for(j=1; j<=(nlstate+ndeath);j++){       means that if the survival funtion is printed every two years of age and if
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficresprobcov," p%1d-%1d ",i,j);       results. So we changed our mind and took the option of the best precision.
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    */
     }      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficresprob,"\n");    agelim = AGESUP;
   fprintf(ficresprobcov,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficresprobcor,"\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   xp=vector(1,npar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);      gp=matrix(0,nhstepm,1,nlstate);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);      gm=matrix(0,nhstepm,1,nlstate);
   first=1;  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);      for(theta=1; theta <=npar; theta++){
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     exit(0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
   else{        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"\n# Routine varprob");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        if (popbased==1) {
     printf("Problem with html file: %s\n", optionfilehtm);          if(mobilav ==0){
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);            for(i=1; i<=nlstate;i++)
     exit(0);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
   else{            for(i=1; i<=nlstate;i++)
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
     fprintf(fichtm,"\n");          }
         }
     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; 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");          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
          }
   cov[1]=1;        /* This for computing probability of death (h=1 means
   tj=cptcoveff;           computed over hstepm matrices product = hstepm*stepm months) 
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}           as a weighted average of prlim.
   j1=0;        */
   for(t=1; t<=tj;t++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(i1=1; i1<=ncodemax[t];i1++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       j1++;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
              }    
       if  (cptcovn>0) {        /* end probability of death */
         fprintf(ficresprob, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         fprintf(ficresprob, "**********\n#");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficresprobcov, "\n#********** Variable ");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficresprobcov, "**********\n#");   
                if (popbased==1) {
         fprintf(ficgp, "\n#********** Variable ");          if(mobilav ==0){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for(i=1; i<=nlstate;i++)
         fprintf(ficgp, "**********\n#");              prlim[i][i]=probs[(int)age][i][ij];
                  }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");              prlim[i][i]=mobaverage[(int)age][i][ij];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");        }
          
         fprintf(ficresprobcor, "\n#********** Variable ");            for(j=1; j<= nlstate; j++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for(h=0; h<=nhstepm; h++){
         fprintf(ficgp, "**********\n#");                for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                }
       for (age=bage; age<=fage; age ++){        }
         cov[2]=age;        /* This for computing probability of death (h=1 means
         for (k=1; k<=cptcovn;k++) {           computed over hstepm matrices product = hstepm*stepm months) 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];           as a weighted average of prlim.
         }        */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (k=1; k<=cptcovprod;k++)          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];           gmp[j] += prlim[i][i]*p3mat[i][j][1];
                }    
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        /* end probability of death */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
         gp=vector(1,(nlstate)*(nlstate+ndeath));        for(j=1; j<= nlstate; j++) /* vareij */
         gm=vector(1,(nlstate)*(nlstate+ndeath));          for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         for(theta=1; theta <=npar; theta++){          }
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                    gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        }
            
           k=0;      } /* End theta */
           for(i=1; i<= (nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
               k=k+1;  
               gp[k]=pmmij[i][j];      for(h=0; h<=nhstepm; h++) /* veij */
             }        for(j=1; j<=nlstate;j++)
           }          for(theta=1; theta <=npar; theta++)
                      trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
            for(theta=1; theta <=npar; theta++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          trgradgp[j][theta]=gradgp[theta][j];
           k=0;    
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               k=k+1;      for(i=1;i<=nlstate;i++)
               gm[k]=pmmij[i][j];        for(j=1;j<=nlstate;j++)
             }          vareij[i][j][(int)age] =0.;
           }  
            for(h=0;h<=nhstepm;h++){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)        for(k=0;k<=nhstepm;k++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)            for(j=1;j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             trgradg[j][theta]=gradg[theta][j];        }
              }
         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);      /* pptj */
              matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         pmij(pmmij,cov,ncovmodel,x,nlstate);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
              for(j=nlstate+1;j<=nlstate+ndeath;j++)
         k=0;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         for(i=1; i<=(nlstate); i++){          varppt[j][i]=doldmp[j][i];
           for(j=1; j<=(nlstate+ndeath);j++){      /* end ppptj */
             k=k+1;      /*  x centered again */
             mu[k][(int) age]=pmmij[i][j];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         }   
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)      if (popbased==1) {
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)        if(mobilav ==0){
             varpij[i][j][(int)age] = doldm[i][j];          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         /*printf("\n%d ",(int)age);        }else{ /* mobilav */ 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          for(i=1; i<=nlstate;i++)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            prlim[i][i]=mobaverage[(int)age][i][ij];
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        }
      }*/      }
                
         fprintf(ficresprob,"\n%d ",(int)age);      /* This for computing probability of death (h=1 means
         fprintf(ficresprobcov,"\n%d ",(int)age);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficresprobcor,"\n%d ",(int)age);         as a weighted average of prlim.
       */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      }    
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      /* end probability of death */
         }  
         i=0;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         for (k=1; k<=(nlstate);k++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for (l=1; l<=(nlstate+ndeath);l++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
             i=i++;        for(i=1; i<=nlstate;i++){
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        }
             for (j=1; j<=i;j++){      } 
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      fprintf(ficresprobmorprev,"\n");
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }      fprintf(ficresvij,"%.0f ",age );
           }      for(i=1; i<=nlstate;i++)
         }/* end of loop for state */        for(j=1; j<=nlstate;j++){
       } /* end of loop for age */          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       /* Confidence intervalle of pij  */      fprintf(ficresvij,"\n");
       /*      free_matrix(gp,0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nset noparametric;unset label");      free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       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);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);    } /* End age */
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       first1=1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       for (k2=1; k2<=(nlstate);k2++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         for (l2=1; l2<=(nlstate+ndeath);l2++){  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           if(l2==k2) continue;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           j=(k2-1)*(nlstate+ndeath)+l2;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           for (k1=1; k1<=(nlstate);k1++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
             for (l1=1; l1<=(nlstate+ndeath);l1++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
               if(l1==k1) continue;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
               i=(k1-1)*(nlstate+ndeath)+l1;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
               if(i<=j) continue;    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);
               for (age=bage; age<=fage; age ++){    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
                 if ((int)age %5==0){  */
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    free_vector(xp,1,npar);
                   mu1=mu[i][(int) age]/stepm*YEARM ;    free_matrix(doldm,1,nlstate,1,nlstate);
                   mu2=mu[j][(int) age]/stepm*YEARM;    free_matrix(dnewm,1,nlstate,1,npar);
                   c12=cv12/sqrt(v1*v2);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   /* Computing eigen value of matrix of covariance */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   /* Eigen vectors */    fclose(ficresprobmorprev);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    fclose(ficgp);
                   /*v21=sqrt(1.-v11*v11); *//* error */    fclose(fichtm);
                   v21=(lc1-v1)/cv12*v11;  }  
                   v12=-v21;  
                   v22=v11;  /************ Variance of prevlim ******************/
                   tnalp=v21/v11;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
                   if(first1==1){  {
                     first1=0;    /* Variance of prevalence limit */
                     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);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                   }    double **newm;
                   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);    double **dnewm,**doldm;
                   /*printf(fignu*/    int i, j, nhstepm, hstepm;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    int k, cptcode;
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    double *xp;
                   if(first==1){    double *gp, *gm;
                     first=0;    double **gradg, **trgradg;
                     fprintf(ficgp,"\nset parametric;unset label");    double age,agelim;
                     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 theta;
                     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(ficresvpl,"# Standard deviation of stable prevalences \n");
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);    fprintf(ficresvpl,"# Age");
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    for(i=1; i<=nlstate;i++)
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);        fprintf(ficresvpl," %1d-%1d",i,i);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    fprintf(ficresvpl,"\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)) not",\  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    xp=vector(1,npar);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    dnewm=matrix(1,nlstate,1,npar);
                   }else{    doldm=matrix(1,nlstate,1,nlstate);
                     first=0;    
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    hstepm=1*YEARM; /* Every year of age */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                     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",\    agelim = AGESUP;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   }/* if first */      if (stepm >= YEARM) hstepm=1;
                 } /* age mod 5 */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               } /* end loop age */      gradg=matrix(1,npar,1,nlstate);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);      gp=vector(1,nlstate);
               first=1;      gm=vector(1,nlstate);
             } /*l12 */  
           } /* k12 */      for(theta=1; theta <=npar; theta++){
         } /*l1 */        for(i=1; i<=npar; i++){ /* Computes gradient */
       }/* k1 */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     } /* loop covariates */        }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        for(i=1;i<=nlstate;i++)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          gp[i] = prlim[i][i];
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(i=1; i<=npar; i++) /* Computes gradient */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_vector(xp,1,npar);        for(i=1;i<=nlstate;i++)
   fclose(ficresprob);          gm[i] = prlim[i][i];
   fclose(ficresprobcov);  
   fclose(ficresprobcor);        for(i=1;i<=nlstate;i++)
   fclose(ficgp);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   fclose(fichtm);      } /* End theta */
 }  
       trgradg =matrix(1,nlstate,1,npar);
   
 /******************* Printing html file ***********/      for(j=1; j<=nlstate;j++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        for(theta=1; theta <=npar; theta++)
                   int lastpass, int stepm, int weightopt, char model[],\          trgradg[j][theta]=gradg[theta][j];
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\  
                   int popforecast, int estepm ,\      for(i=1;i<=nlstate;i++)
                   double jprev1, double mprev1,double anprev1, \        varpl[i][(int)age] =0.;
                   double jprev2, double mprev2,double anprev2){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   int jj1, k1, i1, cpt;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /*char optionfilehtm[FILENAMELENGTH];*/      for(i=1;i<=nlstate;i++)
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     printf("Problem with %s \n",optionfilehtm), exit(0);  
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);      fprintf(ficresvpl,"%.0f ",age );
   }      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      fprintf(ficresvpl,"\n");
  - 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      free_vector(gp,1,nlstate);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n      free_vector(gm,1,nlstate);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      free_matrix(gradg,1,npar,1,nlstate);
  - Life expectancies by age and initial health status (estepm=%2d months):      free_matrix(trgradg,1,nlstate,1,npar);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    } /* End age */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  
     free_vector(xp,1,npar);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  }
   
  jj1=0;  /************ Variance of one-step probabilities  ******************/
  for(k1=1; k1<=m;k1++){  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(i1=1; i1<=ncodemax[k1];i1++){  {
      jj1++;    int i, j=0,  i1, k1, l1, t, tj;
      if (cptcovn > 0) {    int k2, l2, j1,  z1;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int k=0,l, cptcode;
        for (cpt=1; cpt<=cptcoveff;cpt++)    int first=1, first1;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double **dnewm,**doldm;
      }    double *xp;
      /* Pij */    double *gp, *gm;
      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>    double **gradg, **trgradg;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double **mu;
      /* Quasi-incidences */    double age,agelim, cov[NCOVMAX];
      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>    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    int theta;
        /* Stable prevalence in each health state */    char fileresprob[FILENAMELENGTH];
        for(cpt=1; cpt<nlstate;cpt++){    char fileresprobcov[FILENAMELENGTH];
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    char fileresprobcor[FILENAMELENGTH];
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }    double ***varpij;
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    strcpy(fileresprob,"prob"); 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    strcat(fileresprob,fileres);
      }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      printf("Problem with resultfile: %s\n", fileresprob);
 health expectancies in states (1) and (2): e%s%d.png<br>      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
    } /* end i1 */    strcpy(fileresprobcov,"probcov"); 
  }/* End k1 */    strcat(fileresprobcov,fileres);
  fprintf(fichtm,"</ul>");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    }
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    strcpy(fileresprobcor,"probcor"); 
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    strcat(fileresprobcor,fileres);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      printf("Problem with resultfile: %s\n", fileresprobcor);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    }
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  if(popforecast==1) fprintf(fichtm,"\n    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         <br>",fileres,fileres,fileres,fileres);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  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);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  m=cptcoveff;    fprintf(ficresprobcov,"# Age");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
  jj1=0;  
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    for(i=1; i<=nlstate;i++)
      jj1++;      for(j=1; j<=(nlstate+ndeath);j++){
      if (cptcovn > 0) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
        for (cpt=1; cpt<=cptcoveff;cpt++)        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      }  
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");   /* fprintf(ficresprob,"\n");
      }    fprintf(ficresprobcov,"\n");
      for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficresprobcor,"\n");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident   */
 interval) in state (%d): v%s%d%d.png <br>   xp=vector(1,npar);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    } /* end i1 */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
  }/* End k1 */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  fprintf(fichtm,"</ul>");    first=1;
 fclose(fichtm);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
 /******************* Gnuplot file **************/      exit(0);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    }
     else{
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      fprintf(ficgp,"\n# Routine varprob");
   int ng;    }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with html file: %s\n", optionfilehtm);
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   }      exit(0);
     }
 #ifdef windows    else{
     fprintf(ficgp,"cd \"%s\" \n",pathc);      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 #endif      fprintf(fichtm,"\n");
 m=pow(2,cptcoveff);  
        fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
  /* 1eme*/      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 (cpt=1; cpt<= nlstate ; cpt ++) {      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 (k1=1; k1<= m ; k1 ++) {  
     }
 #ifdef windows  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    cov[1]=1;
      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);    tj=cptcoveff;
 #endif    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 #ifdef unix    j1=0;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    for(t=1; t<=tj;t++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      for(i1=1; i1<=ncodemax[t];i1++){ 
 #endif        j1++;
         if  (cptcovn>0) {
 for (i=1; i<= nlstate ; i ++) {          fprintf(ficresprob, "\n#********** Variable "); 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresprob, "**********\n#\n");
 }          fprintf(ficresprobcov, "\n#********** Variable "); 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<= nlstate ; i ++) {          fprintf(ficresprobcov, "**********\n#\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          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,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficgp, "**********\n#\n");
      for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
 }            for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 #ifdef unix          
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          fprintf(ficresprobcor, "\n#********** Variable ");    
 #endif          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    }          fprintf(ficresprobcor, "**********\n#");    
   }        }
   /*2 eme*/        
         for (age=bage; age<=fage; age ++){ 
   for (k1=1; k1<= m ; k1 ++) {          cov[2]=age;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          for (k=1; k<=cptcovn;k++) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
              }
     for (i=1; i<= nlstate+1 ; i ++) {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       k=2*i;          for (k=1; k<=cptcovprod;k++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (j=1; j<= nlstate+1 ; j ++) {          
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   else fprintf(ficgp," \%%*lf (\%%*lf)");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 }            gp=vector(1,(nlstate)*(nlstate+ndeath));
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          gm=vector(1,(nlstate)*(nlstate+ndeath));
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(theta=1; theta <=npar; theta++){
       for (j=1; j<= nlstate+1 ; j ++) {            for(i=1; i<=npar; i++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         else fprintf(ficgp," \%%*lf (\%%*lf)");            
 }              pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficgp,"\" t\"\" w l 0,");            
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            k=0;
       for (j=1; j<= nlstate+1 ; j ++) {            for(i=1; i<= (nlstate); i++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              for(j=1; j<=(nlstate+ndeath);j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");                k=k+1;
 }                  gp[k]=pmmij[i][j];
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              }
       else fprintf(ficgp,"\" t\"\" w l 0,");            }
     }            
   }            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   /*3eme*/      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for (k1=1; k1<= m ; k1 ++) {            k=0;
     for (cpt=1; cpt<= nlstate ; cpt ++) {            for(i=1; i<=(nlstate); i++){
       k=2+nlstate*(2*cpt-2);              for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                k=k+1;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);                gm[k]=pmmij[i][j];
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);       
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          }
   
 */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       for (i=1; i< nlstate ; i ++) {            for(theta=1; theta <=npar; theta++)
         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);              trgradg[j][theta]=gradg[theta][j];
           
       }          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);
   }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   /* CV preval stat */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     for (k1=1; k1<= m ; k1 ++) {          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;          pmij(pmmij,cov,ncovmodel,x,nlstate);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          k=0;
           for(i=1; i<=(nlstate); i++){
       for (i=1; i< nlstate ; i ++)            for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficgp,"+$%d",k+i+1);              k=k+1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              mu[k][(int) age]=pmmij[i][j];
                  }
       l=3+(nlstate+ndeath)*cpt;          }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       for (i=1; i< nlstate ; i ++) {            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         l=3+(nlstate+ndeath)*cpt;              varpij[i][j][(int)age] = doldm[i][j];
         fprintf(ficgp,"+$%d",l+i+1);  
       }          /*printf("\n%d ",(int)age);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              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]));
   }              fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprob,"\n%d ",(int)age);
     for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficresprobcov,"\n%d ",(int)age);
       if (k != i) {          fprintf(ficresprobcor,"\n%d ",(int)age);
         for(j=1; j <=ncovmodel; j++){  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           jk++;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           fprintf(ficgp,"\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     }          }
    }          i=0;
           for (k=1; k<=(nlstate);k++){
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/            for (l=1; l<=(nlstate+ndeath);l++){ 
      for(jk=1; jk <=m; jk++) {              i=i++;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
        if (ng==2)              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");              for (j=1; j<=i;j++){
        else                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
          fprintf(ficgp,"\nset title \"Probability\"\n");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);              }
        i=1;            }
        for(k2=1; k2<=nlstate; k2++) {          }/* end of loop for state */
          k3=i;        } /* end of loop for age */
          for(k=1; k<=(nlstate+ndeath); k++) {  
            if (k != k2){        /* Confidence intervalle of pij  */
              if(ng==2)        /*
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          fprintf(ficgp,"\nset noparametric;unset label");
              else          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              ij=1;          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);
              for(j=3; j <=ncovmodel; j++) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                  ij++;        */
                }  
                else        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        first1=1;
              }        for (k2=1; k2<=(nlstate);k2++){
              fprintf(ficgp,")/(1");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                          if(l2==k2) continue;
              for(k1=1; k1 <=nlstate; k1++){              j=(k2-1)*(nlstate+ndeath)+l2;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            for (k1=1; k1<=(nlstate);k1++){
                ij=1;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                for(j=3; j <=ncovmodel; j++){                if(l1==k1) continue;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                i=(k1-1)*(nlstate+ndeath)+l1;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if(i<=j) continue;
                    ij++;                for (age=bage; age<=fage; age ++){ 
                  }                  if ((int)age %5==0){
                  else                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                fprintf(ficgp,")");                    mu1=mu[i][(int) age]/stepm*YEARM ;
              }                    mu2=mu[j][(int) age]/stepm*YEARM;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    c12=cv12/sqrt(v1*v2);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                    /* Computing eigen value of matrix of covariance */
              i=i+ncovmodel;                    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.;
          } /* end k */                    /* Eigen vectors */
        } /* end k2 */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
      } /* end jk */                    /*v21=sqrt(1.-v11*v11); *//* error */
    } /* end ng */                    v21=(lc1-v1)/cv12*v11;
    fclose(ficgp);                    v12=-v21;
 }  /* end gnuplot */                    v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
 /*************** Moving average **************/                      first1=0;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                      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);
                     }
   int i, cpt, cptcod;                    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);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                    /*printf(fignu*/
       for (i=1; i<=nlstate;i++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           mobaverage[(int)agedeb][i][cptcod]=0.;                    if(first==1){
                          first=0;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                      fprintf(ficgp,"\nset parametric;unset label");
       for (i=1; i<=nlstate;i++){                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           for (cpt=0;cpt<=4;cpt++){                      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);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
           }                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     }                      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",\
                                  mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
 /************** Forecasting ******************/                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
 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){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                      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 *popage;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double *popeffectif,*popcount;                    }/* if first */
   double ***p3mat;                  } /* age mod 5 */
   char fileresf[FILENAMELENGTH];                } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
  agelim=AGESUP;                first=1;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              } /*l12 */
             } /* k12 */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          } /*l1 */
          }/* k1 */
        } /* loop covariates */
   strcpy(fileresf,"f");    }
   strcat(fileresf,fileres);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     printf("Problem with forecast resultfile: %s\n", fileresf);    free_vector(xp,1,npar);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    fclose(ficresprob);
   }    fclose(ficresprobcov);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fclose(ficresprobcor);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    fclose(ficgp);
     fclose(fichtm);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  }
   
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /******************* Printing html file ***********/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  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[],\
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    int popforecast, int estepm ,\
   if (stepm<=12) stepsize=1;                    double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
   agelim=AGESUP;    int jj1, k1, i1, cpt;
      /*char optionfilehtm[FILENAMELENGTH];*/
   hstepm=1;    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   hstepm=hstepm/stepm;      printf("Problem with %s \n",optionfilehtm), exit(0);
   yp1=modf(dateintmean,&yp);      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   anprojmean=yp;    }
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   yp1=modf((yp2*30.5),&yp);   - 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
   jprojmean=yp;   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   if(jprojmean==0) jprojmean=1;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   if(mprojmean==0) jprojmean=1;   - Life expectancies by age and initial health status (estepm=%2d months): 
       <a href=\"e%s\">e%s</a> <br>\n</li>", \
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
    
   for(cptcov=1;cptcov<=i2;cptcov++){  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;   m=cptcoveff;
       fprintf(ficresf,"\n#******");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   jj1=0;
       }   for(k1=1; k1<=m;k1++){
       fprintf(ficresf,"******\n");     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresf,"# StartingAge FinalAge");       jj1++;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);       if (cptcovn > 0) {
               fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               for (cpt=1; cpt<=cptcoveff;cpt++) 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         fprintf(ficresf,"\n");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         }
        /* Pij */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       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>
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           nhstepm = nhstepm/hstepm;       /* 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>
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           oldm=oldms;savm=savms;         /* Stable prevalence in each health state */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           for(cpt=1; cpt<nlstate;cpt++){
                   fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
           for (h=0; h<=nhstepm; h++){  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
             if (h==(int) (calagedate+YEARM*cpt)) {         }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       for(cpt=1; cpt<=nlstate;cpt++) {
             }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
             for(j=1; j<=nlstate+ndeath;j++) {  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
               kk1=0.;kk2=0;       }
               for(i=1; i<=nlstate;i++) {                     fprintf(fichtm,"\n<br>- Total life expectancy by age and
                 if (mobilav==1)  health expectancies in states (1) and (2): e%s%d.png<br>
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
                 else {     } /* end i1 */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   }/* End k1 */
                 }   fprintf(fichtm,"</ul>");
                  
               }  
               if (h==(int)(calagedate+12*cpt)){   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
                 fprintf(ficresf," %.3f", kk1);   - 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
           }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
         }   - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
       }  
     }  /*  if(popforecast==1) fprintf(fichtm,"\n */
   }  /*  - 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 */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   fclose(ficresf);  /*    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); */
 }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 /************** Forecasting ******************/  
 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){   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;   jj1=0;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   for(k1=1; k1<=m;k1++){
   double *popeffectif,*popcount;     for(i1=1; i1<=ncodemax[k1];i1++){
   double ***p3mat,***tabpop,***tabpopprev;       jj1++;
   char filerespop[FILENAMELENGTH];       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   agelim=AGESUP;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       }
         for(cpt=1; cpt<=nlstate;cpt++) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident
    interval) in state (%d): v%s%d%d.png <br>
    <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
   strcpy(filerespop,"pop");       }
   strcat(filerespop,fileres);     } /* end i1 */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   }/* End k1 */
     printf("Problem with forecast resultfile: %s\n", filerespop);   fprintf(fichtm,"</ul>");
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  fclose(fichtm);
   }  }
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   if (mobilav==1) {    int ng;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     movingaverage(agedeb, fage, ageminpar, mobaverage);      printf("Problem with file %s",optionfilegnuplot);
   }      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    /*#ifdef windows */
        fprintf(ficgp,"cd \"%s\" \n",pathc);
   agelim=AGESUP;      /*#endif */
    m=pow(2,cptcoveff);
   hstepm=1;    
   hstepm=hstepm/stepm;   /* 1eme*/
      for (cpt=1; cpt<= nlstate ; cpt ++) {
   if (popforecast==1) {     for (k1=1; k1<= m ; k1 ++) {
     if((ficpop=fopen(popfile,"r"))==NULL) {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
       printf("Problem with population file : %s\n",popfile);exit(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);
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  
     }       for (i=1; i<= nlstate ; i ++) {
     popage=ivector(0,AGESUP);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     popeffectif=vector(0,AGESUP);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     popcount=vector(0,AGESUP);       }
           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);
     i=1;         for (i=1; i<= nlstate ; i ++) {
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     imx=i;       } 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
   }       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   for(cptcov=1;cptcov<=i2;cptcov++){         else fprintf(ficgp," \%%*lf (\%%*lf)");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       }  
       k=k+1;       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       fprintf(ficrespop,"\n#******");     }
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*2 eme*/
       }    
       fprintf(ficrespop,"******\n");    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficrespop,"# Age");      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       if (popforecast==1)  fprintf(ficrespop," [Population]");      
            for (i=1; i<= nlstate+1 ; i ++) {
       for (cpt=0; cpt<=0;cpt++) {        k=2*i;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
                for (j=1; j<= nlstate+1 ; j ++) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          else fprintf(ficgp," \%%*lf (\%%*lf)");
           nhstepm = nhstepm/hstepm;        }   
                  if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           oldm=oldms;savm=savms;        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for (j=1; j<= nlstate+1 ; j ++) {
                  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           for (h=0; h<=nhstepm; h++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
             if (h==(int) (calagedate+YEARM*cpt)) {        }   
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficgp,"\" t\"\" w l 0,");
             }        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
             for(j=1; j<=nlstate+ndeath;j++) {        for (j=1; j<= nlstate+1 ; j ++) {
               kk1=0.;kk2=0;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
               for(i=1; i<=nlstate;i++) {                        else fprintf(ficgp," \%%*lf (\%%*lf)");
                 if (mobilav==1)        }   
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
                 else {        else fprintf(ficgp,"\" t\"\" w l 0,");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      }
                 }    }
               }    
               if (h==(int)(calagedate+12*cpt)){    /*3eme*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    
                   /*fprintf(ficrespop," %.3f", kk1);    for (k1=1; k1<= m ; k1 ++) { 
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      for (cpt=1; cpt<= nlstate ; cpt ++) {
               }        k=2+nlstate*(2*cpt-2);
             }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
             for(i=1; i<=nlstate;i++){        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
               kk1=0.;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                 for(j=1; j<=nlstate;j++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                 }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for (i=1; i< nlstate ; i ++) {
           }          fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
         }        } 
       }      }
      }
   /******/    
     /* CV preval stable (period) */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    for (k1=1; k1<= m ; k1 ++) { 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for (cpt=1; cpt<=nlstate ; cpt ++) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        k=3;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           nhstepm = nhstepm/hstepm;        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);
                  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (i=1; i<= nlstate ; i ++)
           oldm=oldms;savm=savms;          fprintf(ficgp,"+$%d",k+i+1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           for (h=0; h<=nhstepm; h++){        
             if (h==(int) (calagedate+YEARM*cpt)) {        l=3+(nlstate+ndeath)*cpt;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
             }        for (i=1; i< nlstate ; i ++) {
             for(j=1; j<=nlstate+ndeath;j++) {          l=3+(nlstate+ndeath)*cpt;
               kk1=0.;kk2=0;          fprintf(ficgp,"+$%d",l+i+1);
               for(i=1; i<=nlstate;i++) {                      }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
               }      } 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    }  
             }    
           }    /* proba elementaires */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1,jk=1; i <=nlstate; i++){
         }      for(k=1; k <=(nlstate+ndeath); k++){
       }        if (k != i) {
    }          for(j=1; j <=ncovmodel; j++){
   }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
              jk++; 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            fprintf(ficgp,"\n");
           }
   if (popforecast==1) {        }
     free_ivector(popage,0,AGESUP);      }
     free_vector(popeffectif,0,AGESUP);     }
     free_vector(popcount,0,AGESUP);  
   }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       for(jk=1; jk <=m; jk++) {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   fclose(ficrespop);         if (ng==2)
 }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
 /***********************************************/           fprintf(ficgp,"\nset title \"Probability\"\n");
 /**************** Main Program *****************/         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 /***********************************************/         i=1;
          for(k2=1; k2<=nlstate; k2++) {
 int main(int argc, char *argv[])           k3=i;
 {           for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;               if(ng==2)
   double agedeb, agefin,hf;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   double fret;               ij=1;
   double **xi,tmp,delta;               for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   double dum; /* Dummy variable */                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   double ***p3mat;                   ij++;
   int *indx;                 }
   char line[MAXLINE], linepar[MAXLINE];                 else
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   int firstobs=1, lastobs=10;               }
   int sdeb, sfin; /* Status at beginning and end */               fprintf(ficgp,")/(1");
   int c,  h , cpt,l;               
   int ju,jl, mi;               for(k1=1; k1 <=nlstate; k1++){   
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                 ij=1;
   int mobilav=0,popforecast=0;                 for(j=3; j <=ncovmodel; j++){
   int hstepm, nhstepm;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
   double bage, fage, age, agelim, agebase;                   }
   double ftolpl=FTOL;                   else
   double **prlim;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   double *severity;                 }
   double ***param; /* Matrix of parameters */                 fprintf(ficgp,")");
   double  *p;               }
   double **matcov; /* Matrix of covariance */               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   double ***delti3; /* Scale */               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   double *delti; /* Scale */               i=i+ncovmodel;
   double ***eij, ***vareij;             }
   double **varpl; /* Variances of prevalence limits by age */           } /* end k */
   double *epj, vepp;         } /* end k2 */
   double kk1, kk2;       } /* end jk */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;     } /* end ng */
       fclose(ficgp); 
   }  /* end gnuplot */
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   
   /*************** Moving average **************/
   char z[1]="c", occ;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
 #include <sys/time.h>  
 #include <time.h>    int i, cpt, cptcod;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int modcovmax =1;
      int mobilavrange, mob;
   /* long total_usecs;    double age;
   struct timeval start_time, end_time;  
      modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                             a covariate has 2 modalities */
   getcwd(pathcd, size);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
   printf("\n%s",version);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   if(argc <=1){      if(mobilav==1) mobilavrange=5; /* default */
     printf("\nEnter the parameter file name: ");      else mobilavrange=mobilav;
     scanf("%s",pathtot);      for (age=bage; age<=fage; age++)
   }        for (i=1; i<=nlstate;i++)
   else{          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     strcpy(pathtot,argv[1]);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   }      /* We keep the original values on the extreme ages bage, fage and for 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   /*cygwin_split_path(pathtot,path,optionfile);         we use a 5 terms etc. until the borders are no more concerned. 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      */ 
   /* cutv(path,optionfile,pathtot,'\\');*/      for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          for (i=1; i<=nlstate;i++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   chdir(path);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   replace(pathc,path);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
 /*-------- arguments in the command line --------*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
   /* Log file */              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   strcat(filelog, optionfilefiname);            }
   strcat(filelog,".log");    /* */          }
   if((ficlog=fopen(filelog,"w"))==NULL)    {        }/* end age */
     printf("Problem with logfile %s\n",filelog);      }/* end mob */
     goto end;    }else return -1;
   }    return 0;
   fprintf(ficlog,"Log filename:%s\n",filelog);  }/* End movingaverage */
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");  
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  /************** Forecasting ******************/
   fflush(ficlog);  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
   /* */       agemin, agemax range of age
   strcpy(fileres,"r");       dateprev1 dateprev2 range of dates during which prevalence is computed
   strcat(fileres, optionfilefiname);       anproj2 year of en of projection (same day and month as proj1).
   strcat(fileres,".txt");    /* Other files have txt extension */    */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   /*---------arguments file --------*/    int *popage;
     double agec; /* generic age */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     printf("Problem with optionfile %s\n",optionfile);    double *popeffectif,*popcount;
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    double ***p3mat;
     goto end;    double ***mobaverage;
   }    char fileresf[FILENAMELENGTH];
   
   strcpy(filereso,"o");    agelim=AGESUP;
   strcat(filereso,fileres);    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   if((ficparo=fopen(filereso,"w"))==NULL) {   
     printf("Problem with Output resultfile: %s\n", filereso);    strcpy(fileresf,"f"); 
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    strcat(fileresf,fileres);
     goto end;    if((ficresf=fopen(fileresf,"w"))==NULL) {
   }      printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    printf("Computing forecasting: result on file '%s' \n", fileresf);
     ungetc(c,ficpar);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     fputs(line,ficparo);  
   }    if (mobilav!=0) {
   ungetc(c,ficpar);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   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);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   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);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      }
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     puts(line);    if (stepm<=12) stepsize=1;
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
      else  hstepm=estepm;   
      
   covar=matrix(0,NCOVMAX,1,n);    hstepm=hstepm/stepm; 
   cptcovn=0;    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                                 fractional in yp1 */
     anprojmean=yp;
   ncovmodel=2+cptcovn;    yp2=modf((yp1*12),&yp);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    mprojmean=yp;
      yp1=modf((yp2*30.5),&yp);
   /* Read guess parameters */    jprojmean=yp;
   /* Reads comments: lines beginning with '#' */    if(jprojmean==0) jprojmean=1;
   while((c=getc(ficpar))=='#' && c!= EOF){    if(mprojmean==0) jprojmean=1;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    i1=cptcoveff;
     puts(line);    if (cptcovn < 1){i1=1;}
     fputs(line,ficparo);    
   }    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   ungetc(c,ficpar);    
      fprintf(ficresf,"#****** Routine prevforecast **\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)  /*            if (h==(int)(YEARM*yearp)){ */
     for(j=1; j <=nlstate+ndeath-1; j++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fprintf(ficparo,"%1d%1d",i1,j1);        k=k+1;
       if(mle==1)        fprintf(ficresf,"\n#******");
         printf("%1d%1d",i,j);        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficlog,"%1d%1d",i,j);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);        fprintf(ficresf,"******\n");
         if(mle==1){        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
           printf(" %lf",param[i][j][k]);        for(j=1; j<=nlstate+ndeath;j++){ 
           fprintf(ficlog," %lf",param[i][j][k]);          for(i=1; i<=nlstate;i++)              
         }            fprintf(ficresf," p%d%d",i,j);
         else          fprintf(ficresf," p.%d",j);
           fprintf(ficlog," %lf",param[i][j][k]);        }
         fprintf(ficparo," %lf",param[i][j][k]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       }          fprintf(ficresf,"\n");
       fscanf(ficpar,"\n");          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       if(mle==1)  
         printf("\n");          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       fprintf(ficlog,"\n");            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
       fprintf(ficparo,"\n");            nhstepm = nhstepm/hstepm; 
     }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              oldm=oldms;savm=savms;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
   p=param[1][1];            for (h=0; h<=nhstepm; h++){
                if (h*hstepm/YEARM*stepm ==yearp) {
   /* Reads comments: lines beginning with '#' */                fprintf(ficresf,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){                for(j=1;j<=cptcoveff;j++) 
     ungetc(c,ficpar);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     fgets(line, MAXLINE, ficpar);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     puts(line);              } 
     fputs(line,ficparo);              for(j=1; j<=nlstate+ndeath;j++) {
   }                ppij=0.;
   ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                  else {
   for(i=1; i <=nlstate; i++){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
     for(j=1; j <=nlstate+ndeath-1; j++){                  }
       fscanf(ficpar,"%1d%1d",&i1,&j1);                  if (h*hstepm/YEARM*stepm== yearp) {
       printf("%1d%1d",i,j);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       fprintf(ficparo,"%1d%1d",i1,j1);                  }
       for(k=1; k<=ncovmodel;k++){                } /* end i */
         fscanf(ficpar,"%le",&delti3[i][j][k]);                if (h*hstepm/YEARM*stepm==yearp) {
         printf(" %le",delti3[i][j][k]);                  fprintf(ficresf," %.3f", ppij);
         fprintf(ficparo," %le",delti3[i][j][k]);                }
       }              }/* end j */
       fscanf(ficpar,"\n");            } /* end h */
       printf("\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo,"\n");          } /* end agec */
     }        } /* end yearp */
   }      } /* end cptcod */
   delti=delti3[1][1];    } /* end  cptcov */
           
   /* Reads comments: lines beginning with '#' */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    fclose(ficresf);
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /************** 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){
   ungetc(c,ficpar);    
      int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   matcov=matrix(1,npar,1,npar);    int *popage;
   for(i=1; i <=npar; i++){    double calagedatem, agelim, kk1, kk2;
     fscanf(ficpar,"%s",&str);    double *popeffectif,*popcount;
     if(mle==1)    double ***p3mat,***tabpop,***tabpopprev;
       printf("%s",str);    double ***mobaverage;
     fprintf(ficlog,"%s",str);    char filerespop[FILENAMELENGTH];
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fscanf(ficpar," %le",&matcov[i][j]);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if(mle==1){    agelim=AGESUP;
         printf(" %.5le",matcov[i][j]);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
         fprintf(ficlog," %.5le",matcov[i][j]);    
       }    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       else    
         fprintf(ficlog," %.5le",matcov[i][j]);    
       fprintf(ficparo," %.5le",matcov[i][j]);    strcpy(filerespop,"pop"); 
     }    strcat(filerespop,fileres);
     fscanf(ficpar,"\n");    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     if(mle==1)      printf("Problem with forecast resultfile: %s\n", filerespop);
       printf("\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     fprintf(ficlog,"\n");    }
     fprintf(ficparo,"\n");    printf("Computing forecasting: result on file '%s' \n", filerespop);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       matcov[i][j]=matcov[j][i];  
        if (mobilav!=0) {
   if(mle==1)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("\n");      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   fprintf(ficlog,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     /*-------- Rewriting paramater file ----------*/    }
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    stepsize=(int) (stepm+YEARM-1)/YEARM;
      strcat(rfileres,".");    /* */    if (stepm<=12) stepsize=1;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    
     if((ficres =fopen(rfileres,"w"))==NULL) {    agelim=AGESUP;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    hstepm=1;
     }    hstepm=hstepm/stepm; 
     fprintf(ficres,"#%s\n",version);    
        if (popforecast==1) {
     /*-------- data file ----------*/      if((ficpop=fopen(popfile,"r"))==NULL) {
     if((fic=fopen(datafile,"r"))==NULL)    {        printf("Problem with population file : %s\n",popfile);exit(0);
       printf("Problem with datafile: %s\n", datafile);goto end;        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      } 
     }      popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
     n= lastobs;      popcount=vector(0,AGESUP);
     severity = vector(1,maxwav);      
     outcome=imatrix(1,maxwav+1,1,n);      i=1;   
     num=ivector(1,n);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     moisnais=vector(1,n);     
     annais=vector(1,n);      imx=i;
     moisdc=vector(1,n);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     andc=vector(1,n);    }
     agedc=vector(1,n);  
     cod=ivector(1,n);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     weight=vector(1,n);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        k=k+1;
     mint=matrix(1,maxwav,1,n);        fprintf(ficrespop,"\n#******");
     anint=matrix(1,maxwav,1,n);        for(j=1;j<=cptcoveff;j++) {
     s=imatrix(1,maxwav+1,1,n);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     adl=imatrix(1,maxwav+1,1,n);            }
     tab=ivector(1,NCOVMAX);        fprintf(ficrespop,"******\n");
     ncodemax=ivector(1,8);        fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     i=1;        if (popforecast==1)  fprintf(ficrespop," [Population]");
     while (fgets(line, MAXLINE, fic) != NULL)    {        
       if ((i >= firstobs) && (i <=lastobs)) {        for (cpt=0; cpt<=0;cpt++) { 
                  fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         for (j=maxwav;j>=1;j--){          
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           strcpy(line,stra);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            nhstepm = nhstepm/hstepm; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            
         }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    oldm=oldms;savm=savms;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          
             for (h=0; h<=nhstepm; h++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              if (h==(int) (calagedatem+YEARM*cpt)) {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              for(j=1; j<=nlstate+ndeath;j++) {
         for (j=ncovcol;j>=1;j--){                kk1=0.;kk2=0;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                for(i=1; i<=nlstate;i++) {              
         }                  if (mobilav==1) 
         num[i]=atol(stra);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                          else {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/                  }
                 }
         i=i+1;                if (h==(int)(calagedatem+12*cpt)){
       }                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     }                    /*fprintf(ficrespop," %.3f", kk1);
     /* printf("ii=%d", ij);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
        scanf("%d",i);*/                }
   imx=i-1; /* Number of individuals */              }
               for(i=1; i<=nlstate;i++){
   /* for (i=1; i<=imx; i++){                kk1=0.;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                  for(j=1; j<=nlstate;j++){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                  }
     }*/                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
    /*  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]));}*/              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                  fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
              }
   /* Calculation of the number of parameter from char model*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   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);        
            for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
   if (strlen(model) >1){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     j=0, j1=0, k1=1, k2=1;          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     j=nbocc(model,'+');            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     j1=nbocc(model,'*');            nhstepm = nhstepm/hstepm; 
     cptcovn=j+1;            
     cptcovprod=j1;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                oldm=oldms;savm=savms;
     strcpy(modelsav,model);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            for (h=0; h<=nhstepm; h++){
       printf("Error. Non available option model=%s ",model);              if (h==(int) (calagedatem+YEARM*cpt)) {
       fprintf(ficlog,"Error. Non available option model=%s ",model);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       goto end;              } 
     }              for(j=1; j<=nlstate+ndeath;j++) {
                    kk1=0.;kk2=0;
     for(i=(j+1); i>=1;i--){                for(i=1; i<=nlstate;i++) {              
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
       /*scanf("%d",i);*/              }
       if (strchr(strb,'*')) {  /* Model includes a product */            }
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         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;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             /*printf("stre=%s ", stre);*/  
         }    if (popforecast==1) {
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      free_ivector(popage,0,AGESUP);
           cptcovprod--;      free_vector(popeffectif,0,AGESUP);
           cutv(strb,stre,strc,'V');      free_vector(popcount,0,AGESUP);
           Tvar[i]=atoi(stre);    }
           cptcovage++;    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tage[cptcovage]=i;    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }    fclose(ficrespop);
         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 */  /**************** Main Program *****************/
           Tprod[k1]=i;  /***********************************************/
           Tvard[k1][1]=atoi(strc); /* m*/  
           Tvard[k1][2]=atoi(stre); /* n */  int main(int argc, char *argv[])
           Tvar[cptcovn+k2]=Tvard[k1][1];  {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
           for (k=1; k<=lastobs;k++)    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double agedeb, agefin,hf;
           k1++;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
           k2=k2+2;  
         }    double fret;
       }    double **xi,tmp,delta;
       else { /* no more sum */  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double dum; /* Dummy variable */
        /*  scanf("%d",i);*/    double ***p3mat;
       cutv(strd,strc,strb,'V');    double ***mobaverage;
       Tvar[i]=atoi(strc);    int *indx;
       }    char line[MAXLINE], linepar[MAXLINE];
       strcpy(modelsav,stra);      char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    int firstobs=1, lastobs=10;
         scanf("%d",i);*/    int sdeb, sfin; /* Status at beginning and end */
     } /* end of loop + */    int c,  h , cpt,l;
   } /* end model */    int ju,jl, mi;
      int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   printf("cptcovprod=%d ", cptcovprod);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    int mobilav=0,popforecast=0;
   scanf("%d ",i);*/    int hstepm, nhstepm;
     fclose(fic);    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;
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    double bage, fage, age, agelim, agebase;
       for(i=1;i<=n;i++) weight[i]=1.0;    double ftolpl=FTOL;
     }    double **prlim;
     /*-calculation of age at interview from date of interview and age at death -*/    double *severity;
     agev=matrix(1,maxwav,1,imx);    double ***param; /* Matrix of parameters */
     double  *p;
     for (i=1; i<=imx; i++) {    double **matcov; /* Matrix of covariance */
       for(m=2; (m<= maxwav); m++) {    double ***delti3; /* Scale */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double *delti; /* Scale */
          anint[m][i]=9999;    double ***eij, ***vareij;
          s[m][i]=-1;    double **varpl; /* Variances of prevalence limits by age */
        }    double *epj, vepp;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double kk1, kk2;
       }    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     }  
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){    char z[1]="c", occ;
         if(s[m][i] >0){  #include <sys/time.h>
           if (s[m][i] >= nlstate+1) {  #include <time.h>
             if(agedc[i]>0)    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
               if(moisdc[i]!=99 && andc[i]!=9999)   
                 agev[m][i]=agedc[i];    /* long total_usecs;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       struct timeval start_time, end_time;
            else {    
               if (andc[i]!=9999){       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    getcwd(pathcd, size);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    printf("\n%s\n%s",version,fullversion);
               }    if(argc <=1){
             }      printf("\nEnter the parameter file name: ");
           }      scanf("%s",pathtot);
           else if(s[m][i] !=9){ /* Should no more exist */    }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    else{
             if(mint[m][i]==99 || anint[m][i]==9999)      strcpy(pathtot,argv[1]);
               agev[m][i]=1;    }
             else if(agev[m][i] <agemin){    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
               agemin=agev[m][i];    /*cygwin_split_path(pathtot,path,optionfile);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
             }    /* cutv(path,optionfile,pathtot,'\\');*/
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             }    chdir(path);
             /*agev[m][i]=anint[m][i]-annais[i];*/    replace(pathc,path);
             /*   agev[m][i] = age[i]+2*m;*/  
           }    /*-------- arguments in the command line --------*/
           else { /* =9 */  
             agev[m][i]=1;    /* Log file */
             s[m][i]=-1;    strcat(filelog, optionfilefiname);
           }    strcat(filelog,".log");    /* */
         }    if((ficlog=fopen(filelog,"w"))==NULL)    {
         else /*= 0 Unknown */      printf("Problem with logfile %s\n",filelog);
           agev[m][i]=1;      goto end;
       }    }
        fprintf(ficlog,"Log filename:%s\n",filelog);
     }    fprintf(ficlog,"\n%s",version);
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"\nEnter the parameter file name: ");
       for(m=1; (m<= maxwav); m++){    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
         if (s[m][i] > (nlstate+ndeath)) {    fflush(ficlog);
           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;    strcpy(fileres,"r");
         }    strcat(fileres, optionfilefiname);
       }    strcat(fileres,".txt");    /* Other files have txt extension */
     }  
     /*---------arguments file --------*/
 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);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
     free_vector(severity,1,maxwav);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     free_imatrix(outcome,1,maxwav+1,1,n);      goto end;
     free_vector(moisnais,1,n);    }
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);    strcpy(filereso,"o");
        free_matrix(anint,1,maxwav,1,n);*/    strcat(filereso,fileres);
     free_vector(moisdc,1,n);    if((ficparo=fopen(filereso,"w"))==NULL) {
     free_vector(andc,1,n);      printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
          goto end;
     wav=ivector(1,imx);    }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* Reads comments: lines beginning with '#' */
        while((c=getc(ficpar))=='#' && c!= EOF){
     /* Concatenates waves */      ungetc(c,ficpar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
       Tcode=ivector(1,100);    }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    ungetc(c,ficpar);
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
          printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
    codtab=imatrix(1,100,1,10);    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);
    h=0;    while((c=getc(ficpar))=='#' && c!= EOF){
    m=pow(2,cptcoveff);      ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
    for(k=1;k<=cptcoveff; k++){      puts(line);
      for(i=1; i <=(m/pow(2,k));i++){      fputs(line,ficparo);
        for(j=1; j <= ncodemax[k]; j++){    }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    ungetc(c,ficpar);
            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]);*/    covar=matrix(0,NCOVMAX,1,n); 
          }    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
        }    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
      }  
    }    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
       codtab[1][2]=1;codtab[2][2]=2; */    
    /* for(i=1; i <=m ;i++){    /* Read guess parameters */
       for(k=1; k <=cptcovn; k++){    /* Reads comments: lines beginning with '#' */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    while((c=getc(ficpar))=='#' && c!= EOF){
       }      ungetc(c,ficpar);
       printf("\n");      fgets(line, MAXLINE, ficpar);
       }      puts(line);
       scanf("%d",i);*/      fputs(line,ficparo);
        }
    /* Calculates basic frequencies. Computes observed prevalence at single age    ungetc(c,ficpar);
        and prints on file fileres'p'. */    
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
        for(i=1; i <=nlstate; i++)
          for(j=1; j <=nlstate+ndeath-1; j++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fscanf(ficpar,"%1d%1d",&i1,&j1);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficparo,"%1d%1d",i1,j1);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(mle==1)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          printf("%1d%1d",i,j);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficlog,"%1d%1d",i,j);
              for(k=1; k<=ncovmodel;k++){
     /* For Powell, parameters are in a vector p[] starting at p[1]          fscanf(ficpar," %lf",&param[i][j][k]);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          if(mle==1){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
     if(mle==1){          }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          else
     }            fprintf(ficlog," %lf",param[i][j][k]);
              fprintf(ficparo," %lf",param[i][j][k]);
     /*--------- 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);        fscanf(ficpar,"\n");
          if(mle==1)
           printf("\n");
    jk=1;        fprintf(ficlog,"\n");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        fprintf(ficparo,"\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++){    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    p=param[1][1];
          {    
            printf("%d%d ",i,k);    /* Reads comments: lines beginning with '#' */
            fprintf(ficlog,"%d%d ",i,k);    while((c=getc(ficpar))=='#' && c!= EOF){
            fprintf(ficres,"%1d%1d ",i,k);      ungetc(c,ficpar);
            for(j=1; j <=ncovmodel; j++){      fgets(line, MAXLINE, ficpar);
              printf("%f ",p[jk]);      puts(line);
              fprintf(ficlog,"%f ",p[jk]);      fputs(line,ficparo);
              fprintf(ficres,"%f ",p[jk]);    }
              jk++;    ungetc(c,ficpar);
            }  
            printf("\n");    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
            fprintf(ficlog,"\n");    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
            fprintf(ficres,"\n");    for(i=1; i <=nlstate; i++){
          }      for(j=1; j <=nlstate+ndeath-1; j++){
      }        fscanf(ficpar,"%1d%1d",&i1,&j1);
    }        printf("%1d%1d",i,j);
    if(mle==1){        fprintf(ficparo,"%1d%1d",i1,j1);
      /* Computing hessian and covariance matrix */        for(k=1; k<=ncovmodel;k++){
      ftolhess=ftol; /* Usually correct */          fscanf(ficpar,"%le",&delti3[i][j][k]);
      hesscov(matcov, p, npar, delti, ftolhess, func);          printf(" %le",delti3[i][j][k]);
    }          fprintf(ficparo," %le",delti3[i][j][k]);
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        }
    printf("# Scales (for hessian or gradient estimation)\n");        fscanf(ficpar,"\n");
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");        printf("\n");
    for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficparo,"\n");
      for(j=1; j <=nlstate+ndeath; j++){      }
        if (j!=i) {    }
          fprintf(ficres,"%1d%1d",i,j);    delti=delti3[1][1];
          printf("%1d%1d",i,j);  
          fprintf(ficlog,"%1d%1d",i,j);  
          for(k=1; k<=ncovmodel;k++){    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
            printf(" %.5e",delti[jk]);    
            fprintf(ficlog," %.5e",delti[jk]);    /* Reads comments: lines beginning with '#' */
            fprintf(ficres," %.5e",delti[jk]);    while((c=getc(ficpar))=='#' && c!= EOF){
            jk++;      ungetc(c,ficpar);
          }      fgets(line, MAXLINE, ficpar);
          printf("\n");      puts(line);
          fprintf(ficlog,"\n");      fputs(line,ficparo);
          fprintf(ficres,"\n");    }
        }    ungetc(c,ficpar);
      }    
    }    matcov=matrix(1,npar,1,npar);
        for(i=1; i <=npar; i++){
    k=1;      fscanf(ficpar,"%s",&str);
    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)
    if(mle==1)        printf("%s",str);
      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,"%s",str);
    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");      fprintf(ficparo,"%s",str);
    for(i=1;i<=npar;i++){      for(j=1; j <=i; j++){
      /*  if (k>nlstate) k=1;        fscanf(ficpar," %le",&matcov[i][j]);
          i1=(i-1)/(ncovmodel*nlstate)+1;        if(mle==1){
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          printf(" %.5le",matcov[i][j]);
          printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficlog," %.5le",matcov[i][j]);
      fprintf(ficres,"%3d",i);        }
      if(mle==1)        else
        printf("%3d",i);          fprintf(ficlog," %.5le",matcov[i][j]);
      fprintf(ficlog,"%3d",i);        fprintf(ficparo," %.5le",matcov[i][j]);
      for(j=1; j<=i;j++){      }
        fprintf(ficres," %.5e",matcov[i][j]);      fscanf(ficpar,"\n");
        if(mle==1)      if(mle==1)
          printf(" %.5e",matcov[i][j]);        printf("\n");
        fprintf(ficlog," %.5e",matcov[i][j]);      fprintf(ficlog,"\n");
      }      fprintf(ficparo,"\n");
      fprintf(ficres,"\n");    }
      if(mle==1)    for(i=1; i <=npar; i++)
        printf("\n");      for(j=i+1;j<=npar;j++)
      fprintf(ficlog,"\n");        matcov[i][j]=matcov[j][i];
      k++;     
    }    if(mle==1)
          printf("\n");
    while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"\n");
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);  
      puts(line);    /*-------- Rewriting paramater file ----------*/
      fputs(line,ficparo);    strcpy(rfileres,"r");    /* "Rparameterfile */
    }    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
    ungetc(c,ficpar);    strcat(rfileres,".");    /* */
    estepm=0;    strcat(rfileres,optionfilext);    /* Other files have txt extension */
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    if((ficres =fopen(rfileres,"w"))==NULL) {
    if (estepm==0 || estepm < stepm) estepm=stepm;      printf("Problem writing new parameter file: %s\n", fileres);goto end;
    if (fage <= 2) {      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
      bage = ageminpar;    }
      fage = agemaxpar;    fprintf(ficres,"#%s\n",version);
    }      
        /*-------- data file ----------*/
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    if((fic=fopen(datafile,"r"))==NULL)    {
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      printf("Problem with datafile: %s\n", datafile);goto end;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
        }
    while((c=getc(ficpar))=='#' && c!= EOF){  
      ungetc(c,ficpar);    n= lastobs;
      fgets(line, MAXLINE, ficpar);    severity = vector(1,maxwav);
      puts(line);    outcome=imatrix(1,maxwav+1,1,n);
      fputs(line,ficparo);    num=ivector(1,n);
    }    moisnais=vector(1,n);
    ungetc(c,ficpar);    annais=vector(1,n);
      moisdc=vector(1,n);
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    andc=vector(1,n);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    agedc=vector(1,n);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    cod=ivector(1,n);
        weight=vector(1,n);
    while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
      ungetc(c,ficpar);    mint=matrix(1,maxwav,1,n);
      fgets(line, MAXLINE, ficpar);    anint=matrix(1,maxwav,1,n);
      puts(line);    s=imatrix(1,maxwav+1,1,n);
      fputs(line,ficparo);    tab=ivector(1,NCOVMAX);
    }    ncodemax=ivector(1,8);
    ungetc(c,ficpar);  
      i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      if ((i >= firstobs) && (i <=lastobs)) {
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          
         for (j=maxwav;j>=1;j--){
   fscanf(ficpar,"pop_based=%d\n",&popbased);          cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
   fprintf(ficparo,"pop_based=%d\n",popbased);            strcpy(line,stra);
   fprintf(ficres,"pop_based=%d\n",popbased);            cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
            cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
     puts(line);        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
     fputs(line,ficparo);  
   }        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
   ungetc(c,ficpar);        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
   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);        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        for (j=ncovcol;j>=1;j--){
 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);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
 while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
     fgets(line, MAXLINE, ficpar);          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;}*/
     puts(line);  
     fputs(line,ficparo);        i=i+1;
   }      }
   ungetc(c,ficpar);    }
     /* printf("ii=%d", ij);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);       scanf("%d",i);*/
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    imx=i-1; /* Number of individuals */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
     /* for (i=1; i<=imx; i++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      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;
 /*------------ gnuplot -------------*/      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
   strcpy(optionfilegnuplot,optionfilefiname);      }*/
   strcat(optionfilegnuplot,".gp");     /*  for (i=1; i<=imx; i++){
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       if (s[4][i]==9)  s[4][i]=-1; 
     printf("Problem with file %s",optionfilegnuplot);       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]));}*/
   }    
   fclose(ficgp);   for (i=1; i<=imx; i++)
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);   
 /*--------- index.htm --------*/     /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");    /* Calculation of the number of parameter from char model*/
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     printf("Problem with %s \n",optionfilehtm), exit(0);    Tprod=ivector(1,15); 
   }    Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    Tage=ivector(1,15);      
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n     
 \n    if (strlen(model) >1){ /* If there is at least 1 covariate */
 Total number of observations=%d <br>\n      j=0, j1=0, k1=1, k2=1;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      j=nbocc(model,'+'); /* j=Number of '+' */
 <hr  size=\"2\" color=\"#EC5E5E\">      j1=nbocc(model,'*'); /* j1=Number of '*' */
  <ul><li><h4>Parameter files</h4>\n      cptcovn=j+1; 
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      cptcovprod=j1; /*Number of products */
  - 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,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);      strcpy(modelsav,model); 
   fclose(fichtm);      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        fprintf(ficlog,"Error. Non available option model=%s ",model);
          goto end;
 /*------------ free_vector  -------------*/      }
  chdir(path);      
        /* This loop fills the array Tvar from the string 'model'.*/
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      for(i=(j+1); i>=1;i--){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
  free_ivector(num,1,n);        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
  free_vector(agedc,1,n);        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        /*scanf("%d",i);*/
  fclose(ficparo);        if (strchr(strb,'*')) {  /* Model includes a product */
  fclose(ficres);          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
   /*--------------- Prevalence limit --------------*/            cutv(strb,stre,strd,'V');
              Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
   strcpy(filerespl,"pl");            cptcovage++;
   strcat(filerespl,fileres);              Tage[cptcovage]=i;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              /*printf("stre=%s ", stre);*/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          }
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;          else if (strcmp(strd,"age")==0) { /* or age*Vn */
   }            cptcovprod--;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            cutv(strb,stre,strc,'V');
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);            Tvar[i]=atoi(stre);
   fprintf(ficrespl,"#Prevalence limit\n");            cptcovage++;
   fprintf(ficrespl,"#Age ");            Tage[cptcovage]=i;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          }
   fprintf(ficrespl,"\n");          else {  /* Age is not in the model */
              cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
   prlim=matrix(1,nlstate,1,nlstate);            Tvar[i]=ncovcol+k1;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tprod[k1]=i;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tvard[k1][1]=atoi(strc); /* m*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tvard[k1][2]=atoi(stre); /* n */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            Tvar[cptcovn+k2]=Tvard[k1][1];
   k=0;            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   agebase=ageminpar;            for (k=1; k<=lastobs;k++) 
   agelim=agemaxpar;              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
   ftolpl=1.e-10;            k1++;
   i1=cptcoveff;            k2=k2+2;
   if (cptcovn < 1){i1=1;}          }
         }
   for(cptcov=1;cptcov<=i1;cptcov++){        else { /* no more sum */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
         k=k+1;         /*  scanf("%d",i);*/
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        cutv(strd,strc,strb,'V');
         fprintf(ficrespl,"\n#******");        Tvar[i]=atoi(strc);
         printf("\n#******");        }
         fprintf(ficlog,"\n#******");        strcpy(modelsav,stra);  
         for(j=1;j<=cptcoveff;j++) {        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          scanf("%d",i);*/
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* end of loop + */
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    } /* end model */
         }    
         fprintf(ficrespl,"******\n");    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
         printf("******\n");      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
         fprintf(ficlog,"******\n");  
            /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
         for (age=agebase; age<=agelim; age++){    printf("cptcovprod=%d ", cptcovprod);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    scanf("%d ",i);
           fprintf(ficrespl," %.5f", prlim[i][i]);    fclose(fic);*/
           fprintf(ficrespl,"\n");  
         }      /*  if(mle==1){*/
       }    if (weightopt != 1) { /* Maximisation without weights*/
     }      for(i=1;i<=n;i++) weight[i]=1.0;
   fclose(ficrespl);    }
       /*-calculation of age at interview from date of interview and age at death -*/
   /*------------- h Pij x at various ages ------------*/    agev=matrix(1,maxwav,1,imx);
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for (i=1; i<=imx; i++) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for(m=2; (m<= maxwav); m++) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;          anint[m][i]=9999;
   }          s[m][i]=-1;
   printf("Computing pij: result on file '%s' \n", filerespij);        }
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);        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);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          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);
   /*if (stepm<=24) stepsize=2;*/          s[m][i]=-1;
         }
   agelim=AGESUP;        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
   hstepm=stepsize*YEARM; /* Every year of age */          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]); 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          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;
   /* hstepm=1;   aff par mois*/        }
       }
   k=0;    }
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for (i=1; i<=imx; i++)  {
       k=k+1;      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
         fprintf(ficrespij,"\n#****** ");      for(m=firstpass; (m<= lastpass); m++){
         for(j=1;j<=cptcoveff;j++)        if(s[m][i] >0){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if (s[m][i] >= nlstate+1) {
         fprintf(ficrespij,"******\n");            if(agedc[i]>0)
                      if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                agev[m][i]=agedc[i];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              else {
                 if ((int)andc[i]!=9999){
           /*      nhstepm=nhstepm*YEARM; aff par mois*/                  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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  agev[m][i]=-1;
           oldm=oldms;savm=savms;                }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                }
           fprintf(ficrespij,"# Age");          }
           for(i=1; i<=nlstate;i++)          else if(s[m][i] !=9){ /* Standard case, age in fractional
             for(j=1; j<=nlstate+ndeath;j++)                                   years but with the precision of a
               fprintf(ficrespij," %1d-%1d",i,j);                                   month */
           fprintf(ficrespij,"\n");            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
            for (h=0; h<=nhstepm; h++){            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );              agev[m][i]=1;
             for(i=1; i<=nlstate;i++)            else if(agev[m][i] <agemin){ 
               for(j=1; j<=nlstate+ndeath;j++)              agemin=agev[m][i];
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             fprintf(ficrespij,"\n");            }
              }            else if(agev[m][i] >agemax){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              agemax=agev[m][i];
           fprintf(ficrespij,"\n");              /* 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;*/
           }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          else { /* =9 */
             agev[m][i]=1;
   fclose(ficrespij);            s[m][i]=-1;
           }
         }
   /*---------- Forecasting ------------------*/        else /*= 0 Unknown */
   if((stepm == 1) && (strcmp(model,".")==0)){          agev[m][i]=1;
     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);      
   }    }
   else{    for (i=1; i<=imx; i++)  {
     erreur=108;      for(m=firstpass; (m<=lastpass); m++){
     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);        if (s[m][i] > (nlstate+ndeath)) {
     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);          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;
         }
   /*---------- Health expectancies and variances ------------*/      }
     }
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    /*for (i=1; i<=imx; i++){
   if((ficrest=fopen(filerest,"w"))==NULL) {    for (m=firstpass; (m<lastpass); m++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;       printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
     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);  
     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); 
   strcpy(filerese,"e");  
   strcat(filerese,fileres);    free_vector(severity,1,maxwav);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    free_imatrix(outcome,1,maxwav+1,1,n);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_vector(moisnais,1,n);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_vector(annais,1,n);
   }    /* free_matrix(mint,1,maxwav,1,n);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       free_matrix(anint,1,maxwav,1,n);*/
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   strcpy(fileresv,"v");  
   strcat(fileresv,fileres);     
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    wav=ivector(1,imx);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    bh=imatrix(1,lastpass-firstpass+1,1,imx);
   }    mw=imatrix(1,lastpass-firstpass+1,1,imx);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    /* Concatenates waves */
   calagedate=-1;    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    Tcode=ivector(1,100);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
       k=k+1;    ncodemax[1]=1;
       fprintf(ficrest,"\n#****** ");    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
       for(j=1;j<=cptcoveff;j++)        
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
       fprintf(ficrest,"******\n");                                   the estimations*/
     h=0;
       fprintf(ficreseij,"\n#****** ");    m=pow(2,cptcoveff);
       for(j=1;j<=cptcoveff;j++)   
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(k=1;k<=cptcoveff; k++){
       fprintf(ficreseij,"******\n");      for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
       fprintf(ficresvij,"\n#****** ");          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
       for(j=1;j<=cptcoveff;j++)            h++;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
       fprintf(ficresvij,"******\n");            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
       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);      } 
      /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       codtab[1][2]=1;codtab[2][2]=2; */
       oldm=oldms;savm=savms;    /* for(i=1; i <=m ;i++){ 
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);       for(k=1; k <=cptcovn; k++){
       if(popbased==1){       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);       }
        }       printf("\n");
        }
         scanf("%d",i);*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    /* Calculates basic frequencies. Computes observed prevalence at single age
       fprintf(ficrest,"\n");       and prints on file fileres'p'. */
   
       epj=vector(1,nlstate+1);      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       for(age=bage; age <=fage ;age++){      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         if (popbased==1) {      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
           for(i=1; i<=nlstate;i++)      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
             prlim[i][i]=probs[(int)age][i][k];      
         }     
            /* For Powell, parameters are in a vector p[] starting at p[1]
         fprintf(ficrest," %4.0f",age);       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    if(mle>=1){ /* Could be 1 or 2 */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
           }    }
           epj[nlstate+1] +=epj[j];      
         }    /*--------- 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);
         for(i=1, vepp=0.;i <=nlstate;i++)    
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];    jk=1;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         for(j=1;j <=nlstate;j++){    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         }    for(i=1,jk=1; i <=nlstate; i++){
         fprintf(ficrest,"\n");      for(k=1; k <=(nlstate+ndeath); k++){
       }        if (k != i) 
     }          {
   }            printf("%d%d ",i,k);
 free_matrix(mint,1,maxwav,1,n);            fprintf(ficlog,"%d%d ",i,k);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);            fprintf(ficres,"%1d%1d ",i,k);
     free_vector(weight,1,n);            for(j=1; j <=ncovmodel; j++){
   fclose(ficreseij);              printf("%f ",p[jk]);
   fclose(ficresvij);              fprintf(ficlog,"%f ",p[jk]);
   fclose(ficrest);              fprintf(ficres,"%f ",p[jk]);
   fclose(ficpar);              jk++; 
   free_vector(epj,1,nlstate+1);            }
              printf("\n");
   /*------- Variance limit prevalence------*/              fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
   strcpy(fileresvpl,"vpl");          }
   strcat(fileresvpl,fileres);      }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    if(mle==1){
     exit(0);      /* Computing hessian and covariance matrix */
   }      ftolhess=ftol; /* Usually correct */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      hesscov(matcov, p, npar, delti, ftolhess, func);
     }
   k=0;    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("# Scales (for hessian or gradient estimation)\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       k=k+1;    for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficresvpl,"\n#****** ");      for(j=1; j <=nlstate+ndeath; j++){
       for(j=1;j<=cptcoveff;j++)        if (j!=i) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficres,"%1d%1d",i,j);
       fprintf(ficresvpl,"******\n");          printf("%1d%1d",i,j);
                fprintf(ficlog,"%1d%1d",i,j);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          for(k=1; k<=ncovmodel;k++){
       oldm=oldms;savm=savms;            printf(" %.5e",delti[jk]);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            fprintf(ficlog," %.5e",delti[jk]);
     }            fprintf(ficres," %.5e",delti[jk]);
  }            jk++;
           }
   fclose(ficresvpl);          printf("\n");
           fprintf(ficlog,"\n");
   /*---------- End : free ----------------*/          fprintf(ficres,"\n");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        }
        }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);     
      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)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      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");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    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");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(i=1,k=1;i<=npar;i++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      /*  if (k>nlstate) k=1;
            i1=(i-1)/(ncovmodel*nlstate)+1; 
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
   free_vector(delti,1,npar);          printf("%s%d%d",alph[k],i1,tab[i]);
   free_matrix(agev,1,maxwav,1,imx);      */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      fprintf(ficres,"%3d",i);
       if(mle==1)
   fprintf(fichtm,"\n</body>");        printf("%3d",i);
   fclose(fichtm);      fprintf(ficlog,"%3d",i);
   fclose(ficgp);      for(j=1; j<=i;j++){
          fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
   if(erreur >0){          printf(" %.5e",matcov[i][j]);
     printf("End of Imach with error or warning %d\n",erreur);        fprintf(ficlog," %.5e",matcov[i][j]);
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);      }
   }else{      fprintf(ficres,"\n");
    printf("End of Imach\n");      if(mle==1)
    fprintf(ficlog,"End of Imach\n");        printf("\n");
   }      fprintf(ficlog,"\n");
   printf("See log file on %s\n",filelog);      k++;
   fclose(ficlog);    }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     
      while((c=getc(ficpar))=='#' && c!= EOF){
   /* 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);*/      ungetc(c,ficpar);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      fgets(line, MAXLINE, ficpar);
   /*------ End -----------*/      puts(line);
       fputs(line,ficparo);
     }
  end:    ungetc(c,ficpar);
 #ifdef windows  
   /* chdir(pathcd);*/    estepm=0;
 #endif    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
  /*system("wgnuplot graph.plt");*/    if (estepm==0 || estepm < stepm) estepm=stepm;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    if (fage <= 2) {
  /*system("cd ../gp37mgw");*/      bage = ageminpar;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fage = agemaxpar;
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");     
  strcat(plotcmd,optionfilegnuplot);    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
  system(plotcmd);    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);
 #ifdef windows     
   while (z[0] != 'q') {    while((c=getc(ficpar))=='#' && c!= EOF){
     /* chdir(path); */      ungetc(c,ficpar);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      fgets(line, MAXLINE, ficpar);
     scanf("%s",z);      puts(line);
     if (z[0] == 'c') system("./imach");      fputs(line,ficparo);
     else if (z[0] == 'e') system(optionfilehtm);    }
     else if (z[0] == 'g') system(plotcmd);    ungetc(c,ficpar);
     else if (z[0] == 'q') exit(0);    
   }    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);
 #endif    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
 }    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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  Added in v.1.82


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