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version 1.50, 2002/06/26 23:25:02 version 1.81, 2003/06/05 15:41:51
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 /* $Id$  /* $Id$
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
      
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies from
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   first survey ("cross") where individuals from different ages are    first survey ("cross") where individuals from different ages are
   interviewed on their health status or degree of disability (in the    interviewed on their health status or degree of disability (in the
   case of a health survey which is our main interest) -2- at least a    case of a health survey which is our main interest) -2- at least a
   second wave of interviews ("longitudinal") which measure each change    second wave of interviews ("longitudinal") which measure each change
   (if any) in individual health status.  Health expectancies are    (if any) in individual health status.  Health expectancies are
   computed from the time spent in each health state according to a    computed from the time spent in each health state according to a
   model. More health states you consider, more time is necessary to reach the    model. More health states you consider, more time is necessary to reach the
   Maximum Likelihood of the parameters involved in the model.  The    Maximum Likelihood of the parameters involved in the model.  The
   simplest model is the multinomial logistic model where pij is the    simplest model is the multinomial logistic model where pij is the
   probability to be observed in state j at the second wave    probability to be observed in state j at the second wave
   conditional to be observed in state i at the first wave. Therefore    conditional to be observed in state i at the first wave. Therefore
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   'age' is age and 'sex' is a covariate. If you want to have a more    'age' is age and 'sex' is a covariate. If you want to have a more
   complex model than "constant and age", you should modify the program    complex model than "constant and age", you should modify the program
   where the markup *Covariates have to be included here again* invites    where the markup *Covariates have to be included here again* invites
   you to do it.  More covariates you add, slower the    you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
   multinomial logistic model, is clear when the delay between waves is not    multinomial logistic model, is clear when the delay between waves is not
   identical for each individual. Also, if a individual missed an    identical for each individual. Also, if a individual missed an
   intermediate interview, the information is lost, but taken into    intermediate interview, the information is lost, but taken into
   account using an interpolation or extrapolation.      account using an interpolation or extrapolation.  
   
   hPijx is the probability to be observed in state i at age x+h    hPijx is the probability to be observed in state i at age x+h
   conditional to the observed state i at age x. The delay 'h' can be    conditional to the observed state i at age x. The delay 'h' can be
   split into an exact number (nh*stepm) of unobserved intermediate    split into an exact number (nh*stepm) of unobserved intermediate
   states. This elementary transition (by month or quarter trimester,    states. This elementary transition (by month, quarter,
   semester or year) is model as a multinomial logistic.  The hPx    semester or year) is modelled as a multinomial logistic.  The hPx
   matrix is simply the matrix product of nh*stepm elementary matrices    matrix is simply the matrix product of nh*stepm elementary matrices
   and the contribution of each individual to the likelihood is simply    and the contribution of each individual to the likelihood is simply
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the prevalence limits.    of the life expectancies. It also computes the stable prevalence. 
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
   software can be distributed freely for non commercial use. Latest version    software can be distributed freely for non commercial use. Latest version
   can be accessed at http://euroreves.ined.fr/imach .    can be accessed at http://euroreves.ined.fr/imach .
   **********************************************************************/  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #include <math.h>    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #include <stdio.h>    
 #include <stdlib.h>    **********************************************************************/
 #include <unistd.h>  /*
     main
 #define MAXLINE 256    read parameterfile
 #define GNUPLOTPROGRAM "gnuplot"    read datafile
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    concatwav
 #define FILENAMELENGTH 80    if (mle >= 1)
 /*#define DEBUG*/      mlikeli
 #define windows    print results files
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    if mle==1 
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */        begin-prev-date,...
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    open gnuplot file
     open html file
 #define NINTERVMAX 8    stable prevalence
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     for age prevalim()
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    h Pij x
 #define NCOVMAX 8 /* Maximum number of covariates */    variance of p varprob
 #define MAXN 20000    forecasting if prevfcast==1 prevforecast call prevalence()
 #define YEARM 12. /* Number of months per year */    health expectancies
 #define AGESUP 130    Variance-covariance of DFLE
 #define AGEBASE 40    prevalence()
 #ifdef windows     movingaverage()
 #define DIRSEPARATOR '\\'    varevsij() 
 #define ODIRSEPARATOR '/'    if popbased==1 varevsij(,popbased)
 #else    total life expectancies
 #define DIRSEPARATOR '/'    Variance of stable prevalence
 #define ODIRSEPARATOR '\\'   end
 #endif  */
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */  
 int nvar;   
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  #include <math.h>
 int npar=NPARMAX;  #include <stdio.h>
 int nlstate=2; /* Number of live states */  #include <stdlib.h>
 int ndeath=1; /* Number of dead states */  #include <unistd.h>
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 int *wav; /* Number of waves for this individuual 0 is possible */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int maxwav; /* Maxim number of waves */  #define FILENAMELENGTH 80
 int jmin, jmax; /* min, max spacing between 2 waves */  /*#define DEBUG*/
 int mle, weightopt;  #define windows
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;  #define NINTERVMAX 8
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 FILE *ficresprobmorprev;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 FILE *fichtm; /* Html File */  #define NCOVMAX 8 /* Maximum number of covariates */
 FILE *ficreseij;  #define MAXN 20000
 char filerese[FILENAMELENGTH];  #define YEARM 12. /* Number of months per year */
 FILE  *ficresvij;  #define AGESUP 130
 char fileresv[FILENAMELENGTH];  #define AGEBASE 40
 FILE  *ficresvpl;  #ifdef windows
 char fileresvpl[FILENAMELENGTH];  #define DIRSEPARATOR '\\'
 char title[MAXLINE];  #define ODIRSEPARATOR '/'
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  #else
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  #endif
 char filelog[FILENAMELENGTH]; /* Log file */  
 char filerest[FILENAMELENGTH];  /* $Id$ */
 char fileregp[FILENAMELENGTH];  /* $Log$
 char popfile[FILENAMELENGTH];   * Revision 1.81  2003/06/05 15:41:51  brouard
    * *** empty log message ***
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];   *
   /* Revision 1.80  2003/06/05 15:34:14  brouard
 #define NR_END 1  /* Trying to add the true revision in the program and log
 #define FREE_ARG char*  /*
 #define FTOL 1.0e-10  /* Revision 1.79  2003/06/05 15:17:23  brouard
   /* *** empty log message ***
 #define NRANSI  /* */
 #define ITMAX 200  /* $Revision$ */
   /* $Date$ */
 #define TOL 2.0e-4  /* $State$ */
   
 #define CGOLD 0.3819660  char version[80]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 #define ZEPS 1.0e-10  char fullversion[]="$Revision$ $Date$"; 
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  int erreur; /* Error number */
   int nvar;
 #define GOLD 1.618034  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #define GLIMIT 100.0  int npar=NPARMAX;
 #define TINY 1.0e-20  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 static double maxarg1,maxarg2;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  int popbased=0;
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
    int *wav; /* Number of waves for this individuual 0 is possible */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  int maxwav; /* Maxim number of waves */
 #define rint(a) floor(a+0.5)  int jmin, jmax; /* min, max spacing between 2 waves */
   int mle, weightopt;
 static double sqrarg;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int imx;  double jmean; /* Mean space between 2 waves */
 int stepm;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 /* Stepm, step in month: minimum step interpolation*/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int estepm;  FILE *ficlog, *ficrespow;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 int m,nb;  FILE *fichtm; /* Html File */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  FILE *ficreseij;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  char filerese[FILENAMELENGTH];
 double **pmmij, ***probs, ***mobaverage;  FILE  *ficresvij;
 double dateintmean=0;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 double *weight;  char fileresvpl[FILENAMELENGTH];
 int **s; /* Status */  char title[MAXLINE];
 double *agedc, **covar, idx;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double ftolhess; /* Tolerance for computing hessian */  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /**************** split *************************/  char fileregp[FILENAMELENGTH];
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  char popfile[FILENAMELENGTH];
 {  
    char *s;                             /* pointer */  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
    int  l1, l2;                         /* length counters */  
   #define NR_END 1
    l1 = strlen( path );                 /* length of path */  #define FREE_ARG char*
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FTOL 1.0e-10
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */  #define NRANSI 
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  #define ITMAX 200 
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */  #define TOL 2.0e-4 
       extern char       *getwd( );  
   #define CGOLD 0.3819660 
       if ( getwd( dirc ) == NULL ) {  #define ZEPS 1.0e-10 
 #else  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       extern char       *getcwd( );  
   #define GOLD 1.618034 
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define GLIMIT 100.0 
 #endif  #define TINY 1.0e-20 
          return( GLOCK_ERROR_GETCWD );  
       }  static double maxarg1,maxarg2;
       strcpy( name, path );             /* we've got it */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    } else {                             /* strip direcotry from path */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       s++;                              /* after this, the filename */    
       l2 = strlen( s );                 /* length of filename */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define rint(a) floor(a+0.5)
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  static double sqrarg;
       dirc[l1-l2] = 0;                  /* add zero */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  int imx; 
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int stepm;
 #else  /* Stepm, step in month: minimum step interpolation*/
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  int estepm;
    s = strrchr( name, '.' );            /* find last / */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    s++;  
    strcpy(ext,s);                       /* save extension */  int m,nb;
    l1= strlen( name);  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    l2= strlen( s)+1;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    strncpy( finame, name, l1-l2);  double **pmmij, ***probs;
    finame[l1-l2]= 0;  double dateintmean=0;
    return( 0 );                         /* we're done */  
 }  double *weight;
   int **s; /* Status */
   double *agedc, **covar, idx;
 /******************************************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
 void replace(char *s, char*t)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 {  double ftolhess; /* Tolerance for computing hessian */
   int i;  
   int lg=20;  /**************** split *************************/
   i=0;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   lg=strlen(t);  {
   for(i=0; i<= lg; i++) {    char  *ss;                            /* pointer */
     (s[i] = t[i]);    int   l1, l2;                         /* length counters */
     if (t[i]== '\\') s[i]='/';  
   }    l1 = strlen(path );                   /* length of path */
 }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 int nbocc(char *s, char occ)    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   int i,j=0;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   int lg=20;      /* get current working directory */
   i=0;      /*    extern  char* getcwd ( char *buf , int len);*/
   lg=strlen(s);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for(i=0; i<= lg; i++) {        return( GLOCK_ERROR_GETCWD );
   if  (s[i] == occ ) j++;      }
   }      strcpy( name, path );               /* we've got it */
   return j;    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 void cutv(char *u,char *v, char*t, char occ)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   /* cuts string t into u and v where u is ended by char occ excluding it      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)      dirc[l1-l2] = 0;                    /* add zero */
      gives u="abcedf" and v="ghi2j" */    }
   int i,lg,j,p=0;    l1 = strlen( dirc );                  /* length of directory */
   i=0;  #ifdef windows
   for(j=0; j<=strlen(t)-1; j++) {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #else
   }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
   lg=strlen(t);    ss = strrchr( name, '.' );            /* find last / */
   for(j=0; j<p; j++) {    ss++;
     (u[j] = t[j]);    strcpy(ext,ss);                       /* save extension */
   }    l1= strlen( name);
      u[p]='\0';    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
    for(j=0; j<= lg; j++) {    finame[l1-l2]= 0;
     if (j>=(p+1))(v[j-p-1] = t[j]);    return( 0 );                          /* we're done */
   }  }
 }  
   
 /********************** nrerror ********************/  /******************************************/
   
 void nrerror(char error_text[])  void replace(char *s, char*t)
 {  {
   fprintf(stderr,"ERREUR ...\n");    int i;
   fprintf(stderr,"%s\n",error_text);    int lg=20;
   exit(1);    i=0;
 }    lg=strlen(t);
 /*********************** vector *******************/    for(i=0; i<= lg; i++) {
 double *vector(int nl, int nh)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   double *v;    }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  }
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  int nbocc(char *s, char occ)
 }  {
     int i,j=0;
 /************************ free vector ******************/    int lg=20;
 void free_vector(double*v, int nl, int nh)    i=0;
 {    lg=strlen(s);
   free((FREE_ARG)(v+nl-NR_END));    for(i=0; i<= lg; i++) {
 }    if  (s[i] == occ ) j++;
     }
 /************************ivector *******************************/    return j;
 int *ivector(long nl,long nh)  }
 {  
   int *v;  void cutv(char *u,char *v, char*t, char occ)
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  {
   if (!v) nrerror("allocation failure in ivector");    /* cuts string t into u and v where u is ended by char occ excluding it
   return v-nl+NR_END;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /******************free ivector **************************/    i=0;
 void free_ivector(int *v, long nl, long nh)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   free((FREE_ARG)(v+nl-NR_END));    }
 }  
     lg=strlen(t);
 /******************* imatrix *******************************/    for(j=0; j<p; j++) {
 int **imatrix(long nrl, long nrh, long ncl, long nch)      (u[j] = t[j]);
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    }
 {       u[p]='\0';
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
   /* allocate pointers to rows */    }
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /********************** nrerror ********************/
   m -= nrl;  
    void nrerror(char error_text[])
    {
   /* allocate rows and set pointers to them */    fprintf(stderr,"ERREUR ...\n");
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    fprintf(stderr,"%s\n",error_text);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    exit(EXIT_FAILURE);
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  /*********************** vector *******************/
    double *vector(int nl, int nh)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  {
      double *v;
   /* return pointer to array of pointers to rows */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   return m;    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  /************************ free vector ******************/
       int **m;  void free_vector(double*v, int nl, int nh)
       long nch,ncl,nrh,nrl;  {
      /* free an int matrix allocated by imatrix() */    free((FREE_ARG)(v+nl-NR_END));
 {  }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /************************ivector *******************************/
 }  char *cvector(long nl,long nh)
   {
 /******************* matrix *******************************/    char *v;
 double **matrix(long nrl, long nrh, long ncl, long nch)    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
 {    if (!v) nrerror("allocation failure in cvector");
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    return v-nl+NR_END;
   double **m;  }
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /******************free ivector **************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  void free_cvector(char *v, long nl, long nh)
   m += NR_END;  {
   m -= nrl;    free((FREE_ARG)(v+nl-NR_END));
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /************************ivector *******************************/
   m[nrl] += NR_END;  int *ivector(long nl,long nh)
   m[nrl] -= ncl;  {
     int *v;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   return m;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /******************free ivector **************************/
 {  void free_ivector(int *v, long nl, long nh)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /******************* ma3x *******************************/  /******************* imatrix *******************************/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  { 
   double ***m;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    /* allocate pointers to rows */ 
   m += NR_END;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   m -= nrl;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    m -= nrl; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    m[nrl] -= ncl; 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    
   m[nrl][ncl] += NR_END;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   m[nrl][ncl] -= nll;    
   for (j=ncl+1; j<=nch; j++)    /* return pointer to array of pointers to rows */ 
     m[nrl][j]=m[nrl][j-1]+nlay;    return m; 
    } 
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /****************** free_imatrix *************************/
     for (j=ncl+1; j<=nch; j++)  void free_imatrix(m,nrl,nrh,ncl,nch)
       m[i][j]=m[i][j-1]+nlay;        int **m;
   }        long nch,ncl,nrh,nrl; 
   return m;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 /*************************free ma3x ************************/    free((FREE_ARG) (m+nrl-NR_END)); 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  } 
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /******************* matrix *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double **matrix(long nrl, long nrh, long ncl, long nch)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 /***************** f1dim *************************/  
 extern int ncom;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 extern double *pcom,*xicom;    if (!m) nrerror("allocation failure 1 in matrix()");
 extern double (*nrfunc)(double []);    m += NR_END;
      m -= nrl;
 double f1dim(double x)  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int j;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double f;    m[nrl] += NR_END;
   double *xt;    m[nrl] -= ncl;
    
   xt=vector(1,ncom);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    return m;
   f=(*nrfunc)(xt);    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
   free_vector(xt,1,ncom);     */
   return f;  }
 }  
   /*************************free matrix ************************/
 /*****************brent *************************/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int iter;    free((FREE_ARG)(m+nrl-NR_END));
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /******************* ma3x *******************************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double e=0.0;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   a=(ax < cx ? ax : cx);    double ***m;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   fw=fv=fx=(*f)(x);    if (!m) nrerror("allocation failure 1 in matrix()");
   for (iter=1;iter<=ITMAX;iter++) {    m += NR_END;
     xm=0.5*(a+b);    m -= nrl;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     printf(".");fflush(stdout);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     fprintf(ficlog,".");fflush(ficlog);    m[nrl] += NR_END;
 #ifdef DEBUG    m[nrl] -= ncl;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       *xmin=x;    m[nrl][ncl] += NR_END;
       return fx;    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
     ftemp=fu;      m[nrl][j]=m[nrl][j-1]+nlay;
     if (fabs(e) > tol1) {    
       r=(x-w)*(fx-fv);    for (i=nrl+1; i<=nrh; i++) {
       q=(x-v)*(fx-fw);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       p=(x-v)*q-(x-w)*r;      for (j=ncl+1; j<=nch; j++) 
       q=2.0*(q-r);        m[i][j]=m[i][j-1]+nlay;
       if (q > 0.0) p = -p;    }
       q=fabs(q);    return m; 
       etemp=e;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       e=d;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       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 {  
         d=p/q;  /*************************free ma3x ************************/
         u=x+d;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         if (u-a < tol2 || b-u < tol2)  {
           d=SIGN(tol1,xm-x);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     } else {    free((FREE_ARG)(m+nrl-NR_END));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /***************** f1dim *************************/
     fu=(*f)(u);  extern int ncom; 
     if (fu <= fx) {  extern double *pcom,*xicom;
       if (u >= x) a=x; else b=x;  extern double (*nrfunc)(double []); 
       SHFT(v,w,x,u)   
         SHFT(fv,fw,fx,fu)  double f1dim(double x) 
         } else {  { 
           if (u < x) a=u; else b=u;    int j; 
           if (fu <= fw || w == x) {    double f;
             v=w;    double *xt; 
             w=u;   
             fv=fw;    xt=vector(1,ncom); 
             fw=fu;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
           } else if (fu <= fv || v == x || v == w) {    f=(*nrfunc)(xt); 
             v=u;    free_vector(xt,1,ncom); 
             fv=fu;    return f; 
           }  } 
         }  
   }  /*****************brent *************************/
   nrerror("Too many iterations in brent");  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *xmin=x;  { 
   return fx;    int iter; 
 }    double a,b,d,etemp;
     double fu,fv,fw,fx;
 /****************** mnbrak ***********************/    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    double e=0.0; 
             double (*func)(double))   
 {    a=(ax < cx ? ax : cx); 
   double ulim,u,r,q, dum;    b=(ax > cx ? ax : cx); 
   double fu;    x=w=v=bx; 
      fw=fv=fx=(*f)(x); 
   *fa=(*func)(*ax);    for (iter=1;iter<=ITMAX;iter++) { 
   *fb=(*func)(*bx);      xm=0.5*(a+b); 
   if (*fb > *fa) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     SHFT(dum,*ax,*bx,dum)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       SHFT(dum,*fb,*fa,dum)      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
   *cx=(*bx)+GOLD*(*bx-*ax);  #ifdef DEBUG
   *fc=(*func)(*cx);      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);
   while (*fb > *fc) {      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);
     r=(*bx-*ax)*(*fb-*fc);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     q=(*bx-*cx)*(*fb-*fa);  #endif
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        *xmin=x; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);        return fx; 
     if ((*bx-u)*(u-*cx) > 0.0) {      } 
       fu=(*func)(u);      ftemp=fu;
     } else if ((*cx-u)*(u-ulim) > 0.0) {      if (fabs(e) > tol1) { 
       fu=(*func)(u);        r=(x-w)*(fx-fv); 
       if (fu < *fc) {        q=(x-v)*(fx-fw); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))        p=(x-v)*q-(x-w)*r; 
           SHFT(*fb,*fc,fu,(*func)(u))        q=2.0*(q-r); 
           }        if (q > 0.0) p = -p; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {        q=fabs(q); 
       u=ulim;        etemp=e; 
       fu=(*func)(u);        e=d; 
     } else {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       u=(*cx)+GOLD*(*cx-*bx);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       fu=(*func)(u);        else { 
     }          d=p/q; 
     SHFT(*ax,*bx,*cx,u)          u=x+d; 
       SHFT(*fa,*fb,*fc,fu)          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /*************** linmin ************************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 int ncom;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 double *pcom,*xicom;      fu=(*f)(u); 
 double (*nrfunc)(double []);      if (fu <= fx) { 
          if (u >= x) a=x; else b=x; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        SHFT(v,w,x,u) 
 {          SHFT(fv,fw,fx,fu) 
   double brent(double ax, double bx, double cx,          } else { 
                double (*f)(double), double tol, double *xmin);            if (u < x) a=u; else b=u; 
   double f1dim(double x);            if (fu <= fw || w == x) { 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,              v=w; 
               double *fc, double (*func)(double));              w=u; 
   int j;              fv=fw; 
   double xx,xmin,bx,ax;              fw=fu; 
   double fx,fb,fa;            } else if (fu <= fv || v == x || v == w) { 
                v=u; 
   ncom=n;              fv=fu; 
   pcom=vector(1,n);            } 
   xicom=vector(1,n);          } 
   nrfunc=func;    } 
   for (j=1;j<=n;j++) {    nrerror("Too many iterations in brent"); 
     pcom[j]=p[j];    *xmin=x; 
     xicom[j]=xi[j];    return fx; 
   }  } 
   ax=0.0;  
   xx=1.0;  /****************** mnbrak ***********************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 #ifdef DEBUG              double (*func)(double)) 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  { 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    double ulim,u,r,q, dum;
 #endif    double fu; 
   for (j=1;j<=n;j++) {   
     xi[j] *= xmin;    *fa=(*func)(*ax); 
     p[j] += xi[j];    *fb=(*func)(*bx); 
   }    if (*fb > *fa) { 
   free_vector(xicom,1,n);      SHFT(dum,*ax,*bx,dum) 
   free_vector(pcom,1,n);        SHFT(dum,*fb,*fa,dum) 
 }        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 /*************** powell ************************/    *fc=(*func)(*cx); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    while (*fb > *fc) { 
             double (*func)(double []))      r=(*bx-*ax)*(*fb-*fc); 
 {      q=(*bx-*cx)*(*fb-*fa); 
   void linmin(double p[], double xi[], int n, double *fret,      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
               double (*func)(double []));        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   int i,ibig,j;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double del,t,*pt,*ptt,*xit;      if ((*bx-u)*(u-*cx) > 0.0) { 
   double fp,fptt;        fu=(*func)(u); 
   double *xits;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   pt=vector(1,n);        fu=(*func)(u); 
   ptt=vector(1,n);        if (fu < *fc) { 
   xit=vector(1,n);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   xits=vector(1,n);            SHFT(*fb,*fc,fu,(*func)(u)) 
   *fret=(*func)(p);            } 
   for (j=1;j<=n;j++) pt[j]=p[j];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (*iter=1;;++(*iter)) {        u=ulim; 
     fp=(*fret);        fu=(*func)(u); 
     ibig=0;      } else { 
     del=0.0;        u=(*cx)+GOLD*(*cx-*bx); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);        fu=(*func)(u); 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      } 
     for (i=1;i<=n;i++)      SHFT(*ax,*bx,*cx,u) 
       printf(" %d %.12f",i, p[i]);        SHFT(*fa,*fb,*fc,fu) 
     fprintf(ficlog," %d %.12f",i, p[i]);        } 
     printf("\n");  } 
     fprintf(ficlog,"\n");  
     for (i=1;i<=n;i++) {  /*************** linmin ************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  int ncom; 
 #ifdef DEBUG  double *pcom,*xicom;
       printf("fret=%lf \n",*fret);  double (*nrfunc)(double []); 
       fprintf(ficlog,"fret=%lf \n",*fret);   
 #endif  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf("%d",i);fflush(stdout);  { 
       fprintf(ficlog,"%d",i);fflush(ficlog);    double brent(double ax, double bx, double cx, 
       linmin(p,xit,n,fret,func);                 double (*f)(double), double tol, double *xmin); 
       if (fabs(fptt-(*fret)) > del) {    double f1dim(double x); 
         del=fabs(fptt-(*fret));    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         ibig=i;                double *fc, double (*func)(double)); 
       }    int j; 
 #ifdef DEBUG    double xx,xmin,bx,ax; 
       printf("%d %.12e",i,(*fret));    double fx,fb,fa;
       fprintf(ficlog,"%d %.12e",i,(*fret));   
       for (j=1;j<=n;j++) {    ncom=n; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    pcom=vector(1,n); 
         printf(" x(%d)=%.12e",j,xit[j]);    xicom=vector(1,n); 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
       for(j=1;j<=n;j++) {      pcom[j]=p[j]; 
         printf(" p=%.12e",p[j]);      xicom[j]=xi[j]; 
         fprintf(ficlog," p=%.12e",p[j]);    } 
       }    ax=0.0; 
       printf("\n");    xx=1.0; 
       fprintf(ficlog,"\n");    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 #endif    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #ifdef DEBUG    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       int k[2],l;  #endif
       k[0]=1;    for (j=1;j<=n;j++) { 
       k[1]=-1;      xi[j] *= xmin; 
       printf("Max: %.12e",(*func)(p));      p[j] += xi[j]; 
       fprintf(ficlog,"Max: %.12e",(*func)(p));    } 
       for (j=1;j<=n;j++) {    free_vector(xicom,1,n); 
         printf(" %.12e",p[j]);    free_vector(pcom,1,n); 
         fprintf(ficlog," %.12e",p[j]);  } 
       }  
       printf("\n");  /*************** powell ************************/
       fprintf(ficlog,"\n");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(l=0;l<=1;l++) {              double (*func)(double [])) 
         for (j=1;j<=n;j++) {  { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    void linmin(double p[], double xi[], int n, double *fret, 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);                double (*func)(double [])); 
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    int i,ibig,j; 
         }    double del,t,*pt,*ptt,*xit;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double fp,fptt;
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double *xits;
       }    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
     xit=vector(1,n); 
     xits=vector(1,n); 
       free_vector(xit,1,n);    *fret=(*func)(p); 
       free_vector(xits,1,n);    for (j=1;j<=n;j++) pt[j]=p[j]; 
       free_vector(ptt,1,n);    for (*iter=1;;++(*iter)) { 
       free_vector(pt,1,n);      fp=(*fret); 
       return;      ibig=0; 
     }      del=0.0; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for (j=1;j<=n;j++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       ptt[j]=2.0*p[j]-pt[j];      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       xit[j]=p[j]-pt[j];      for (i=1;i<=n;i++) {
       pt[j]=p[j];        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
     fptt=(*func)(ptt);        fprintf(ficrespow," %.12lf", p[i]);
     if (fptt < fp) {      }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      printf("\n");
       if (t < 0.0) {      fprintf(ficlog,"\n");
         linmin(p,xit,n,fret,func);      fprintf(ficrespow,"\n");
         for (j=1;j<=n;j++) {      for (i=1;i<=n;i++) { 
           xi[j][ibig]=xi[j][n];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
           xi[j][n]=xit[j];        fptt=(*fret); 
         }  #ifdef DEBUG
 #ifdef DEBUG        printf("fret=%lf \n",*fret);
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        fprintf(ficlog,"fret=%lf \n",*fret);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #endif
         for(j=1;j<=n;j++){        printf("%d",i);fflush(stdout);
           printf(" %.12e",xit[j]);        fprintf(ficlog,"%d",i);fflush(ficlog);
           fprintf(ficlog," %.12e",xit[j]);        linmin(p,xit,n,fret,func); 
         }        if (fabs(fptt-(*fret)) > del) { 
         printf("\n");          del=fabs(fptt-(*fret)); 
         fprintf(ficlog,"\n");          ibig=i; 
 #endif        } 
       }  #ifdef DEBUG
     }        printf("%d %.12e",i,(*fret));
   }        fprintf(ficlog,"%d %.12e",i,(*fret));
 }        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 /**** Prevalence limit ****************/          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        }
 {        for(j=1;j<=n;j++) {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit          printf(" p=%.12e",p[j]);
      matrix by transitions matrix until convergence is reached */          fprintf(ficlog," p=%.12e",p[j]);
         }
   int i, ii,j,k;        printf("\n");
   double min, max, maxmin, maxmax,sumnew=0.;        fprintf(ficlog,"\n");
   double **matprod2();  #endif
   double **out, cov[NCOVMAX], **pmij();      } 
   double **newm;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double agefin, delaymax=50 ; /* Max number of years to converge */  #ifdef DEBUG
         int k[2],l;
   for (ii=1;ii<=nlstate+ndeath;ii++)        k[0]=1;
     for (j=1;j<=nlstate+ndeath;j++){        k[1]=-1;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
    cov[1]=1.;          printf(" %.12e",p[j]);
            fprintf(ficlog," %.12e",p[j]);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        printf("\n");
     newm=savm;        fprintf(ficlog,"\n");
     /* Covariates have to be included here again */        for(l=0;l<=1;l++) {
      cov[2]=agefin;          for (j=1;j<=n;j++) {
              ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for (k=1; k<=cptcovn;k++) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       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]]];  #endif
   
       /*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]);*/        free_vector(xit,1,n); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        free_vector(xits,1,n); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
     savm=oldm;        return; 
     oldm=newm;      } 
     maxmax=0.;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for(j=1;j<=nlstate;j++){      for (j=1;j<=n;j++) { 
       min=1.;        ptt[j]=2.0*p[j]-pt[j]; 
       max=0.;        xit[j]=p[j]-pt[j]; 
       for(i=1; i<=nlstate; i++) {        pt[j]=p[j]; 
         sumnew=0;      } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      fptt=(*func)(ptt); 
         prlim[i][j]= newm[i][j]/(1-sumnew);      if (fptt < fp) { 
         max=FMAX(max,prlim[i][j]);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         min=FMIN(min,prlim[i][j]);        if (t < 0.0) { 
       }          linmin(p,xit,n,fret,func); 
       maxmin=max-min;          for (j=1;j<=n;j++) { 
       maxmax=FMAX(maxmax,maxmin);            xi[j][ibig]=xi[j][n]; 
     }            xi[j][n]=xit[j]; 
     if(maxmax < ftolpl){          }
       return prlim;  #ifdef DEBUG
     }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 /*************** transition probabilities ***************/            fprintf(ficlog," %.12e",xit[j]);
           }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          printf("\n");
 {          fprintf(ficlog,"\n");
   double s1, s2;  #endif
   /*double t34;*/        }
   int i,j,j1, nc, ii, jj;      } 
     } 
     for(i=1; i<= nlstate; i++){  } 
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /**** Prevalence limit (stable prevalence)  ****************/
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       ps[i][j]=s2;       matrix by transitions matrix until convergence is reached */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }    int i, ii,j,k;
     for(j=i+1; j<=nlstate+ndeath;j++){    double min, max, maxmin, maxmax,sumnew=0.;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double **matprod2();
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double **out, cov[NCOVMAX], **pmij();
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double **newm;
       }    double agefin, delaymax=50 ; /* Max number of years to converge */
       ps[i][j]=s2;  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
     /*ps[3][2]=1;*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   for(i=1; i<= nlstate; i++){  
      s1=0;     cov[1]=1.;
     for(j=1; j<i; j++)   
       s1+=exp(ps[i][j]);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(j=i+1; j<=nlstate+ndeath; j++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       s1+=exp(ps[i][j]);      newm=savm;
     ps[i][i]=1./(s1+1.);      /* Covariates have to be included here again */
     for(j=1; j<i; j++)       cov[2]=agefin;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    
     for(j=i+1; j<=nlstate+ndeath; j++)        for (k=1; k<=cptcovn;k++) {
       ps[i][j]= exp(ps[i][j])*ps[i][i];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 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]]);*/
   } /* end i */        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        for (k=1; k<=cptcovprod;k++)
     for(jj=1; jj<= nlstate+ndeath; jj++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       ps[ii][jj]=0;  
       ps[ii][ii]=1;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      savm=oldm;
     for(jj=1; jj<= nlstate+ndeath; jj++){      oldm=newm;
      printf("%lf ",ps[ii][jj]);      maxmax=0.;
    }      for(j=1;j<=nlstate;j++){
     printf("\n ");        min=1.;
     }        max=0.;
     printf("\n ");printf("%lf ",cov[2]);*/        for(i=1; i<=nlstate; i++) {
 /*          sumnew=0;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   goto end;*/          prlim[i][j]= newm[i][j]/(1-sumnew);
     return ps;          max=FMAX(max,prlim[i][j]);
 }          min=FMIN(min,prlim[i][j]);
         }
 /**************** Product of 2 matrices ******************/        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      }
 {      if(maxmax < ftolpl){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        return prlim;
      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  }
      a pointer to pointers identical to out */  
   long i, j, k;  /*************** transition probabilities ***************/ 
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    double s1, s2;
     /*double t34;*/
   return out;    int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
 /************* Higher Matrix Product ***************/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          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);*/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        }
      duration (i.e. until        ps[i][j]=s2;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        /*printf("s1=%.17e, s2=%.17e\n",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).      for(j=i+1; j<=nlstate+ndeath;j++){
      Model is determined by parameters x and covariates have to be        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      included manually here.          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
      */        }
         ps[i][j]=s2;
   int i, j, d, h, k;      }
   double **out, cov[NCOVMAX];    }
   double **newm;      /*ps[3][2]=1;*/
   
   /* Hstepm could be zero and should return the unit matrix */    for(i=1; i<= nlstate; i++){
   for (i=1;i<=nlstate+ndeath;i++)       s1=0;
     for (j=1;j<=nlstate+ndeath;j++){      for(j=1; j<i; j++)
       oldm[i][j]=(i==j ? 1.0 : 0.0);        s1+=exp(ps[i][j]);
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for(j=i+1; j<=nlstate+ndeath; j++)
     }        s1+=exp(ps[i][j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      ps[i][i]=1./(s1+1.);
   for(h=1; h <=nhstepm; h++){      for(j=1; j<i; j++)
     for(d=1; d <=hstepm; d++){        ps[i][j]= exp(ps[i][j])*ps[i][i];
       newm=savm;      for(j=i+1; j<=nlstate+ndeath; j++)
       /* Covariates have to be included here again */        ps[i][j]= exp(ps[i][j])*ps[i][i];
       cov[1]=1.;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    } /* end i */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for(jj=1; jj<= nlstate+ndeath; jj++){
       for (k=1; k<=cptcovprod;k++)        ps[ii][jj]=0;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        ps[ii][ii]=1;
       }
     }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      for(jj=1; jj<= nlstate+ndeath; jj++){
       savm=oldm;       printf("%lf ",ps[ii][jj]);
       oldm=newm;     }
     }      printf("\n ");
     for(i=1; i<=nlstate+ndeath; i++)      }
       for(j=1;j<=nlstate+ndeath;j++) {      printf("\n ");printf("%lf ",cov[2]);*/
         po[i][j][h]=newm[i][j];  /*
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
          */    goto end;*/
       }      return ps;
   } /* end h */  }
   return po;  
 }  /**************** Product of 2 matrices ******************/
   
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 /*************** log-likelihood *************/  {
 double func( double *x)    /* 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(...) */
   int i, ii, j, k, mi, d, kk;    /* in, b, out are matrice of pointers which should have been initialized 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];       before: only the contents of out is modified. The function returns
   double **out;       a pointer to pointers identical to out */
   double sw; /* Sum of weights */    long i, j, k;
   double lli; /* Individual log likelihood */    for(i=nrl; i<= nrh; i++)
   long ipmx;      for(k=ncolol; k<=ncoloh; k++)
   /*extern weight */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   /* We are differentiating ll according to initial status */          out[i][k] +=in[i][j]*b[j][k];
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)    return out;
     printf(" %d\n",s[4][i]);  }
   */  
   cov[1]=1.;  
   /************* Higher Matrix Product ***************/
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    /* Computes the transition matrix starting at age 'age' over 
       for (ii=1;ii<=nlstate+ndeath;ii++)       'nhstepm*hstepm*stepm' months (i.e. until
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       for(d=0; d<dh[mi][i]; d++){       nhstepm*hstepm matrices. 
         newm=savm;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;       (typically every 2 years instead of every month which is too big 
         for (kk=1; kk<=cptcovage;kk++) {       for the memory).
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];       Model is determined by parameters x and covariates have to be 
         }       included manually here. 
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;    int i, j, d, h, k;
         oldm=newm;    double **out, cov[NCOVMAX];
            double **newm;
          
       } /* end mult */    /* Hstepm could be zero and should return the unit matrix */
          for (i=1;i<=nlstate+ndeath;i++)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      for (j=1;j<=nlstate+ndeath;j++){
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        oldm[i][j]=(i==j ? 1.0 : 0.0);
       ipmx +=1;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     } /* end of wave */    for(h=1; h <=nhstepm; h++){
   } /* end of individual */      for(d=1; d <=hstepm; d++){
         newm=savm;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        /* Covariates have to be included here again */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        cov[1]=1.;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   return -l;        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++)
 /*********** Maximum Likelihood Estimation ***************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int i,j, iter;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double **xi,*delti;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double fret;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   xi=matrix(1,npar,1,npar);        savm=oldm;
   for (i=1;i<=npar;i++)        oldm=newm;
     for (j=1;j<=npar;j++)      }
       xi[i][j]=(i==j ? 1.0 : 0.0);      for(i=1; i<=nlstate+ndeath; i++)
   printf("Powell\n");  fprintf(ficlog,"Powell\n");        for(j=1;j<=nlstate+ndeath;j++) {
   powell(p,xi,npar,ftol,&iter,&fret,func);          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]);
    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));    } /* end h */
     return po;
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*************** log-likelihood *************/
 {  double func( double *x)
   double  **a,**y,*x,pd;  {
   double **hess;    int i, ii, j, k, mi, d, kk;
   int i, j,jk;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   int *indx;    double **out;
     double sw; /* Sum of weights */
   double hessii(double p[], double delta, int theta, double delti[]);    double lli; /* Individual log likelihood */
   double hessij(double p[], double delti[], int i, int j);    int s1, s2;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double bbh, survp;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    long ipmx;
     /*extern weight */
   hess=matrix(1,npar,1,npar);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   printf("\nCalculation of the hessian matrix. Wait...\n");    /*for(i=1;i<imx;i++) 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");      printf(" %d\n",s[4][i]);
   for (i=1;i<=npar;i++){    */
     printf("%d",i);fflush(stdout);    cov[1]=1.;
     fprintf(ficlog,"%d",i);fflush(ficlog);  
     hess[i][i]=hessii(p,ftolhess,i,delti);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    if(mle==1){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (i=1;i<=npar;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (j=1;j<=npar;j++)  {          for (ii=1;ii<=nlstate+ndeath;ii++)
       if (j>i) {            for (j=1;j<=nlstate+ndeath;j++){
         printf(".%d%d",i,j);fflush(stdout);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         hess[i][j]=hessij(p,delti,i,j);            }
         hess[j][i]=hess[i][j];              for(d=0; d<dh[mi][i]; d++){
         /*printf(" %lf ",hess[i][j]);*/            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];
   printf("\n");            }
   fprintf(ficlog,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            savm=oldm;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");            oldm=newm;
            } /* end mult */
   a=matrix(1,npar,1,npar);        
   y=matrix(1,npar,1,npar);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   x=vector(1,npar);          /* But now since version 0.9 we anticipate for bias and large stepm.
   indx=ivector(1,npar);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=npar;i++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];           * the nearest (and in case of equal distance, to the lowest) interval but now
   ludcmp(a,npar,indx,&pd);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for (j=1;j<=npar;j++) {           * probability in order to take into account the bias as a fraction of the way
     for (i=1;i<=npar;i++) x[i]=0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     x[j]=1;           * -stepm/2 to stepm/2 .
     lubksb(a,npar,indx,x);           * For stepm=1 the results are the same as for previous versions of Imach.
     for (i=1;i<=npar;i++){           * For stepm > 1 the results are less biased than in previous versions. 
       matcov[i][j]=x[i];           */
     }          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   printf("\n#Hessian matrix#\n");          /* bias is positive if real duration
   fprintf(ficlog,"\n#Hessian matrix#\n");           * is higher than the multiple of stepm and negative otherwise.
   for (i=1;i<=npar;i++) {           */
     for (j=1;j<=npar;j++) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       printf("%.3e ",hess[i][j]);          if( s2 > nlstate){ 
       fprintf(ficlog,"%.3e ",hess[i][j]);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     }               to the likelihood is the probability to die between last step unit time and current 
     printf("\n");               step unit time, which is also the differences between probability to die before dh 
     fprintf(ficlog,"\n");               and probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   /* Recompute Inverse */          health state: the date of the interview describes the actual state
   for (i=1;i<=npar;i++)          and not the date of a change in health state. The former idea was
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          to consider that at each interview the state was recorded
   ludcmp(a,npar,indx,&pd);          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   /*  printf("\n#Hessian matrix recomputed#\n");          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
   for (j=1;j<=npar;j++) {          stepm. It is no more the probability to die between last interview
     for (i=1;i<=npar;i++) x[i]=0;          and month of death but the probability to survive from last
     x[j]=1;          interview up to one month before death multiplied by the
     lubksb(a,npar,indx,x);          probability to die within a month. Thanks to Chris
     for (i=1;i<=npar;i++){          Jackson for correcting this bug.  Former versions increased
       y[i][j]=x[i];          mortality artificially. The bad side is that we add another loop
       printf("%.3e ",y[i][j]);          which slows down the processing. The difference can be up to 10%
       fprintf(ficlog,"%.3e ",y[i][j]);          lower mortality.
     }            */
     printf("\n");            lli=log(out[s1][s2] - savm[s1][s2]);
     fprintf(ficlog,"\n");          }else{
   }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
   free_matrix(a,1,npar,1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   free_matrix(y,1,npar,1,npar);          /*if(lli ==000.0)*/
   free_vector(x,1,npar);          /*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); */
   free_ivector(indx,1,npar);          ipmx +=1;
   free_matrix(hess,1,npar,1,npar);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 }      } /* end of individual */
     }  else if(mle==2){
 /*************** hessian matrix ****************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 double hessii( double x[], double delta, int theta, double delti[])        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   int i;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int l=1, lmax=20;            for (j=1;j<=nlstate+ndeath;j++){
   double k1,k2;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double p2[NPARMAX+1];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double res;            }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          for(d=0; d<=dh[mi][i]; d++){
   double fx;            newm=savm;
   int k=0,kmax=10;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double l1;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fx=func(x);            }
   for (i=1;i<=npar;i++) p2[i]=x[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(l=0 ; l <=lmax; l++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     l1=pow(10,l);            savm=oldm;
     delts=delt;            oldm=newm;
     for(k=1 ; k <kmax; k=k+1){          } /* end mult */
       delt = delta*(l1*k);        
       p2[theta]=x[theta] +delt;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       k1=func(p2)-fx;          /* But now since version 0.9 we anticipate for bias and large stepm.
       p2[theta]=x[theta]-delt;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       k2=func(p2)-fx;           * (in months) between two waves is not a multiple of stepm, we rounded to 
       /*res= (k1-2.0*fx+k2)/delt/delt; */           * the nearest (and in case of equal distance, to the lowest) interval but now
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                 * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 #ifdef DEBUG           * probability in order to take into account the bias as a fraction of the way
       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);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       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);           * -stepm/2 to stepm/2 .
 #endif           * For stepm=1 the results are the same as for previous versions of Imach.
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */           * For stepm > 1 the results are less biased than in previous versions. 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){           */
         k=kmax;          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          bbh=(double)bh[mi][i]/(double)stepm; 
         k=kmax; l=lmax*10.;          /* bias is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           */
         delts=delt;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     }          /*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]);*/
   delti[theta]=delts;          /*if(lli ==000.0)*/
   return res;          /*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;
 double hessij( double x[], double delti[], int thetai,int thetaj)        } /* end of wave */
 {      } /* end of individual */
   int i;    }  else if(mle==3){  /* exponential inter-extrapolation */
   int l=1, l1, lmax=20;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double k1,k2,k3,k4,res,fx;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double p2[NPARMAX+1];        for(mi=1; mi<= wav[i]-1; mi++){
   int k;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   fx=func(x);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=1; k<=2; k++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++) p2[i]=x[i];            }
     p2[thetai]=x[thetai]+delti[thetai]/k;          for(d=0; d<dh[mi][i]; d++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            newm=savm;
     k1=func(p2)-fx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            }
     k2=func(p2)-fx;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetai]=x[thetai]-delti[thetai]/k;            savm=oldm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            oldm=newm;
     k3=func(p2)-fx;          } /* end mult */
          
     p2[thetai]=x[thetai]-delti[thetai]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /* But now since version 0.9 we anticipate for bias and large stepm.
     k4=func(p2)-fx;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * (in months) between two waves is not a multiple of stepm, we rounded to 
 #ifdef DEBUG           * the nearest (and in case of equal distance, to the lowest) interval but now
     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);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     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);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 #endif           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   return res;           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 /************** Inverse of matrix **************/           */
 void ludcmp(double **a, int n, int *indx, double *d)          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   int i,imax,j,k;          bbh=(double)bh[mi][i]/(double)stepm; 
   double big,dum,sum,temp;          /* bias is positive if real duration
   double *vv;           * is higher than the multiple of stepm and negative otherwise.
             */
   vv=vector(1,n);          /* 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 */
   *d=1.0;          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 */
   for (i=1;i<=n;i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     big=0.0;          /*if(lli ==000.0)*/
     for (j=1;j<=n;j++)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       if ((temp=fabs(a[i][j])) > big) big=temp;          ipmx +=1;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          sw += weight[i];
     vv[i]=1.0/big;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   for (j=1;j<=n;j++) {      } /* end of individual */
     for (i=1;i<j;i++) {    }else{  /* ml=4 no inter-extrapolation */
       sum=a[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       a[i][j]=sum;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     big=0.0;            for (j=1;j<=nlstate+ndeath;j++){
     for (i=j;i<=n;i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       sum=a[i][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<j;k++)            }
         sum -= a[i][k]*a[k][j];          for(d=0; d<dh[mi][i]; d++){
       a[i][j]=sum;            newm=savm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         big=dum;            for (kk=1; kk<=cptcovage;kk++) {
         imax=i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
     }          
     if (j != imax) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=1;k<=n;k++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         dum=a[imax][k];            savm=oldm;
         a[imax][k]=a[j][k];            oldm=newm;
         a[j][k]=dum;          } /* end mult */
       }        
       *d = -(*d);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       vv[imax]=vv[j];          ipmx +=1;
     }          sw += weight[i];
     indx[j]=imax;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (a[j][j] == 0.0) a[j][j]=TINY;        } /* end of wave */
     if (j != n) {      } /* end of individual */
       dum=1.0/(a[j][j]);    } /* End of if */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   free_vector(vv,1,n);  /* Doesn't work */    return -l;
 ;  }
 }  
   
 void lubksb(double **a, int n, int *indx, double b[])  /*********** Maximum Likelihood Estimation ***************/
 {  
   int i,ii=0,ip,j;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double sum;  {
      int i,j, iter;
   for (i=1;i<=n;i++) {    double **xi;
     ip=indx[i];    double fret;
     sum=b[ip];    char filerespow[FILENAMELENGTH];
     b[ip]=b[i];    xi=matrix(1,npar,1,npar);
     if (ii)    for (i=1;i<=npar;i++)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      for (j=1;j<=npar;j++)
     else if (sum) ii=i;        xi[i][j]=(i==j ? 1.0 : 0.0);
     b[i]=sum;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   }    strcpy(filerespow,"pow"); 
   for (i=n;i>=1;i--) {    strcat(filerespow,fileres);
     sum=b[i];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      printf("Problem with resultfile: %s\n", filerespow);
     b[i]=sum/a[i][i];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
 }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
 /************ Frequencies ********************/      for(j=1;j<=nlstate+ndeath;j++)
 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)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 {  /* Some frequencies */    fprintf(ficrespow,"\n");
      powell(p,xi,npar,ftol,&iter,&fret,func);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   int first;    fclose(ficrespow);
   double ***freq; /* Frequencies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double *pp;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double pos, k2, dateintsum=0,k2cpt=0;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  }
    
   pp=vector(1,nlstate);  /**** Computes Hessian and covariance matrix ***/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   strcpy(fileresp,"p");  {
   strcat(fileresp,fileres);    double  **a,**y,*x,pd;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double **hess;
     printf("Problem with prevalence resultfile: %s\n", fileresp);    int i, j,jk;
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    int *indx;
     exit(0);  
   }    double hessii(double p[], double delta, int theta, double delti[]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double hessij(double p[], double delti[], int i, int j);
   j1=0;    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    hess=matrix(1,npar,1,npar);
   
   first=1;    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for(k1=1; k1<=j;k1++){    for (i=1;i<=npar;i++){
     for(i1=1; i1<=ncodemax[k1];i1++){      printf("%d",i);fflush(stdout);
       j1++;      fprintf(ficlog,"%d",i);fflush(ficlog);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      hess[i][i]=hessii(p,ftolhess,i,delti);
         scanf("%d", i);*/      /*printf(" %f ",p[i]);*/
       for (i=-1; i<=nlstate+ndeath; i++)        /*printf(" %lf ",hess[i][i]);*/
         for (jk=-1; jk<=nlstate+ndeath; jk++)      }
           for(m=agemin; m <= agemax+3; m++)    
             freq[i][jk][m]=0;    for (i=1;i<=npar;i++) {
            for (j=1;j<=npar;j++)  {
       dateintsum=0;        if (j>i) { 
       k2cpt=0;          printf(".%d%d",i,j);fflush(stdout);
       for (i=1; i<=imx; i++) {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         bool=1;          hess[i][j]=hessij(p,delti,i,j);
         if  (cptcovn>0) {          hess[j][i]=hess[i][j];    
           for (z1=1; z1<=cptcoveff; z1++)          /*printf(" %lf ",hess[i][j]);*/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;      }
         }    }
         if (bool==1) {    printf("\n");
           for(m=firstpass; m<=lastpass; m++){    fprintf(ficlog,"\n");
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
               if(agev[m][i]==1) agev[m][i]=agemax+2;    
               if (m<lastpass) {    a=matrix(1,npar,1,npar);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    y=matrix(1,npar,1,npar);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    x=vector(1,npar);
               }    indx=ivector(1,npar);
                  for (i=1;i<=npar;i++)
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                 dateintsum=dateintsum+k2;    ludcmp(a,npar,indx,&pd);
                 k2cpt++;  
               }    for (j=1;j<=npar;j++) {
             }      for (i=1;i<=npar;i++) x[i]=0;
           }      x[j]=1;
         }      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
                matcov[i][j]=x[i];
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
     }
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");    printf("\n#Hessian matrix#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n#Hessian matrix#\n");
         fprintf(ficresp, "**********\n#");    for (i=1;i<=npar;i++) { 
       }      for (j=1;j<=npar;j++) { 
       for(i=1; i<=nlstate;i++)        printf("%.3e ",hess[i][j]);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        fprintf(ficlog,"%.3e ",hess[i][j]);
       fprintf(ficresp, "\n");      }
            printf("\n");
       for(i=(int)agemin; i <= (int)agemax+3; i++){      fprintf(ficlog,"\n");
         if(i==(int)agemax+3){    }
           fprintf(ficlog,"Total");  
         }else{    /* Recompute Inverse */
           if(first==1){    for (i=1;i<=npar;i++)
             first=0;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             printf("See log file for details...\n");    ludcmp(a,npar,indx,&pd);
           }  
           fprintf(ficlog,"Age %d", i);    /*  printf("\n#Hessian matrix recomputed#\n");
         }  
         for(jk=1; jk <=nlstate ; jk++){    for (j=1;j<=npar;j++) {
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1;i<=npar;i++) x[i]=0;
             pp[jk] += freq[jk][m][i];      x[j]=1;
         }      lubksb(a,npar,indx,x);
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=npar;i++){ 
           for(m=-1, pos=0; m <=0 ; m++)        y[i][j]=x[i];
             pos += freq[jk][m][i];        printf("%.3e ",y[i][j]);
           if(pp[jk]>=1.e-10){        fprintf(ficlog,"%.3e ",y[i][j]);
             if(first==1){      }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      printf("\n");
             }      fprintf(ficlog,"\n");
             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);    free_matrix(a,1,npar,1,npar);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    free_matrix(y,1,npar,1,npar);
           }    free_vector(x,1,npar);
         }    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  }
         }  
   /*************** hessian matrix ****************/
         for(jk=1,pos=0; jk <=nlstate ; jk++)  double hessii( double x[], double delta, int theta, double delti[])
           pos += pp[jk];  {
         for(jk=1; jk <=nlstate ; jk++){    int i;
           if(pos>=1.e-5){    int l=1, lmax=20;
             if(first==1)    double k1,k2;
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double p2[NPARMAX+1];
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double res;
           }else{    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
             if(first==1)    double fx;
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    int k=0,kmax=10;
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double l1;
           }  
           if( i <= (int) agemax){    fx=func(x);
             if(pos>=1.e-5){    for (i=1;i<=npar;i++) p2[i]=x[i];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    for(l=0 ; l <=lmax; l++){
               probs[i][jk][j1]= pp[jk]/pos;      l1=pow(10,l);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      delts=delt;
             }      for(k=1 ; k <kmax; k=k+1){
             else        delt = delta*(l1*k);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        p2[theta]=x[theta] +delt;
           }        k1=func(p2)-fx;
         }        p2[theta]=x[theta]-delt;
                k2=func(p2)-fx;
         for(jk=-1; jk <=nlstate+ndeath; jk++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
           for(m=-1; m <=nlstate+ndeath; m++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             if(freq[jk][m][i] !=0 ) {        
             if(first==1)  #ifdef DEBUG
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][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);
             }  #endif
         if(i <= (int) agemax)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           fprintf(ficresp,"\n");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         if(first==1)          k=kmax;
           printf("Others in log...\n");        }
         fprintf(ficlog,"\n");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       }          k=kmax; l=lmax*10.;
     }        }
   }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   dateintmean=dateintsum/k2cpt;          delts=delt;
          }
   fclose(ficresp);      }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }
   free_vector(pp,1,nlstate);    delti[theta]=delts;
      return res; 
   /* End of Freq */    
 }  }
   
 /************ Prevalence ********************/  double hessij( double x[], double delti[], int thetai,int thetaj)
 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)  {
 {  /* Some frequencies */    int i;
      int l=1, l1, lmax=20;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double k1,k2,k3,k4,res,fx;
   double ***freq; /* Frequencies */    double p2[NPARMAX+1];
   double *pp;    int k;
   double pos, k2;  
     fx=func(x);
   pp=vector(1,nlstate);    for (k=1; k<=2; k++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   j1=0;      k1=func(p2)-fx;
      
   j=cptcoveff;      p2[thetai]=x[thetai]+delti[thetai]/k;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
   for(k1=1; k1<=j;k1++){    
     for(i1=1; i1<=ncodemax[k1];i1++){      p2[thetai]=x[thetai]-delti[thetai]/k;
       j1++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            k3=func(p2)-fx;
       for (i=-1; i<=nlstate+ndeath; i++)      
         for (jk=-1; jk<=nlstate+ndeath; jk++)        p2[thetai]=x[thetai]-delti[thetai]/k;
           for(m=agemin; m <= agemax+3; m++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             freq[i][jk][m]=0;      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<=imx; i++) {  #ifdef DEBUG
         bool=1;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         if  (cptcovn>0) {      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 (z1=1; z1<=cptcoveff; z1++)  #endif
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    }
               bool=0;    return res;
         }  }
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  /************** Inverse of matrix **************/
             k2=anint[m][i]+(mint[m][i]/12.);  void ludcmp(double **a, int n, int *indx, double *d) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int i,imax,j,k; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double big,dum,sum,temp; 
               if (m<lastpass) {    double *vv; 
                 if (calagedate>0)   
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    vv=vector(1,n); 
                 else    *d=1.0; 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for (i=1;i<=n;i++) { 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      big=0.0; 
               }      for (j=1;j<=n;j++) 
             }        if ((temp=fabs(a[i][j])) > big) big=temp; 
           }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
       }    } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for (j=1;j<=n;j++) { 
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<j;i++) { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        sum=a[i][j]; 
             pp[jk] += freq[jk][m][i];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
         for(jk=1; jk <=nlstate ; jk++){      } 
           for(m=-1, pos=0; m <=0 ; m++)      big=0.0; 
             pos += freq[jk][m][i];      for (i=j;i<=n;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=0, pp[jk]=0; m <=nlstate+ndeath; m++)        a[i][j]=sum; 
             pp[jk] += freq[jk][m][i];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         }          big=dum; 
                  imax=i; 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        } 
              } 
         for(jk=1; jk <=nlstate ; jk++){          if (j != imax) { 
           if( i <= (int) agemax){        for (k=1;k<=n;k++) { 
             if(pos>=1.e-5){          dum=a[imax][k]; 
               probs[i][jk][j1]= pp[jk]/pos;          a[imax][k]=a[j][k]; 
             }          a[j][k]=dum; 
           }        } 
         }/* end jk */        *d = -(*d); 
       }/* end i */        vv[imax]=vv[j]; 
     } /* end i1 */      } 
   } /* end k1 */      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
        if (j != n) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        dum=1.0/(a[j][j]); 
   free_vector(pp,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
        } 
 }  /* End of Freq */    } 
     free_vector(vv,1,n);  /* Doesn't work */
 /************* Waves Concatenation ***************/  ;
   } 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  void lubksb(double **a, int n, int *indx, double b[]) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  { 
      Death is a valid wave (if date is known).    int i,ii=0,ip,j; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double sum; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]   
      and mw[mi+1][i]. dh depends on stepm.    for (i=1;i<=n;i++) { 
      */      ip=indx[i]; 
       sum=b[ip]; 
   int i, mi, m;      b[ip]=b[i]; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      if (ii) 
      double sum=0., jmean=0.;*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int first;      else if (sum) ii=i; 
   int j, k=0,jk, ju, jl;      b[i]=sum; 
   double sum=0.;    } 
   first=0;    for (i=n;i>=1;i--) { 
   jmin=1e+5;      sum=b[i]; 
   jmax=-1;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   jmean=0.;      b[i]=sum/a[i][i]; 
   for(i=1; i<=imx; i++){    } 
     mi=0;  } 
     m=firstpass;  
     while(s[m][i] <= nlstate){  /************ Frequencies ********************/
       if(s[m][i]>=1)  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)
         mw[++mi][i]=m;  {  /* Some frequencies */
       if(m >=lastpass)    
         break;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       else    int first;
         m++;    double ***freq; /* Frequencies */
     }/* end while */    double *pp, **prop;
     if (s[m][i] > nlstate){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       mi++;     /* Death is another wave */    FILE *ficresp;
       /* if(mi==0)  never been interviewed correctly before death */    char fileresp[FILENAMELENGTH];
          /* Only death is a correct wave */    
       mw[mi][i]=m;    pp=vector(1,nlstate);
     }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
     wav[i]=mi;    strcat(fileresp,fileres);
     if(mi==0){    if((ficresp=fopen(fileresp,"w"))==NULL) {
       if(first==0){      printf("Problem with prevalence resultfile: %s\n", fileresp);
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         first=1;      exit(0);
       }    }
       if(first==1){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);    j1=0;
       }    
     } /* end mi==0 */    j=cptcoveff;
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   for(i=1; i<=imx; i++){    first=1;
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)    for(k1=1; k1<=j;k1++){
         dh[mi][i]=1;      for(i1=1; i1<=ncodemax[k1];i1++){
       else{        j1++;
         if (s[mw[mi+1][i]][i] > nlstate) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           if (agedc[i] < 2*AGESUP) {          scanf("%d", i);*/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for (i=-1; i<=nlstate+ndeath; i++)  
           if(j==0) j=1;  /* Survives at least one month after exam */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           k=k+1;            for(m=iagemin; m <= iagemax+3; m++)
           if (j >= jmax) jmax=j;              freq[i][jk][m]=0;
           if (j <= jmin) jmin=j;  
           sum=sum+j;      for (i=1; i<=nlstate; i++)  
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(m=iagemin; m <= iagemax+3; m++)
           }          prop[i][m]=0;
         }        
         else{        dateintsum=0;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        k2cpt=0;
           k=k+1;        for (i=1; i<=imx; i++) {
           if (j >= jmax) jmax=j;          bool=1;
           else if (j <= jmin)jmin=j;          if  (cptcovn>0) {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for (z1=1; z1<=cptcoveff; z1++) 
           sum=sum+j;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         }                bool=0;
         jk= j/stepm;          }
         jl= j -jk*stepm;          if (bool==1){
         ju= j -(jk+1)*stepm;            for(m=firstpass; m<=lastpass; m++){
         if(jl <= -ju)              k2=anint[m][i]+(mint[m][i]/12.);
           dh[mi][i]=jk;              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         else                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           dh[mi][i]=jk+1;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         if(dh[mi][i]==0)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           dh[mi][i]=1; /* At least one step */                if (m<lastpass) {
       }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   }                }
   jmean=sum/k;                
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);                  dateintsum=dateintsum+k2;
  }                  k2cpt++;
                 }
 /*********** Tricode ****************************/              }
 void tricode(int *Tvar, int **nbcode, int imx)            }
 {          }
   int Ndum[20],ij=1, k, j, i;        }
   int cptcode=0;         
   cptcoveff=0;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
    
   for (k=0; k<19; k++) Ndum[k]=0;        if  (cptcovn>0) {
   for (k=1; k<=7; k++) ncodemax[k]=0;          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          fprintf(ficresp, "**********\n#");
     for (i=1; i<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);        for(i=1; i<=nlstate;i++) 
       Ndum[ij]++;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        fprintf(ficresp, "\n");
       if (ij > cptcode) cptcode=ij;        
     }        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
     for (i=0; i<=cptcode; i++) {            fprintf(ficlog,"Total");
       if(Ndum[i]!=0) ncodemax[j]++;          }else{
     }            if(first==1){
     ij=1;              first=0;
               printf("See log file for details...\n");
             }
     for (i=1; i<=ncodemax[j]; i++) {            fprintf(ficlog,"Age %d", i);
       for (k=0; k<=19; k++) {          }
         if (Ndum[k] != 0) {          for(jk=1; jk <=nlstate ; jk++){
           nbcode[Tvar[j]][ij]=k;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                        pp[jk] += freq[jk][m][i]; 
           ij++;          }
         }          for(jk=1; jk <=nlstate ; jk++){
         if (ij > ncodemax[j]) break;            for(m=-1, pos=0; m <=0 ; m++)
       }                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]);
  for (k=0; k<19; k++) Ndum[k]=0;              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
  for (i=1; i<=ncovmodel-2; i++) {            }else{
    ij=Tvar[i];              if(first==1)
    Ndum[ij]++;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
  ij=1;          }
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){          for(jk=1; jk <=nlstate ; jk++){
      Tvaraff[ij]=i;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
      ij++;              pp[jk] += freq[jk][m][i];
    }          }       
  }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
  cptcoveff=ij-1;            posprop += prop[jk][i];
 }          }
           for(jk=1; jk <=nlstate ; jk++){
 /*********** Health Expectancies ****************/            if(pos>=1.e-5){
               if(first==1)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )                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)
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double age, agelim, hf;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double ***p3mat,***varhe;            }
   double **dnewm,**doldm;            if( i <= iagemax){
   double *xp;              if(pos>=1.e-5){
   double **gp, **gm;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double ***gradg, ***trgradg;                probs[i][jk][j1]= pp[jk]/pos;
   int theta;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);              else
   xp=vector(1,npar);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   dnewm=matrix(1,nlstate*2,1,npar);            }
   doldm=matrix(1,nlstate*2,1,nlstate*2);          }
            
   fprintf(ficreseij,"# Health expectancies\n");          for(jk=-1; jk <=nlstate+ndeath; jk++)
   fprintf(ficreseij,"# Age");            for(m=-1; m <=nlstate+ndeath; m++)
   for(i=1; i<=nlstate;i++)              if(freq[jk][m][i] !=0 ) {
     for(j=1; j<=nlstate;j++)              if(first==1)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficreseij,"\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
   if(estepm < stepm){          if(i <= iagemax)
     printf ("Problem %d lower than %d\n",estepm, stepm);            fprintf(ficresp,"\n");
   }          if(first==1)
   else  hstepm=estepm;              printf("Others in log...\n");
   /* We compute the life expectancy from trapezoids spaced every estepm months          fprintf(ficlog,"\n");
    * This is mainly to measure the difference between two models: for example        }
    * if stepm=24 months pijx are given only every 2 years and by summing them      }
    * we are calculating an estimate of the Life Expectancy assuming a linear    }
    * progression inbetween and thus overestimating or underestimating according    dateintmean=dateintsum/k2cpt; 
    * to the curvature of the survival function. If, for the same date, we   
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    fclose(ficresp);
    * to compare the new estimate of Life expectancy with the same linear    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    * hypothesis. A more precise result, taking into account a more precise    free_vector(pp,1,nlstate);
    * curvature will be obtained if estepm is as small as stepm. */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   /* For example we decided to compute the life expectancy with the smallest unit */  }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  
      nhstepm is the number of hstepm from age to agelim  /************ Prevalence ********************/
      nstepm is the number of stepm from age to agelin.  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)
      Look at hpijx to understand the reason of that which relies in memory size  {  
      and note for a fixed period like estepm months */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the       in each health status at the date of interview (if between dateprev1 and dateprev2).
      survival function given by stepm (the optimization length). Unfortunately it       We still use firstpass and lastpass as another selection.
      means that if the survival funtion is printed only each two years of age and if    */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same   
      results. So we changed our mind and took the option of the best precision.    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   */    double ***freq; /* Frequencies */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double *pp, **prop;
     double pos,posprop; 
   agelim=AGESUP;    double  y2; /* in fractional years */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int iagemin, iagemax;
     /* nhstepm age range expressed in number of stepm */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    iagemin= (int) agemin;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    iagemax= (int) agemax;
     /* if (stepm >= YEARM) hstepm=1;*/    /*pp=vector(1,nlstate);*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    j1=0;
     gp=matrix(0,nhstepm,1,nlstate*2);    
     gm=matrix(0,nhstepm,1,nlstate*2);    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    for(k1=1; k1<=j;k1++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
         
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
     /* Computing Variances of health expectancies */            prop[i][m]=0.0;
        
      for(theta=1; theta <=npar; theta++){        for (i=1; i<=imx; i++) { /* Each individual */
       for(i=1; i<=npar; i++){          bool=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          if  (cptcovn>0) {
       }            for (z1=1; z1<=cptcoveff; z1++) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
       cptj=0;          } 
       for(j=1; j<= nlstate; j++){          if (bool==1) { 
         for(i=1; i<=nlstate; i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           cptj=cptj+1;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                        /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                        prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(i=1; i<=npar; i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                }
                  } /* end selection of waves */
       cptj=0;          }
       for(j=1; j<= nlstate; j++){        }
         for(i=1;i<=nlstate;i++){        for(i=iagemin; i <= iagemax+3; i++){  
           cptj=cptj+1;          
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            posprop += prop[jk][i]; 
           }          } 
         }  
       }          for(jk=1; jk <=nlstate ; jk++){     
       for(j=1; j<= nlstate*2; j++)            if( i <=  iagemax){ 
         for(h=0; h<=nhstepm-1; h++){              if(posprop>=1.e-5){ 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                probs[i][jk][j1]= prop[jk][i]/posprop;
         }              } 
      }            } 
              }/* end jk */ 
 /* End theta */        }/* end i */ 
       } /* end i1 */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    } /* end k1 */
     
      for(h=0; h<=nhstepm-1; h++)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       for(j=1; j<=nlstate*2;j++)    /*free_vector(pp,1,nlstate);*/
         for(theta=1; theta <=npar; theta++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           trgradg[h][j][theta]=gradg[h][theta][j];  }  /* End of prevalence */
        
   /************* Waves Concatenation ***************/
      for(i=1;i<=nlstate*2;i++)  
       for(j=1;j<=nlstate*2;j++)  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)
         varhe[i][j][(int)age] =0.;  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      printf("%d|",(int)age);fflush(stdout);       Death is a valid wave (if date is known).
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      for(h=0;h<=nhstepm-1;h++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(k=0;k<=nhstepm-1;k++){       and mw[mi+1][i]. dh depends on stepm.
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);       */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)    int i, mi, m;
           for(j=1;j<=nlstate*2;j++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;       double sum=0., jmean=0.;*/
       }    int first;
     }    int j, k=0,jk, ju, jl;
     /* Computing expectancies */    double sum=0.;
     for(i=1; i<=nlstate;i++)    first=0;
       for(j=1; j<=nlstate;j++)    jmin=1e+5;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    jmax=-1;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    jmean=0.;
              for(i=1; i<=imx; i++){
 /* 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]);*/      mi=0;
       m=firstpass;
         }      while(s[m][i] <= nlstate){
         if(s[m][i]>=1)
     fprintf(ficreseij,"%3.0f",age );          mw[++mi][i]=m;
     cptj=0;        if(m >=lastpass)
     for(i=1; i<=nlstate;i++)          break;
       for(j=1; j<=nlstate;j++){        else
         cptj++;          m++;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      }/* end while */
       }      if (s[m][i] > nlstate){
     fprintf(ficreseij,"\n");        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     free_matrix(gm,0,nhstepm,1,nlstate*2);           /* Only death is a correct wave */
     free_matrix(gp,0,nhstepm,1,nlstate*2);        mw[mi][i]=m;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      }
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      wav[i]=mi;
   }      if(mi==0){
   printf("\n");        if(first==0){
   fprintf(ficlog,"\n");          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
   free_vector(xp,1,npar);        }
   free_matrix(dnewm,1,nlstate*2,1,npar);        if(first==1){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        }
 }      } /* end mi==0 */
     } /* End individuals */
 /************ Variance ******************/  
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)    for(i=1; i<=imx; i++){
 {      for(mi=1; mi<wav[i];mi++){
   /* Variance of health expectancies */        if (stepm <=0)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          dh[mi][i]=1;
   /* double **newm;*/        else{
   double **dnewm,**doldm;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   double **dnewmp,**doldmp;            if (agedc[i] < 2*AGESUP) {
   int i, j, nhstepm, hstepm, h, nstepm ;            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   int k, cptcode;            if(j==0) j=1;  /* Survives at least one month after exam */
   double *xp;            k=k+1;
   double **gp, **gm;  /* for var eij */            if (j >= jmax) jmax=j;
   double ***gradg, ***trgradg; /*for var eij */            if (j <= jmin) jmin=j;
   double **gradgp, **trgradgp; /* for var p point j */            sum=sum+j;
   double *gpp, *gmp; /* for var p point j */            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double ***p3mat;            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 age,agelim, hf;            }
   int theta;          }
   char digit[4];          else{
   char digitp[16];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   char fileresprobmorprev[FILENAMELENGTH];            k=k+1;
             if (j >= jmax) jmax=j;
   if(popbased==1)            else if (j <= jmin)jmin=j;
     strcpy(digitp,"-populbased-");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   else            /*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]);*/
     strcpy(digitp,"-stablbased-");            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;
   strcpy(fileresprobmorprev,"prmorprev");          }
   sprintf(digit,"%-d",ij);          jk= j/stepm;
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/          jl= j -jk*stepm;
   strcat(fileresprobmorprev,digit); /* Tvar to be done */          ju= j -(jk+1)*stepm;
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          if(mle <=1){ 
   strcat(fileresprobmorprev,fileres);            if(jl==0){
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {              dh[mi][i]=jk;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);              bh[mi][i]=0;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);            }else{ /* We want a negative bias in order to only have interpolation ie
   }                    * at the price of an extra matrix product in likelihood */
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              dh[mi][i]=jk+1;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);              bh[mi][i]=ju;
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");            }
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          }else{
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){            if(jl <= -ju){
     fprintf(ficresprobmorprev," p.%-d SE",j);              dh[mi][i]=jk;
     for(i=1; i<=nlstate;i++)              bh[mi][i]=jl;       /* bias is positive if real duration
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);                                   * is higher than the multiple of stepm and negative otherwise.
   }                                     */
   fprintf(ficresprobmorprev,"\n");            }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            else{
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              dh[mi][i]=jk+1;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);              bh[mi][i]=ju;
     exit(0);            }
   }            if(dh[mi][i]==0){
   else{              dh[mi][i]=1; /* At least one step */
     fprintf(ficgp,"\n# Routine varevsij");              bh[mi][i]=ju; /* At least one step */
   }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            }
     printf("Problem with html file: %s\n", optionfilehtm);          }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        } /* end if mle */
     exit(0);      } /* end wave */
   }    }
   else{    jmean=sum/k;
     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");    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);
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);   }
   
   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");  /*********** Tricode ****************************/
   fprintf(ficresvij,"# Age");  void tricode(int *Tvar, int **nbcode, int imx)
   for(i=1; i<=nlstate;i++)  {
     for(j=1; j<=nlstate;j++)    
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficresvij,"\n");    int cptcode=0;
     cptcoveff=0; 
   xp=vector(1,npar);   
   dnewm=matrix(1,nlstate,1,npar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   doldm=matrix(1,nlstate,1,nlstate);    for (k=1; k<=7; k++) ncodemax[k]=0;
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);  
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);                                 modality*/ 
   gpp=vector(nlstate+1,nlstate+ndeath);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   gmp=vector(nlstate+1,nlstate+ndeath);        Ndum[ij]++; /*store the modality */
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        /*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 
   if(estepm < stepm){                                         Tvar[j]. If V=sex and male is 0 and 
     printf ("Problem %d lower than %d\n",estepm, stepm);                                         female is 1, then  cptcode=1.*/
   }      }
   else  hstepm=estepm;    
   /* For example we decided to compute the life expectancy with the smallest unit */      for (i=0; i<=cptcode; i++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is 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 */
      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      ij=1; 
      and note for a fixed period like k years */      for (i=1; i<=ncodemax[j]; i++) {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for (k=0; k<= maxncov; k++) {
      survival function given by stepm (the optimization length). Unfortunately it          if (Ndum[k] != 0) {
      means that if the survival funtion is printed only each two years of age and if            nbcode[Tvar[j]][ij]=k; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            /* 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; */
      results. So we changed our mind and took the option of the best precision.            
   */            ij++;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          }
   agelim = AGESUP;          if (ij > ncodemax[j]) break; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    }  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
     for(theta=1; theta <=npar; theta++){     Ndum[ij]++;
       for(i=1; i<=npar; i++){ /* Computes gradient */   }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }   ij=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     for (i=1; i<= maxncov; i++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
       if (popbased==1) {       ij++;
         for(i=1; i<=nlstate;i++)     }
           prlim[i][i]=probs[(int)age][i][ij];   }
       }   
     cptcoveff=ij-1; /*Number of simple covariates*/
       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];  
         }  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 )
       }  
       /* This for computing forces of mortality (h=1)as a weighted average */  {
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    /* Health expectancies */
         for(i=1; i<= nlstate; i++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    double age, agelim, hf;
       }        double ***p3mat,***varhe;
       /* end force of mortality */    double **dnewm,**doldm;
     double *xp;
       for(i=1; i<=npar; i++) /* Computes gradient */    double **gp, **gm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double ***gradg, ***trgradg;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int theta;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       if (popbased==1) {    xp=vector(1,npar);
         for(i=1; i<=nlstate;i++)    dnewm=matrix(1,nlstate*nlstate,1,npar);
           prlim[i][i]=probs[(int)age][i][ij];    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       }    
     fprintf(ficreseij,"# Health expectancies\n");
       for(j=1; j<= nlstate; j++){    fprintf(ficreseij,"# Age");
         for(h=0; h<=nhstepm; h++){    for(i=1; i<=nlstate;i++)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(j=1; j<=nlstate;j++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        fprintf(ficreseij," %1d-%1d (SE)",i,j);
         }    fprintf(ficreseij,"\n");
       }  
       /* This for computing force of mortality (h=1)as a weighted average */    if(estepm < stepm){
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(i=1; i<= nlstate; i++)    }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];    else  hstepm=estepm;   
       }        /* We compute the life expectancy from trapezoids spaced every estepm months
       /* end force of mortality */     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
       for(j=1; j<= nlstate; j++) /* vareij */     * we are calculating an estimate of the Life Expectancy assuming a linear 
         for(h=0; h<=nhstepm; h++){     * progression in between and thus overestimating or underestimating according
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     * to the curvature of the survival function. If, for the same date, we 
         }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */     * to compare the new estimate of Life expectancy with the same linear 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];     * hypothesis. A more precise result, taking into account a more precise
       }     * curvature will be obtained if estepm is as small as stepm. */
   
     } /* End theta */    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
     for(h=0; h<=nhstepm; h++) /* veij */       Look at hpijx to understand the reason of that which relies in memory size
       for(j=1; j<=nlstate;j++)       and note for a fixed period like estepm months */
         for(theta=1; theta <=npar; theta++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           trgradg[h][j][theta]=gradg[h][theta][j];       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(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for(theta=1; theta <=npar; theta++)       results. So we changed our mind and took the option of the best precision.
         trgradgp[j][theta]=gradgp[theta][j];    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)    agelim=AGESUP;
       for(j=1;j<=nlstate;j++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         vareij[i][j][(int)age] =0.;      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     for(h=0;h<=nhstepm;h++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(k=0;k<=nhstepm;k++){      /* if (stepm >= YEARM) hstepm=1;*/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(i=1;i<=nlstate;i++)      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           for(j=1;j<=nlstate;j++)      gp=matrix(0,nhstepm,1,nlstate*nlstate);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       }  
     }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     /* pptj */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     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(j=nlstate+1;j<=nlstate+ndeath;j++)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=nlstate+1;i<=nlstate+ndeath;i++)  
         varppt[j][i]=doldmp[j][i];      /* Computing Variances of health expectancies */
     /* end ppptj */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);         for(theta=1; theta <=npar; theta++){
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
     if (popbased==1) {        }
       for(i=1; i<=nlstate;i++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prlim[i][i]=probs[(int)age][i][ij];    
     }        cptj=0;
            for(j=1; j<= nlstate; j++){
     /* This for computing force of mortality (h=1)as a weighted average */          for(i=1; i<=nlstate; i++){
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            cptj=cptj+1;
       for(i=1; i<= nlstate; i++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         gmp[j] += prlim[i][i]*p3mat[i][j][1];              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     }                }
     /* end force of mortality */          }
         }
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);       
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){       
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        for(i=1; i<=npar; i++) 
       for(i=1; i<=nlstate;i++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        
     }        cptj=0;
     fprintf(ficresprobmorprev,"\n");        for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
     fprintf(ficresvij,"%.0f ",age );            cptj=cptj+1;
     for(i=1; i<=nlstate;i++)            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       }            }
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);        }
     free_matrix(gm,0,nhstepm,1,nlstate);        for(j=1; j<= nlstate*nlstate; j++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          for(h=0; h<=nhstepm-1; h++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   } /* End age */       } 
   free_vector(gpp,nlstate+1,nlstate+ndeath);     
   free_vector(gmp,nlstate+1,nlstate+ndeath);  /* End theta */
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");  
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */       for(h=0; h<=nhstepm-1; h++)
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");        for(j=1; j<=nlstate*nlstate;j++)
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);          for(theta=1; theta <=npar; theta++)
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);            trgradg[h][j][theta]=gradg[h][theta][j];
   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);  
   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);       for(i=1;i<=nlstate*nlstate;i++)
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,nlstate);       printf("%d|",(int)age);fflush(stdout);
   free_matrix(dnewm,1,nlstate,1,npar);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);       for(h=0;h<=nhstepm-1;h++){
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);        for(k=0;k<=nhstepm-1;k++){
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   fclose(ficresprobmorprev);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   fclose(ficgp);          for(i=1;i<=nlstate*nlstate;i++)
   fclose(fichtm);            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 }        }
       }
 /************ Variance of prevlim ******************/      /* Computing expectancies */
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      for(i=1; i<=nlstate;i++)
 {        for(j=1; j<=nlstate;j++)
   /* Variance of prevalence limit */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   double **newm;            
   double **dnewm,**doldm;  /* 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]);*/
   int i, j, nhstepm, hstepm;  
   int k, cptcode;          }
   double *xp;  
   double *gp, *gm;      fprintf(ficreseij,"%3.0f",age );
   double **gradg, **trgradg;      cptj=0;
   double age,agelim;      for(i=1; i<=nlstate;i++)
   int theta;        for(j=1; j<=nlstate;j++){
              cptj++;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   fprintf(ficresvpl,"# Age");        }
   for(i=1; i<=nlstate;i++)      fprintf(ficreseij,"\n");
       fprintf(ficresvpl," %1d-%1d",i,i);     
   fprintf(ficresvpl,"\n");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   xp=vector(1,npar);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   dnewm=matrix(1,nlstate,1,npar);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }
   hstepm=1*YEARM; /* Every year of age */    printf("\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    fprintf(ficlog,"\n");
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_vector(xp,1,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     if (stepm >= YEARM) hstepm=1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     gradg=matrix(1,npar,1,nlstate);  }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* Variance of health expectancies */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       }    /* double **newm;*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double **dnewm,**doldm;
       for(i=1;i<=nlstate;i++)    double **dnewmp,**doldmp;
         gp[i] = prlim[i][i];    int i, j, nhstepm, hstepm, h, nstepm ;
        int k, cptcode;
       for(i=1; i<=npar; i++) /* Computes gradient */    double *xp;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **gp, **gm;  /* for var eij */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double ***gradg, ***trgradg; /*for var eij */
       for(i=1;i<=nlstate;i++)    double **gradgp, **trgradgp; /* for var p point j */
         gm[i] = prlim[i][i];    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       for(i=1;i<=nlstate;i++)    double ***p3mat;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double age,agelim, hf;
     } /* End theta */    double ***mobaverage;
     int theta;
     trgradg =matrix(1,nlstate,1,npar);    char digit[4];
     char digitp[25];
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)    char fileresprobmorprev[FILENAMELENGTH];
         trgradg[j][theta]=gradg[theta][j];  
     if(popbased==1){
     for(i=1;i<=nlstate;i++)      if(mobilav!=0)
       varpl[i][(int)age] =0.;        strcpy(digitp,"-populbased-mobilav-");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      else strcpy(digitp,"-populbased-nomobil-");
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    }
     for(i=1;i<=nlstate;i++)    else 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      strcpy(digitp,"-stablbased-");
   
     fprintf(ficresvpl,"%.0f ",age );    if (mobilav!=0) {
     for(i=1; i<=nlstate;i++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     fprintf(ficresvpl,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     free_vector(gp,1,nlstate);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     free_vector(gm,1,nlstate);      }
     free_matrix(gradg,1,npar,1,nlstate);    }
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   free_vector(xp,1,npar);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   free_matrix(doldm,1,nlstate,1,npar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   free_matrix(dnewm,1,nlstate,1,nlstate);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
 }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
 /************ Variance of one-step probabilities  ******************/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    }
 {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   int i, j=0,  i1, k1, l1, t, tj;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   int k2, l2, j1,  z1;    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);
   int k=0,l, cptcode;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   int first=1, first1;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      fprintf(ficresprobmorprev," p.%-d SE",j);
   double **dnewm,**doldm;      for(i=1; i<=nlstate;i++)
   double *xp;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   double *gp, *gm;    }  
   double **gradg, **trgradg;    fprintf(ficresprobmorprev,"\n");
   double **mu;    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   double age,agelim, cov[NCOVMAX];      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   int theta;      exit(0);
   char fileresprob[FILENAMELENGTH];    }
   char fileresprobcov[FILENAMELENGTH];    else{
   char fileresprobcor[FILENAMELENGTH];      fprintf(ficgp,"\n# Routine varevsij");
     }
   double ***varpij;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
       printf("Problem with html file: %s\n", optionfilehtm);
   strcpy(fileresprob,"prob");      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
   strcat(fileresprob,fileres);      exit(0);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprob);    else{
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   }      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   strcpy(fileresprobcov,"probcov");    }
   strcat(fileresprobcov,fileres);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcov);    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(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   strcpy(fileresprobcor,"probcor");      for(j=1; j<=nlstate;j++)
   strcat(fileresprobcor,fileres);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    fprintf(ficresvij,"\n");
     printf("Problem with resultfile: %s\n", fileresprobcor);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate,1,npar);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    doldm=matrix(1,nlstate,1,nlstate);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   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);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficresprob,"# Age");    
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    if(estepm < stepm){
   fprintf(ficresprobcov,"# Age");      printf ("Problem %d lower than %d\n",estepm, stepm);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    }
   fprintf(ficresprobcov,"# Age");    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   for(i=1; i<=nlstate;i++)       nhstepm is the number of hstepm from age to agelim 
     for(j=1; j<=(nlstate+ndeath);j++){       nstepm is the number of stepm from age to agelin. 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficresprobcov," p%1d-%1d ",i,j);       and note for a fixed period like k years */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     }         survival function given by stepm (the optimization length). Unfortunately it
   fprintf(ficresprob,"\n");       means that if the survival funtion is printed every two years of age and if
   fprintf(ficresprobcov,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fprintf(ficresprobcor,"\n");       results. So we changed our mind and took the option of the best precision.
   xp=vector(1,npar);    */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    agelim = AGESUP;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   first=1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);      gp=matrix(0,nhstepm,1,nlstate);
     exit(0);      gm=matrix(0,nhstepm,1,nlstate);
   }  
   else{  
     fprintf(ficgp,"\n# Routine varprob");      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("Problem with html file: %s\n", optionfilehtm);        }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     exit(0);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }  
   else{        if (popbased==1) {
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");          if(mobilav ==0){
     fprintf(fichtm,"\n");            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");          }else{ /* mobilav */ 
     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(i=1; i<=nlstate;i++)
     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");              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   }        }
     
          for(j=1; j<= nlstate; j++){
   cov[1]=1;          for(h=0; h<=nhstepm; h++){
   tj=cptcoveff;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   j1=0;          }
   for(t=1; t<=tj;t++){        }
     for(i1=1; i1<=ncodemax[t];i1++){        /* This for computing probability of death (h=1 means
       j1++;           computed over hstepm matrices product = hstepm*stepm months) 
                 as a weighted average of prlim.
       if  (cptcovn>0) {        */
         fprintf(ficresprob, "\n#********** Variable ");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         fprintf(ficresprob, "**********\n#");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(ficresprobcov, "\n#********** Variable ");        }    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        /* end probability of death */
         fprintf(ficresprobcov, "**********\n#");  
                for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         fprintf(ficgp, "\n#********** Variable ");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficgp, "**********\n#");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           
                if (popbased==1) {
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          if(mobilav ==0){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for(i=1; i<=nlstate;i++)
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");              prlim[i][i]=probs[(int)age][i][ij];
                  }else{ /* mobilav */ 
         fprintf(ficresprobcor, "\n#********** Variable ");                for(i=1; i<=nlstate;i++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficgp, "**********\n#");              }
       }        }
        
       for (age=bage; age<=fage; age ++){        for(j=1; j<= nlstate; j++){
         cov[2]=age;          for(h=0; h<=nhstepm; h++){
         for (k=1; k<=cptcovn;k++) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        }
         for (k=1; k<=cptcovprod;k++)        /* This for computing probability of death (h=1 means
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];           computed over hstepm matrices product = hstepm*stepm months) 
                   as a weighted average of prlim.
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));        */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         gp=vector(1,(nlstate)*(nlstate+ndeath));          for(i=1,gmp[j]=0.; i<= nlstate; i++)
         gm=vector(1,(nlstate)*(nlstate+ndeath));           gmp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
         for(theta=1; theta <=npar; theta++){        /* end probability of death */
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(j=1; j<= nlstate; j++) /* vareij */
                    for(h=0; h<=nhstepm; h++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                    }
           k=0;  
           for(i=1; i<= (nlstate); i++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
             for(j=1; j<=(nlstate+ndeath);j++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
               k=k+1;        }
               gp[k]=pmmij[i][j];  
             }      } /* End theta */
           }  
                trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(h=0; h<=nhstepm; h++) /* veij */
            for(j=1; j<=nlstate;j++)
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          for(theta=1; theta <=npar; theta++)
           k=0;            trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
               k=k+1;        for(theta=1; theta <=npar; theta++)
               gm[k]=pmmij[i][j];          trgradgp[j][theta]=gradgp[theta][j];
             }    
           }  
            hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)      for(i=1;i<=nlstate;i++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          for(j=1;j<=nlstate;j++)
         }          vareij[i][j][(int)age] =0.;
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      for(h=0;h<=nhstepm;h++){
           for(theta=1; theta <=npar; theta++)        for(k=0;k<=nhstepm;k++){
             trgradg[j][theta]=gradg[theta][j];          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                  matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          for(i=1;i<=nlstate;i++)
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);            for(j=1;j<=nlstate;j++)
                      vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         pmij(pmmij,cov,ncovmodel,x,nlstate);        }
              }
         k=0;    
         for(i=1; i<=(nlstate); i++){      /* pptj */
           for(j=1; j<=(nlstate+ndeath);j++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
             k=k+1;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             mu[k][(int) age]=pmmij[i][j];      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)      /* end ppptj */
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      /*  x centered again */
             varpij[i][j][(int)age] = doldm[i][j];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         /*printf("\n%d ",(int)age);   
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      if (popbased==1) {
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        if(mobilav ==0){
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          for(i=1; i<=nlstate;i++)
      }*/            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
         fprintf(ficresprob,"\n%d ",(int)age);          for(i=1; i<=nlstate;i++)
         fprintf(ficresprobcov,"\n%d ",(int)age);            prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficresprobcor,"\n%d ",(int)age);        }
       }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)               
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      /* This for computing probability of death (h=1 means
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);         as a weighted average of prlim.
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      */
         }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         i=0;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         for (k=1; k<=(nlstate);k++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           for (l=1; l<=(nlstate+ndeath);l++){      }    
             i=i++;      /* end probability of death */
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
             for (j=1; j<=i;j++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        for(i=1; i<=nlstate;i++){
             }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           }        }
         }/* end of loop for state */      } 
       } /* end of loop for age */      fprintf(ficresprobmorprev,"\n");
   
       /* Confidence intervalle of pij  */      fprintf(ficresvij,"%.0f ",age );
       /*      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\nset noparametric;unset label");        for(j=1; j<=nlstate;j++){
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        }
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);      fprintf(ficresvij,"\n");
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);      free_matrix(gp,0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       */      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    } /* End age */
       first1=1;    free_vector(gpp,nlstate+1,nlstate+ndeath);
       for (k1=1; k1<=(nlstate);k1++){    free_vector(gmp,nlstate+1,nlstate+ndeath);
         for (l1=1; l1<=(nlstate+ndeath);l1++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           if(l1==k1) continue;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           i=(k1-1)*(nlstate+ndeath)+l1;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           for (k2=1; k2<=(nlstate);k2++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             for (l2=1; l2<=(nlstate+ndeath);l2++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
               if(l2==k2) continue;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
               j=(k2-1)*(nlstate+ndeath)+l2;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
               if(j<=i) continue;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
               for (age=bage; age<=fage; age ++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
                 if ((int)age %5==0){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    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);
                   mu1=mu[i][(int) age]/stepm*YEARM ;    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
                   mu2=mu[j][(int) age]/stepm*YEARM;  */
                   /* Computing eigen value of matrix of covariance */    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));  
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    free_vector(xp,1,npar);
                   if(first1==1){    free_matrix(doldm,1,nlstate,1,nlstate);
                     first1=0;    free_matrix(dnewm,1,nlstate,1,npar);
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   /* Eigen vectors */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    fclose(ficresprobmorprev);
                   v21=sqrt(1.-v11*v11);    fclose(ficgp);
                   v12=-v21;    fclose(fichtm);
                   v22=v11;  }  
                   /*printf(fignu*/  
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  /************ Variance of prevlim ******************/
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */  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(first==1){  {
                     first=0;    /* Variance of prevalence limit */
                     fprintf(ficgp,"\nset parametric;set nolabel");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);    double **newm;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    double **dnewm,**doldm;
                     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>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);    int i, j, nhstepm, hstepm;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    int k, cptcode;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    double *xp;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    double *gp, *gm;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double **gradg, **trgradg;
                     /*              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    double age,agelim;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    int theta;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);     
                     */    fprintf(ficresvpl,"# Standard deviation of stable prevalences \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",\    fprintf(ficresvpl,"# Age");
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    for(i=1; i<=nlstate;i++)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));        fprintf(ficresvpl," %1d-%1d",i,i);
                   }else{    fprintf(ficresvpl,"\n");
                     first=0;  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    xp=vector(1,npar);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    dnewm=matrix(1,nlstate,1,npar);
                     /*    doldm=matrix(1,nlstate,1,nlstate);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    hstepm=1*YEARM; /* Every year of age */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                     */    agelim = AGESUP;
                     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",\    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      if (stepm >= YEARM) hstepm=1;
                   }/* if first */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                 } /* age mod 5 */      gradg=matrix(1,npar,1,nlstate);
               } /* end loop age */      gp=vector(1,nlstate);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);      gm=vector(1,nlstate);
               first=1;  
             } /*l12 */      for(theta=1; theta <=npar; theta++){
           } /* k12 */        for(i=1; i<=npar; i++){ /* Computes gradient */
         } /*l1 */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }/* k1 */        }
     } /* loop covariates */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        for(i=1;i<=nlstate;i++)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          gp[i] = prlim[i][i];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        for(i=1; i<=npar; i++) /* Computes gradient */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }        for(i=1;i<=nlstate;i++)
   free_vector(xp,1,npar);          gm[i] = prlim[i][i];
   fclose(ficresprob);  
   fclose(ficresprobcov);        for(i=1;i<=nlstate;i++)
   fclose(ficresprobcor);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   fclose(ficgp);      } /* End theta */
   fclose(fichtm);  
 }      trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
 /******************* Printing html file ***********/        for(theta=1; theta <=npar; theta++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          trgradg[j][theta]=gradg[theta][j];
                   int lastpass, int stepm, int weightopt, char model[],\  
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      for(i=1;i<=nlstate;i++)
                   int popforecast, int estepm ,\        varpl[i][(int)age] =0.;
                   double jprev1, double mprev1,double anprev1, \      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   double jprev2, double mprev2,double anprev2){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   int jj1, k1, i1, cpt;      for(i=1;i<=nlstate;i++)
   /*char optionfilehtm[FILENAMELENGTH];*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);      fprintf(ficresvpl,"%.0f ",age );
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      free_vector(gp,1,nlstate);
  - 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(gm,1,nlstate);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n      free_matrix(gradg,1,npar,1,nlstate);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      free_matrix(trgradg,1,nlstate,1,npar);
  - Life expectancies by age and initial health status (estepm=%2d months):    } /* End age */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    free_matrix(dnewm,1,nlstate,1,nlstate);
   
  m=cptcoveff;  }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   /************ Variance of one-step probabilities  ******************/
  jj1=0;  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(k1=1; k1<=m;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    int i, j=0,  i1, k1, l1, t, tj;
      jj1++;    int k2, l2, j1,  z1;
      if (cptcovn > 0) {    int k=0,l, cptcode;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int first=1, first1;
        for (cpt=1; cpt<=cptcoveff;cpt++)    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double **dnewm,**doldm;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double *xp;
      }    double *gp, *gm;
      /* Pij */    double **gradg, **trgradg;
      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 **mu;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double age,agelim, cov[NCOVMAX];
      /* Quasi-incidences */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      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>    int theta;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    char fileresprob[FILENAMELENGTH];
        /* Stable prevalence in each health state */    char fileresprobcov[FILENAMELENGTH];
        for(cpt=1; cpt<nlstate;cpt++){    char fileresprobcor[FILENAMELENGTH];
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>  
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double ***varpij;
        }  
      for(cpt=1; cpt<=nlstate;cpt++) {    strcpy(fileresprob,"prob"); 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    strcat(fileresprob,fileres);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      }      printf("Problem with resultfile: %s\n", fileresprob);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 health expectancies in states (1) and (2): e%s%d.png<br>    }
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    strcpy(fileresprobcov,"probcov"); 
    } /* end i1 */    strcat(fileresprobcov,fileres);
  }/* End k1 */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
  fprintf(fichtm,"</ul>");      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    strcpy(fileresprobcor,"probcor"); 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    strcat(fileresprobcor,fileres);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n      printf("Problem with resultfile: %s\n", fileresprobcor);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      fprintf(ficlog,"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    }
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  - 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);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
  if(popforecast==1) fprintf(fichtm,"\n    fprintf(ficlog,"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    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         <br>",fileres,fileres,fileres,fileres);    
  else    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    fprintf(ficresprob,"# Age");
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
  m=cptcoveff;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(ficresprobcov,"# Age");
   
  jj1=0;  
  for(k1=1; k1<=m;k1++){    for(i=1; i<=nlstate;i++)
    for(i1=1; i1<=ncodemax[k1];i1++){      for(j=1; j<=(nlstate+ndeath);j++){
      jj1++;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
      if (cptcovn > 0) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        for (cpt=1; cpt<=cptcoveff;cpt++)      }  
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);   /* fprintf(ficresprob,"\n");
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficresprobcov,"\n");
      }    fprintf(ficresprobcor,"\n");
      for(cpt=1; cpt<=nlstate;cpt++) {   */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident   xp=vector(1,npar);
 interval) in state (%d): v%s%d%d.png <br>    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
    } /* end i1 */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  }/* End k1 */    first=1;
  fprintf(fichtm,"</ul>");    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 fclose(fichtm);      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 }      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
 /******************* Gnuplot file **************/    }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    else{
       fprintf(ficgp,"\n# Routine varprob");
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    }
   int ng;    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      printf("Problem with html file: %s\n", optionfilehtm);
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);      exit(0);
   }    }
     else{
 #ifdef windows      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(ficgp,"cd \"%s\" \n",pathc);      fprintf(fichtm,"\n");
 #endif  
 m=pow(2,cptcoveff);      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");
  /* 1eme*/      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 (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    }
   
 #ifdef windows    cov[1]=1;
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    tj=cptcoveff;
      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);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 #endif    j1=0;
 #ifdef unix    for(t=1; t<=tj;t++){
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      for(i1=1; i1<=ncodemax[t];i1++){ 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        j1++;
 #endif        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
 for (i=1; i<= nlstate ; i ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresprob, "**********\n#\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresprobcov, "\n#********** Variable "); 
 }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficresprobcov, "**********\n#\n");
     for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficgp, "\n#********** Variable "); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }          fprintf(ficgp, "**********\n#\n");
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          
      for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }            fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          
 #ifdef unix          fprintf(ficresprobcor, "\n#********** Variable ");    
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficresprobcor, "**********\n#");    
    }        }
   }        
   /*2 eme*/        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   for (k1=1; k1<= m ; k1 ++) {          for (k=1; k<=cptcovn;k++) {
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          }
              for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1; i<= nlstate+1 ; i ++) {          for (k=1; k<=cptcovprod;k++)
       k=2*i;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          
       for (j=1; j<= nlstate+1 ; j ++) {          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          gp=vector(1,(nlstate)*(nlstate+ndeath));
 }            gm=vector(1,(nlstate)*(nlstate+ndeath));
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(theta=1; theta <=npar; theta++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(i=1; i<=npar; i++)
       for (j=1; j<= nlstate+1 ; j ++) {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            
         else fprintf(ficgp," \%%*lf (\%%*lf)");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
 }              
       fprintf(ficgp,"\" t\"\" w l 0,");            k=0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(i=1; i<= (nlstate); i++){
       for (j=1; j<= nlstate+1 ; j ++) {              for(j=1; j<=(nlstate+ndeath);j++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                k=k+1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                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);
             k=0;
   for (k1=1; k1<= m ; k1 ++) {            for(i=1; i<=(nlstate); i++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {              for(j=1; j<=(nlstate+ndeath);j++){
       k=2+nlstate*(2*cpt-2);                k=k+1;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                gm[k]=pmmij[i][j];
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);              }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");       
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 */            for(theta=1; theta <=npar; theta++)
       for (i=1; i< nlstate ; i ++) {              trgradg[j][theta]=gradg[theta][j];
         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);          
           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));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   /* CV preval stat */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {          pmij(pmmij,cov,ncovmodel,x,nlstate);
       k=3;          
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          k=0;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
       for (i=1; i< nlstate ; i ++)              k=k+1;
         fprintf(ficgp,"+$%d",k+i+1);              mu[k][(int) age]=pmmij[i][j];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            }
                }
       l=3+(nlstate+ndeath)*cpt;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       for (i=1; i< nlstate ; i ++) {              varpij[i][j][(int)age] = doldm[i][j];
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);          /*printf("\n%d ",(int)age);
       }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              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 */          fprintf(ficresprob,"\n%d ",(int)age);
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprobcov,"\n%d ",(int)age);
     for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficresprobcor,"\n%d ",(int)age);
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           jk++;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           fprintf(ficgp,"\n");            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 (l=1; l<=(nlstate+ndeath);l++){ 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/              i=i++;
      for(jk=1; jk <=m; jk++) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
        if (ng==2)              for (j=1; j<=i;j++){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
        else                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
          fprintf(ficgp,"\nset title \"Probability\"\n");              }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            }
        i=1;          }/* end of loop for state */
        for(k2=1; k2<=nlstate; k2++) {        } /* end of loop for age */
          k3=i;  
          for(k=1; k<=(nlstate+ndeath); k++) {        /* Confidence intervalle of pij  */
            if (k != k2){        /*
              if(ng==2)          fprintf(ficgp,"\nset noparametric;unset label");
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
              else          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                fprintf(ficgp," exp(p%d+p%d*x",i,i+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);
              ij=1;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
              for(j=3; j <=ncovmodel; j++) {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        */
                  ij++;  
                }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                else        first1=1;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for (k2=1; k2<=(nlstate);k2++){
              }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              fprintf(ficgp,")/(1");            if(l2==k2) continue;
                          j=(k2-1)*(nlstate+ndeath)+l2;
              for(k1=1; k1 <=nlstate; k1++){              for (k1=1; k1<=(nlstate);k1++){
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                ij=1;                if(l1==k1) continue;
                for(j=3; j <=ncovmodel; j++){                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                if(i<=j) continue;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                for (age=bage; age<=fage; age ++){ 
                    ij++;                  if ((int)age %5==0){
                  }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                  else                    v2=varpij[j][j][(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]]);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                fprintf(ficgp,")");                    mu2=mu[j][(int) age]/stepm*YEARM;
              }                    c12=cv12/sqrt(v1*v2);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    /* Computing eigen value of matrix of covariance */
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
              i=i+ncovmodel;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
            }                    /* Eigen vectors */
          } /* end k */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
        } /* end k2 */                    /*v21=sqrt(1.-v11*v11); *//* error */
      } /* end jk */                    v21=(lc1-v1)/cv12*v11;
    } /* end ng */                    v12=-v21;
    fclose(ficgp);                    v22=v11;
 }  /* end gnuplot */                    tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
 /*************** Moving average **************/                      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);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                    }
                     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);
   int i, cpt, cptcod;                    /*printf(fignu*/
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       for (i=1; i<=nlstate;i++)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                    if(first==1){
           mobaverage[(int)agedeb][i][cptcod]=0.;                      first=0;
                          fprintf(ficgp,"\nset parametric;unset label");
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                      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 (i=1; i<=nlstate;i++){                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                      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);
           for (cpt=0;cpt<=4;cpt++){                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",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> Correlation at age %d (%.3f),",(int) age, c12);
           }                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                      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;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
 /************** Forecasting ******************/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
 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,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   int *popage;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                    }/* if first */
   double *popeffectif,*popcount;                  } /* age mod 5 */
   double ***p3mat;                } /* end loop age */
   char fileresf[FILENAMELENGTH];                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
  agelim=AGESUP;              } /*l12 */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            } /* k12 */
           } /*l1 */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }/* k1 */
        } /* loop covariates */
      }
   strcpy(fileresf,"f");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   strcat(fileresf,fileres);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    free_vector(xp,1,npar);
     printf("Problem with forecast resultfile: %s\n", fileresf);    fclose(ficresprob);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    fclose(ficresprobcov);
   }    fclose(ficresprobcor);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fclose(ficgp);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    fclose(fichtm);
   }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   
   if (mobilav==1) {  /******************* Printing html file ***********/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     movingaverage(agedeb, fage, ageminpar, mobaverage);                    int lastpass, int stepm, int weightopt, char model[],\
   }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    double jprev1, double mprev1,double anprev1, \
   if (stepm<=12) stepsize=1;                    double jprev2, double mprev2,double anprev2){
      int jj1, k1, i1, cpt;
   agelim=AGESUP;    /*char optionfilehtm[FILENAMELENGTH];*/
      if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   hstepm=1;      printf("Problem with %s \n",optionfilehtm), exit(0);
   hstepm=hstepm/stepm;      fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   yp1=modf(dateintmean,&yp);    }
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   mprojmean=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
   yp1=modf((yp2*30.5),&yp);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
   jprojmean=yp;   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   if(jprojmean==0) jprojmean=1;   - Life expectancies by age and initial health status (estepm=%2d months): 
   if(mprojmean==0) jprojmean=1;     <a href=\"e%s\">e%s</a> <br>\n</li>", \
      jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   m=cptcoveff;
       k=k+1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {   jj1=0;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   for(k1=1; k1<=m;k1++){
       }     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresf,"******\n");       jj1++;
       fprintf(ficresf,"# StartingAge FinalAge");       if (cptcovn > 0) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               for (cpt=1; cpt<=cptcoveff;cpt++) 
                 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         fprintf(ficresf,"\n");       }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       /* Quasi-incidences */
           nhstepm = nhstepm/hstepm;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
            <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         /* Stable prevalence in each health state */
           oldm=oldms;savm=savms;         for(cpt=1; cpt<nlstate;cpt++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
          <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           for (h=0; h<=nhstepm; h++){         }
             if (h==(int) (calagedate+YEARM*cpt)) {       for(cpt=1; cpt<=nlstate;cpt++) {
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
             }  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
             for(j=1; j<=nlstate+ndeath;j++) {       }
               kk1=0.;kk2=0;       fprintf(fichtm,"\n<br>- Total life expectancy by age and
               for(i=1; i<=nlstate;i++) {                health expectancies in states (1) and (2): e%s%d.png<br>
                 if (mobilav==1)  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     } /* end i1 */
                 else {   }/* End k1 */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   fprintf(fichtm,"</ul>");
                 }  
                  
               }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
               if (h==(int)(calagedate+12*cpt)){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
                 fprintf(ficresf," %.3f", kk1);   - 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 
           }   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - 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 */
          /*      <br>",fileres,fileres,fileres,fileres); */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*  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); */
   fclose(ficresf);  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 }  
 /************** Forecasting ******************/   m=cptcoveff;
 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){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   jj1=0;
   int *popage;   for(k1=1; k1<=m;k1++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;     for(i1=1; i1<=ncodemax[k1];i1++){
   double *popeffectif,*popcount;       jj1++;
   double ***p3mat,***tabpop,***tabpopprev;       if (cptcovn > 0) {
   char filerespop[FILENAMELENGTH];         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   agelim=AGESUP;       }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  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");     } /* end i1 */
   strcat(filerespop,fileres);   }/* End k1 */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   fprintf(fichtm,"</ul>");
     printf("Problem with forecast resultfile: %s\n", filerespop);  fclose(fichtm);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  }
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);  /******************* Gnuplot file **************/
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  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;
     int ng;
   if (mobilav==1) {    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with file %s",optionfilegnuplot);
     movingaverage(agedeb, fage, ageminpar, mobaverage);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
   }    }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*#ifdef windows */
   if (stepm<=12) stepsize=1;      fprintf(ficgp,"cd \"%s\" \n",pathc);
        /*#endif */
   agelim=AGESUP;  m=pow(2,cptcoveff);
      
   hstepm=1;   /* 1eme*/
   hstepm=hstepm/stepm;    for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) {
   if (popforecast==1) {       fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
     if((ficpop=fopen(popfile,"r"))==NULL) {       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);
       printf("Problem with population file : %s\n",popfile);exit(0);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);       for (i=1; i<= nlstate ; i ++) {
     }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     popage=ivector(0,AGESUP);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     popeffectif=vector(0,AGESUP);       }
     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);
           for (i=1; i<= nlstate ; i ++) {
     i=1;           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
           } 
     imx=i;       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   for(cptcov=1;cptcov<=i2;cptcov++){       }  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
       k=k+1;     }
       fprintf(ficrespop,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    /*2 eme*/
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       }    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficrespop,"******\n");      fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficrespop,"# Age");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      
       if (popforecast==1)  fprintf(ficrespop," [Population]");      for (i=1; i<= nlstate+1 ; i ++) {
              k=2*i;
       for (cpt=0; cpt<=0;cpt++) {        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for (j=1; j<= nlstate+1 ; j ++) {
                  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          else fprintf(ficgp," \%%*lf (\%%*lf)");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }   
           nhstepm = nhstepm/hstepm;        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                  else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
           oldm=oldms;savm=savms;        for (j=1; j<= nlstate+1 ; j ++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                  else fprintf(ficgp," \%%*lf (\%%*lf)");
           for (h=0; h<=nhstepm; h++){        }   
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficgp,"\" t\"\" w l 0,");
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
             }        for (j=1; j<= nlstate+1 ; j ++) {
             for(j=1; j<=nlstate+ndeath;j++) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
               kk1=0.;kk2=0;          else fprintf(ficgp," \%%*lf (\%%*lf)");
               for(i=1; i<=nlstate;i++) {                      }   
                 if (mobilav==1)        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        else fprintf(ficgp,"\" t\"\" w l 0,");
                 else {      }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    }
                 }    
               }    /*3eme*/
               if (h==(int)(calagedate+12*cpt)){    
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    for (k1=1; k1<= m ; k1 ++) { 
                   /*fprintf(ficrespop," %.3f", kk1);      for (cpt=1; cpt<= nlstate ; cpt ++) {
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        k=2+nlstate*(2*cpt-2);
               }        fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
             }        fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
             for(i=1; i<=nlstate;i++){        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
               kk1=0.;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                 for(j=1; j<=nlstate;j++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                 }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             }          
         */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        for (i=1; i< nlstate ; i ++) {
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          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 (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      for (cpt=1; cpt<=nlstate ; cpt ++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          k=3;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
           nhstepm = nhstepm/hstepm;        
                  for (i=1; i<= nlstate ; i ++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp,"+$%d",k+i+1);
           oldm=oldms;savm=savms;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          
           for (h=0; h<=nhstepm; h++){        l=3+(nlstate+ndeath)*cpt;
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for (i=1; i< nlstate ; i ++) {
             }          l=3+(nlstate+ndeath)*cpt;
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficgp,"+$%d",l+i+1);
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                      fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          } 
               }    }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    
             }    /* proba elementaires */
           }    for(i=1,jk=1; i <=nlstate; i++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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++; 
              fprintf(ficgp,"\n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
         }
   if (popforecast==1) {      }
     free_ivector(popage,0,AGESUP);     }
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   }       for(jk=1; jk <=m; jk++) {
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         if (ng==2)
   fclose(ficrespop);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
 }         else
            fprintf(ficgp,"\nset title \"Probability\"\n");
 /***********************************************/         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 /**************** Main Program *****************/         i=1;
 /***********************************************/         for(k2=1; k2<=nlstate; k2++) {
            k3=i;
 int main(int argc, char *argv[])           for(k=1; k<=(nlstate+ndeath); k++) {
 {             if (k != k2){
                if(ng==2)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   double agedeb, agefin,hf;               else
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
   double fret;               for(j=3; j <=ncovmodel; j++) {
   double **xi,tmp,delta;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   double dum; /* Dummy variable */                   ij++;
   double ***p3mat;                 }
   int *indx;                 else
   char line[MAXLINE], linepar[MAXLINE];                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];               }
   int firstobs=1, lastobs=10;               fprintf(ficgp,")/(1");
   int sdeb, sfin; /* Status at beginning and end */               
   int c,  h , cpt,l;               for(k1=1; k1 <=nlstate; k1++){   
   int ju,jl, mi;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                 ij=1;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                 for(j=3; j <=ncovmodel; j++){
   int mobilav=0,popforecast=0;                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   int hstepm, nhstepm;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                     ij++;
                    }
   double bage, fage, age, agelim, agebase;                   else
   double ftolpl=FTOL;                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   double **prlim;                 }
   double *severity;                 fprintf(ficgp,")");
   double ***param; /* Matrix of parameters */               }
   double  *p;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   double **matcov; /* Matrix of covariance */               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   double ***delti3; /* Scale */               i=i+ncovmodel;
   double *delti; /* Scale */             }
   double ***eij, ***vareij;           } /* end k */
   double **varpl; /* Variances of prevalence limits by age */         } /* end k2 */
   double *epj, vepp;       } /* end jk */
   double kk1, kk2;     } /* end ng */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;     fclose(ficgp); 
    }  /* end gnuplot */
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   char z[1]="c", occ;  
 #include <sys/time.h>    int i, cpt, cptcod;
 #include <time.h>    int modcovmax =1;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int mobilavrange, mob;
      double age;
   /* long total_usecs;  
   struct timeval start_time, end_time;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                               a covariate has 2 modalities */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   getcwd(pathcd, size);  
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
   printf("\n%s",version);      if(mobilav==1) mobilavrange=5; /* default */
   if(argc <=1){      else mobilavrange=mobilav;
     printf("\nEnter the parameter file name: ");      for (age=bage; age<=fage; age++)
     scanf("%s",pathtot);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   else{            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     strcpy(pathtot,argv[1]);      /* We keep the original values on the extreme ages bage, fage and for 
   }         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/         we use a 5 terms etc. until the borders are no more concerned. 
   /*cygwin_split_path(pathtot,path,optionfile);      */ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      for (mob=3;mob <=mobilavrange;mob=mob+2){
   /* cutv(path,optionfile,pathtot,'\\');*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   chdir(path);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   replace(pathc,path);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
 /*-------- arguments in the command line --------*/                }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   /* Log file */            }
   strcat(filelog, optionfilefiname);          }
   strcat(filelog,".log");    /* */        }/* end age */
   if((ficlog=fopen(filelog,"w"))==NULL)    {      }/* end mob */
     printf("Problem with logfile %s\n",filelog);    }else return -1;
     goto end;    return 0;
   }  }/* End movingaverage */
   fprintf(ficlog,"Log filename:%s\n",filelog);  
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");  /************** Forecasting ******************/
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  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){
   fflush(ficlog);    /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
   /* */       dateprev1 dateprev2 range of dates during which prevalence is computed
   strcpy(fileres,"r");       anproj2 year of en of projection (same day and month as proj1).
   strcat(fileres, optionfilefiname);    */
   strcat(fileres,".txt");    /* Other files have txt extension */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
   /*---------arguments file --------*/    double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double *popeffectif,*popcount;
     printf("Problem with optionfile %s\n",optionfile);    double ***p3mat;
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    double ***mobaverage;
     goto end;    char fileresf[FILENAMELENGTH];
   }  
     agelim=AGESUP;
   strcpy(filereso,"o");    prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   strcat(filereso,fileres);   
   if((ficparo=fopen(filereso,"w"))==NULL) {    strcpy(fileresf,"f"); 
     printf("Problem with Output resultfile: %s\n", filereso);    strcat(fileresf,fileres);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    if((ficresf=fopen(fileresf,"w"))==NULL) {
     goto end;      printf("Problem with forecast resultfile: %s\n", fileresf);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
   /* Reads comments: lines beginning with '#' */    printf("Computing forecasting: result on file '%s' \n", fileresf);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     puts(line);  
     fputs(line,ficparo);    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   ungetc(c,ficpar);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   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(" 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);      }
   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);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     fgets(line, MAXLINE, ficpar);    if (stepm<=12) stepsize=1;
     puts(line);    if(estepm < stepm){
     fputs(line,ficparo);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
   ungetc(c,ficpar);    else  hstepm=estepm;   
    
        hstepm=hstepm/stepm; 
   covar=matrix(0,NCOVMAX,1,n);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   cptcovn=0;                                 fractional in yp1 */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    anprojmean=yp;
     yp2=modf((yp1*12),&yp);
   ncovmodel=2+cptcovn;    mprojmean=yp;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    yp1=modf((yp2*30.5),&yp);
      jprojmean=yp;
   /* Read guess parameters */    if(jprojmean==0) jprojmean=1;
   /* Reads comments: lines beginning with '#' */    if(mprojmean==0) jprojmean=1;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    i1=cptcoveff;
     fgets(line, MAXLINE, ficpar);    if (cptcovn < 1){i1=1;}
     puts(line);    
     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);  /*            if (h==(int)(YEARM*yearp)){ */
     for(i=1; i <=nlstate; i++)    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     for(j=1; j <=nlstate+ndeath-1; j++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        k=k+1;
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficresf,"\n#******");
       if(mle==1)        for(j=1;j<=cptcoveff;j++) {
         printf("%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]]);
       fprintf(ficlog,"%1d%1d",i,j);        }
       for(k=1; k<=ncovmodel;k++){        fprintf(ficresf,"******\n");
         fscanf(ficpar," %lf",&param[i][j][k]);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         if(mle==1){        for(j=1; j<=nlstate+ndeath;j++){ 
           printf(" %lf",param[i][j][k]);          for(i=1; i<=nlstate;i++)              
           fprintf(ficlog," %lf",param[i][j][k]);            fprintf(ficresf," p%d%d",i,j);
         }          fprintf(ficresf," p.%d",j);
         else        }
           fprintf(ficlog," %lf",param[i][j][k]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
         fprintf(ficparo," %lf",param[i][j][k]);          fprintf(ficresf,"\n");
       }          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       fscanf(ficpar,"\n");  
       if(mle==1)          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         printf("\n");            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
       fprintf(ficlog,"\n");            nhstepm = nhstepm/hstepm; 
       fprintf(ficparo,"\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }            oldm=oldms;savm=savms;
              hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          
             for (h=0; h<=nhstepm; h++){
   p=param[1][1];              if (h*hstepm/YEARM*stepm ==yearp) {
                  fprintf(ficresf,"\n");
   /* Reads comments: lines beginning with '#' */                for(j=1;j<=cptcoveff;j++) 
   while((c=getc(ficpar))=='#' && c!= EOF){                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     ungetc(c,ficpar);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     fgets(line, MAXLINE, ficpar);              } 
     puts(line);              for(j=1; j<=nlstate+ndeath;j++) {
     fputs(line,ficparo);                ppij=0.;
   }                for(i=1; i<=nlstate;i++) {
   ungetc(c,ficpar);                  if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                  else {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   for(i=1; i <=nlstate; i++){                  }
     for(j=1; j <=nlstate+ndeath-1; j++){                  if (h*hstepm/YEARM*stepm== yearp) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       printf("%1d%1d",i,j);                  }
       fprintf(ficparo,"%1d%1d",i1,j1);                } /* end i */
       for(k=1; k<=ncovmodel;k++){                if (h*hstepm/YEARM*stepm==yearp) {
         fscanf(ficpar,"%le",&delti3[i][j][k]);                  fprintf(ficresf," %.3f", ppij);
         printf(" %le",delti3[i][j][k]);                }
         fprintf(ficparo," %le",delti3[i][j][k]);              }/* end j */
       }            } /* end h */
       fscanf(ficpar,"\n");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("\n");          } /* end agec */
       fprintf(ficparo,"\n");        } /* end yearp */
     }      } /* end cptcod */
   }    } /* end  cptcov */
   delti=delti3[1][1];         
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    fclose(ficresf);
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************** Forecasting *****not tested NB*************/
     fputs(line,ficparo);  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;
      int *popage;
   matcov=matrix(1,npar,1,npar);    double calagedatem, agelim, kk1, kk2;
   for(i=1; i <=npar; i++){    double *popeffectif,*popcount;
     fscanf(ficpar,"%s",&str);    double ***p3mat,***tabpop,***tabpopprev;
     if(mle==1)    double ***mobaverage;
       printf("%s",str);    char filerespop[FILENAMELENGTH];
     fprintf(ficlog,"%s",str);  
     fprintf(ficparo,"%s",str);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(j=1; j <=i; j++){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fscanf(ficpar," %le",&matcov[i][j]);    agelim=AGESUP;
       if(mle==1){    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
         printf(" %.5le",matcov[i][j]);    
         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]);    strcpy(filerespop,"pop"); 
       fprintf(ficparo," %.5le",matcov[i][j]);    strcat(filerespop,fileres);
     }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     fscanf(ficpar,"\n");      printf("Problem with forecast resultfile: %s\n", filerespop);
     if(mle==1)      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       printf("\n");    }
     fprintf(ficlog,"\n");    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficparo,"\n");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   }  
   for(i=1; i <=npar; i++)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    if (mobilav!=0) {
          mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if(mle==1)      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     printf("\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficlog,"\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */    stepsize=(int) (stepm+YEARM-1)/YEARM;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    if (stepm<=12) stepsize=1;
      strcat(rfileres,".");    /* */    
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    agelim=AGESUP;
     if((ficres =fopen(rfileres,"w"))==NULL) {    
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    hstepm=1;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    hstepm=hstepm/stepm; 
     }    
     fprintf(ficres,"#%s\n",version);    if (popforecast==1) {
          if((ficpop=fopen(popfile,"r"))==NULL) {
     /*-------- data file ----------*/        printf("Problem with population file : %s\n",popfile);exit(0);
     if((fic=fopen(datafile,"r"))==NULL)    {        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       printf("Problem with datafile: %s\n", datafile);goto end;      } 
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      popage=ivector(0,AGESUP);
     }      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
     n= lastobs;      
     severity = vector(1,maxwav);      i=1;   
     outcome=imatrix(1,maxwav+1,1,n);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     num=ivector(1,n);     
     moisnais=vector(1,n);      imx=i;
     annais=vector(1,n);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     moisdc=vector(1,n);    }
     andc=vector(1,n);  
     agedc=vector(1,n);    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     cod=ivector(1,n);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     weight=vector(1,n);        k=k+1;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        fprintf(ficrespop,"\n#******");
     mint=matrix(1,maxwav,1,n);        for(j=1;j<=cptcoveff;j++) {
     anint=matrix(1,maxwav,1,n);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
     s=imatrix(1,maxwav+1,1,n);        }
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficrespop,"******\n");
     tab=ivector(1,NCOVMAX);        fprintf(ficrespop,"# Age");
     ncodemax=ivector(1,8);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
     i=1;        
     while (fgets(line, MAXLINE, fic) != NULL)    {        for (cpt=0; cpt<=0;cpt++) { 
       if ((i >= firstobs) && (i <=lastobs)) {          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                  
         for (j=maxwav;j>=1;j--){          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           strcpy(line,stra);            nhstepm = nhstepm/hstepm; 
           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);            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);  
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              } 
               for(j=1; j<=nlstate+ndeath;j++) {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                kk1=0.;kk2=0;
         for (j=ncovcol;j>=1;j--){                for(i=1; i<=nlstate;i++) {              
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                  if (mobilav==1) 
         }                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         num[i]=atol(stra);                  else {
                            kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                  }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/                }
                 if (h==(int)(calagedatem+12*cpt)){
         i=i+1;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
       }                    /*fprintf(ficrespop," %.3f", kk1);
     }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     /* printf("ii=%d", ij);                }
        scanf("%d",i);*/              }
   imx=i-1; /* Number of individuals */              for(i=1; i<=nlstate;i++){
                 kk1=0.;
   /* for (i=1; i<=imx; i++){                  for(j=1; j<=nlstate;j++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                  }
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                    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;              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
              }
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* Calculation of the number of parameter from char model*/          }
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */        }
   Tprod=ivector(1,15);   
   Tvaraff=ivector(1,15);    /******/
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);              for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
              fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   if (strlen(model) >1){          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     j=0, j1=0, k1=1, k2=1;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
     j=nbocc(model,'+');            nhstepm = nhstepm/hstepm; 
     j1=nbocc(model,'*');            
     cptcovn=j+1;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     cptcovprod=j1;            oldm=oldms;savm=savms;
                hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     strcpy(modelsav,model);            for (h=0; h<=nhstepm; h++){
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){              if (h==(int) (calagedatem+YEARM*cpt)) {
       printf("Error. Non available option model=%s ",model);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       fprintf(ficlog,"Error. Non available option model=%s ",model);              } 
       goto end;              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
                    for(i=1; i<=nlstate;i++) {              
     for(i=(j+1); i>=1;i--){                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/              }
       /*scanf("%d",i);*/            }
       if (strchr(strb,'*')) {  /* Model includes a product */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/          }
         if (strcmp(strc,"age")==0) { /* Vn*age */        }
           cptcovprod--;     } 
           cutv(strb,stre,strd,'V');    }
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/   
           cptcovage++;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/    if (popforecast==1) {
         }      free_ivector(popage,0,AGESUP);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      free_vector(popeffectif,0,AGESUP);
           cptcovprod--;      free_vector(popcount,0,AGESUP);
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=atoi(stre);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cptcovage++;    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tage[cptcovage]=i;    fclose(ficrespop);
         }  }
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  /***********************************************/
           Tvar[i]=ncovcol+k1;  /**************** Main Program *****************/
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */  /***********************************************/
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc); /* m*/  int main(int argc, char *argv[])
           Tvard[k1][2]=atoi(stre); /* n */  {
           Tvar[cptcovn+k2]=Tvard[k1][1];    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
           for (k=1; k<=lastobs;k++)    double agedeb, agefin,hf;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
           k1++;  
           k2=k2+2;    double fret;
         }    double **xi,tmp,delta;
       }  
       else { /* no more sum */    double dum; /* Dummy variable */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double ***p3mat;
        /*  scanf("%d",i);*/    double ***mobaverage;
       cutv(strd,strc,strb,'V');    int *indx;
       Tvar[i]=atoi(strc);    char line[MAXLINE], linepar[MAXLINE];
       }    char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
       strcpy(modelsav,stra);      int firstobs=1, lastobs=10;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    int sdeb, sfin; /* Status at beginning and end */
         scanf("%d",i);*/    int c,  h , cpt,l;
     } /* end of loop + */    int ju,jl, mi;
   } /* end model */    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
      int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   printf("cptcovprod=%d ", cptcovprod);    int mobilav=0,popforecast=0;
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    int hstepm, nhstepm;
   scanf("%d ",i);*/    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     fclose(fic);    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     /*  if(mle==1){*/    double bage, fage, age, agelim, agebase;
     if (weightopt != 1) { /* Maximisation without weights*/    double ftolpl=FTOL;
       for(i=1;i<=n;i++) weight[i]=1.0;    double **prlim;
     }    double *severity;
     /*-calculation of age at interview from date of interview and age at death -*/    double ***param; /* Matrix of parameters */
     agev=matrix(1,maxwav,1,imx);    double  *p;
     double **matcov; /* Matrix of covariance */
     for (i=1; i<=imx; i++) {    double ***delti3; /* Scale */
       for(m=2; (m<= maxwav); m++) {    double *delti; /* Scale */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double ***eij, ***vareij;
          anint[m][i]=9999;    double **varpl; /* Variances of prevalence limits by age */
          s[m][i]=-1;    double *epj, vepp;
        }    double kk1, kk2;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    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]);    char z[1]="c", occ;
       for(m=1; (m<= maxwav); m++){  #include <sys/time.h>
         if(s[m][i] >0){  #include <time.h>
           if (s[m][i] >= nlstate+1) {    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
             if(agedc[i]>0)   
               if(moisdc[i]!=99 && andc[i]!=9999)    /* long total_usecs;
                 agev[m][i]=agedc[i];       struct timeval start_time, end_time;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    
            else {       gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
               if (andc[i]!=9999){    getcwd(pathcd, size);
               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);    printf("\n%s\n%s",version,fullversion);
               agev[m][i]=-1;    if(argc <=1){
               }      printf("\nEnter the parameter file name: ");
             }      scanf("%s",pathtot);
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */    else{
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      strcpy(pathtot,argv[1]);
             if(mint[m][i]==99 || anint[m][i]==9999)    }
               agev[m][i]=1;    /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
             else if(agev[m][i] <agemin){    /*cygwin_split_path(pathtot,path,optionfile);
               agemin=agev[m][i];      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    /* cutv(path,optionfile,pathtot,'\\');*/
             }  
             else if(agev[m][i] >agemax){    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
               agemax=agev[m][i];    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",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);*/    chdir(path);
             }    replace(pathc,path);
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/    /*-------- arguments in the command line --------*/
           }  
           else { /* =9 */    /* Log file */
             agev[m][i]=1;    strcat(filelog, optionfilefiname);
             s[m][i]=-1;    strcat(filelog,".log");    /* */
           }    if((ficlog=fopen(filelog,"w"))==NULL)    {
         }      printf("Problem with logfile %s\n",filelog);
         else /*= 0 Unknown */      goto end;
           agev[m][i]=1;    }
       }    fprintf(ficlog,"Log filename:%s\n",filelog);
        fprintf(ficlog,"\n%s",version);
     }    fprintf(ficlog,"\nEnter the parameter file name: ");
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
       for(m=1; (m<= maxwav); m++){    fflush(ficlog);
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);      /* */
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);      strcpy(fileres,"r");
           goto end;    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);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     free_vector(severity,1,maxwav);      goto end;
     free_imatrix(outcome,1,maxwav+1,1,n);    }
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    strcpy(filereso,"o");
     /* free_matrix(mint,1,maxwav,1,n);    strcat(filereso,fileres);
        free_matrix(anint,1,maxwav,1,n);*/    if((ficparo=fopen(filereso,"w"))==NULL) {
     free_vector(moisdc,1,n);      printf("Problem with Output resultfile: %s\n", filereso);
     free_vector(andc,1,n);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
        }
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    /* Reads comments: lines beginning with '#' */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    while((c=getc(ficpar))=='#' && c!= EOF){
          ungetc(c,ficpar);
     /* Concatenates waves */      fgets(line, MAXLINE, ficpar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      puts(line);
       fputs(line,ficparo);
     }
       Tcode=ivector(1,100);    ungetc(c,ficpar);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    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);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
          fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
    codtab=imatrix(1,100,1,10);    while((c=getc(ficpar))=='#' && c!= EOF){
    h=0;      ungetc(c,ficpar);
    m=pow(2,cptcoveff);      fgets(line, MAXLINE, ficpar);
        puts(line);
    for(k=1;k<=cptcoveff; k++){      fputs(line,ficparo);
      for(i=1; i <=(m/pow(2,k));i++){    }
        for(j=1; j <= ncodemax[k]; j++){    ungetc(c,ficpar);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    
            h++;     
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    covar=matrix(0,NCOVMAX,1,n); 
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
          }    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
        }  
      }    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
    }    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    
       codtab[1][2]=1;codtab[2][2]=2; */    /* Read guess parameters */
    /* for(i=1; i <=m ;i++){    /* Reads comments: lines beginning with '#' */
       for(k=1; k <=cptcovn; k++){    while((c=getc(ficpar))=='#' && c!= EOF){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      ungetc(c,ficpar);
       }      fgets(line, MAXLINE, ficpar);
       printf("\n");      puts(line);
       }      fputs(line,ficparo);
       scanf("%d",i);*/    }
        ungetc(c,ficpar);
    /* Calculates basic frequencies. Computes observed prevalence at single age    
        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++){
            fscanf(ficpar,"%1d%1d",&i1,&j1);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficparo,"%1d%1d",i1,j1);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(mle==1)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          printf("%1d%1d",i,j);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficlog,"%1d%1d",i,j);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(k=1; k<=ncovmodel;k++){
                fscanf(ficpar," %lf",&param[i][j][k]);
     /* For Powell, parameters are in a vector p[] starting at p[1]          if(mle==1){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            printf(" %lf",param[i][j][k]);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            fprintf(ficlog," %lf",param[i][j][k]);
           }
     if(mle==1){          else
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            fprintf(ficlog," %lf",param[i][j][k]);
     }          fprintf(ficparo," %lf",param[i][j][k]);
            }
     /*--------- results files --------------*/        fscanf(ficpar,"\n");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);        if(mle==1)
            printf("\n");
         fprintf(ficlog,"\n");
    jk=1;        fprintf(ficparo,"\n");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      }
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){    p=param[1][1];
        if (k != i)    
          {    /* Reads comments: lines beginning with '#' */
            printf("%d%d ",i,k);    while((c=getc(ficpar))=='#' && c!= EOF){
            fprintf(ficlog,"%d%d ",i,k);      ungetc(c,ficpar);
            fprintf(ficres,"%1d%1d ",i,k);      fgets(line, MAXLINE, ficpar);
            for(j=1; j <=ncovmodel; j++){      puts(line);
              printf("%f ",p[jk]);      fputs(line,ficparo);
              fprintf(ficlog,"%f ",p[jk]);    }
              fprintf(ficres,"%f ",p[jk]);    ungetc(c,ficpar);
              jk++;  
            }    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
            printf("\n");    /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
            fprintf(ficlog,"\n");    for(i=1; i <=nlstate; i++){
            fprintf(ficres,"\n");      for(j=1; j <=nlstate+ndeath-1; j++){
          }        fscanf(ficpar,"%1d%1d",&i1,&j1);
      }        printf("%1d%1d",i,j);
    }        fprintf(ficparo,"%1d%1d",i1,j1);
    if(mle==1){        for(k=1; k<=ncovmodel;k++){
      /* Computing hessian and covariance matrix */          fscanf(ficpar,"%le",&delti3[i][j][k]);
      ftolhess=ftol; /* Usually correct */          printf(" %le",delti3[i][j][k]);
      hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(ficparo," %le",delti3[i][j][k]);
    }        }
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        fscanf(ficpar,"\n");
    printf("# Scales (for hessian or gradient estimation)\n");        printf("\n");
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");        fprintf(ficparo,"\n");
    for(i=1,jk=1; i <=nlstate; i++){      }
      for(j=1; j <=nlstate+ndeath; j++){    }
        if (j!=i) {    delti=delti3[1][1];
          fprintf(ficres,"%1d%1d",i,j);  
          printf("%1d%1d",i,j);  
          fprintf(ficlog,"%1d%1d",i,j);    /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
          for(k=1; k<=ncovmodel;k++){    
            printf(" %.5e",delti[jk]);    /* Reads comments: lines beginning with '#' */
            fprintf(ficlog," %.5e",delti[jk]);    while((c=getc(ficpar))=='#' && c!= EOF){
            fprintf(ficres," %.5e",delti[jk]);      ungetc(c,ficpar);
            jk++;      fgets(line, MAXLINE, ficpar);
          }      puts(line);
          printf("\n");      fputs(line,ficparo);
          fprintf(ficlog,"\n");    }
          fprintf(ficres,"\n");    ungetc(c,ficpar);
        }    
      }    matcov=matrix(1,npar,1,npar);
    }    for(i=1; i <=npar; i++){
          fscanf(ficpar,"%s",&str);
    k=1;      if(mle==1)
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        printf("%s",str);
    if(mle==1)      fprintf(ficlog,"%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(ficparo,"%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");      for(j=1; j <=i; j++){
    for(i=1;i<=npar;i++){        fscanf(ficpar," %le",&matcov[i][j]);
      /*  if (k>nlstate) k=1;        if(mle==1){
          i1=(i-1)/(ncovmodel*nlstate)+1;          printf(" %.5le",matcov[i][j]);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          fprintf(ficlog," %.5le",matcov[i][j]);
          printf("%s%d%d",alph[k],i1,tab[i]);*/        }
      fprintf(ficres,"%3d",i);        else
      if(mle==1)          fprintf(ficlog," %.5le",matcov[i][j]);
        printf("%3d",i);        fprintf(ficparo," %.5le",matcov[i][j]);
      fprintf(ficlog,"%3d",i);      }
      for(j=1; j<=i;j++){      fscanf(ficpar,"\n");
        fprintf(ficres," %.5e",matcov[i][j]);      if(mle==1)
        if(mle==1)        printf("\n");
          printf(" %.5e",matcov[i][j]);      fprintf(ficlog,"\n");
        fprintf(ficlog," %.5e",matcov[i][j]);      fprintf(ficparo,"\n");
      }    }
      fprintf(ficres,"\n");    for(i=1; i <=npar; i++)
      if(mle==1)      for(j=i+1;j<=npar;j++)
        printf("\n");        matcov[i][j]=matcov[j][i];
      fprintf(ficlog,"\n");     
      k++;    if(mle==1)
    }      printf("\n");
        fprintf(ficlog,"\n");
    while((c=getc(ficpar))=='#' && c!= EOF){  
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);    /*-------- Rewriting paramater file ----------*/
      puts(line);    strcpy(rfileres,"r");    /* "Rparameterfile */
      fputs(line,ficparo);    strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
    }    strcat(rfileres,".");    /* */
    ungetc(c,ficpar);    strcat(rfileres,optionfilext);    /* Other files have txt extension */
    estepm=0;    if((ficres =fopen(rfileres,"w"))==NULL) {
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      printf("Problem writing new parameter file: %s\n", fileres);goto end;
    if (estepm==0 || estepm < stepm) estepm=stepm;      fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
    if (fage <= 2) {    }
      bage = ageminpar;    fprintf(ficres,"#%s\n",version);
      fage = agemaxpar;      
    }    /*-------- data file ----------*/
        if((fic=fopen(datafile,"r"))==NULL)    {
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      printf("Problem with datafile: %s\n", datafile);goto end;
    fprintf(ficres,"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;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    }
      
    while((c=getc(ficpar))=='#' && c!= EOF){    n= lastobs;
      ungetc(c,ficpar);    severity = vector(1,maxwav);
      fgets(line, MAXLINE, ficpar);    outcome=imatrix(1,maxwav+1,1,n);
      puts(line);    num=ivector(1,n);
      fputs(line,ficparo);    moisnais=vector(1,n);
    }    annais=vector(1,n);
    ungetc(c,ficpar);    moisdc=vector(1,n);
      andc=vector(1,n);
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    agedc=vector(1,n);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    cod=ivector(1,n);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    weight=vector(1,n);
        for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
    while((c=getc(ficpar))=='#' && c!= EOF){    mint=matrix(1,maxwav,1,n);
      ungetc(c,ficpar);    anint=matrix(1,maxwav,1,n);
      fgets(line, MAXLINE, ficpar);    s=imatrix(1,maxwav+1,1,n);
      puts(line);    tab=ivector(1,NCOVMAX);
      fputs(line,ficparo);    ncodemax=ivector(1,8);
    }  
    ungetc(c,ficpar);    i=1;
      while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
   fscanf(ficpar,"pop_based=%d\n",&popbased);          strcpy(line,stra);
   fprintf(ficparo,"pop_based=%d\n",popbased);            cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
   fprintf(ficres,"pop_based=%d\n",popbased);            cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
          }
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
     fgets(line, MAXLINE, ficpar);        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
     puts(line);  
     fputs(line,ficparo);        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
   }        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   ungetc(c,ficpar);  
         cutv(stra, strb,line,' '); weight[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);        for (j=ncovcol;j>=1;j--){
 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);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 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);        } 
         num[i]=atol(stra);
           
 while((c=getc(ficpar))=='#' && c!= EOF){        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
     ungetc(c,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;}*/
     fgets(line, MAXLINE, ficpar);  
     puts(line);        i=i+1;
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);    /* printf("ii=%d", ij);
        scanf("%d",i);*/
   fscanf(ficpar,"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(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);    /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
 /*------------ gnuplot -------------*/      }*/
   strcpy(optionfilegnuplot,optionfilefiname);     /*  for (i=1; i<=imx; i++){
   strcat(optionfilegnuplot,".gp");       if (s[4][i]==9)  s[4][i]=-1; 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       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]));}*/
     printf("Problem with file %s",optionfilegnuplot);    
   }   for (i=1; i<=imx; i++)
   fclose(ficgp);   
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);     /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
 /*--------- index.htm --------*/       else weight[i]=1;*/
   
   strcpy(optionfilehtm,optionfile);    /* Calculation of the number of parameter from char model*/
   strcat(optionfilehtm,".htm");    Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    Tprod=ivector(1,15); 
     printf("Problem with %s \n",optionfilehtm), exit(0);    Tvaraff=ivector(1,15); 
   }    Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
   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    if (strlen(model) >1){ /* If there is at least 1 covariate */
 \n      j=0, j1=0, k1=1, k2=1;
 Total number of observations=%d <br>\n      j=nbocc(model,'+'); /* j=Number of '+' */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      j1=nbocc(model,'*'); /* j1=Number of '*' */
 <hr  size=\"2\" color=\"#EC5E5E\">      cptcovn=j+1; 
  <ul><li><h4>Parameter files</h4>\n      cptcovprod=j1; /*Number of products */
  - 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      strcpy(modelsav,model); 
  - 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);      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
   fclose(fichtm);        printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"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);        goto end;
        }
 /*------------ free_vector  -------------*/      
  chdir(path);      /* This loop fills the array Tvar from the string 'model'.*/
    
  free_ivector(wav,1,imx);      for(i=(j+1); i>=1;i--){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
  free_ivector(num,1,n);        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
  free_vector(agedc,1,n);        /*scanf("%d",i);*/
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        if (strchr(strb,'*')) {  /* Model includes a product */
  fclose(ficparo);          cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
  fclose(ficres);          if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
   /*--------------- Prevalence limit --------------*/            Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
              cptcovage++;
   strcpy(filerespl,"pl");              Tage[cptcovage]=i;
   strcat(filerespl,fileres);              /*printf("stre=%s ", stre);*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          else if (strcmp(strd,"age")==0) { /* or age*Vn */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;            cptcovprod--;
   }            cutv(strb,stre,strc,'V');
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            Tvar[i]=atoi(stre);
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);            cptcovage++;
   fprintf(ficrespl,"#Prevalence limit\n");            Tage[cptcovage]=i;
   fprintf(ficrespl,"#Age ");          }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          else {  /* Age is not in the model */
   fprintf(ficrespl,"\n");            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
              Tvar[i]=ncovcol+k1;
   prlim=matrix(1,nlstate,1,nlstate);            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tprod[k1]=i;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tvard[k1][1]=atoi(strc); /* m*/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tvard[k1][2]=atoi(stre); /* n */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            Tvar[cptcovn+k2]=Tvard[k1][1];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
   k=0;            for (k=1; k<=lastobs;k++) 
   agebase=ageminpar;              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
   agelim=agemaxpar;            k1++;
   ftolpl=1.e-10;            k2=k2+2;
   i1=cptcoveff;          }
   if (cptcovn < 1){i1=1;}        }
         else { /* no more sum */
   for(cptcov=1;cptcov<=i1;cptcov++){          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         /*  scanf("%d",i);*/
         k=k+1;        cutv(strd,strc,strb,'V');
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        Tvar[i]=atoi(strc);
         fprintf(ficrespl,"\n#******");        }
         printf("\n#******");        strcpy(modelsav,stra);  
         fprintf(ficlog,"\n#******");        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
         for(j=1;j<=cptcoveff;j++) {          scanf("%d",i);*/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* end of loop + */
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    } /* end model */
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         }    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
         fprintf(ficrespl,"******\n");      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
         printf("******\n");  
         fprintf(ficlog,"******\n");    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
            printf("cptcovprod=%d ", cptcovprod);
         for (age=agebase; age<=agelim; age++){    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    scanf("%d ",i);
           for(i=1; i<=nlstate;i++)    fclose(fic);*/
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           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 -*/
     agev=matrix(1,maxwav,1,imx);
   /*------------- h Pij x at various ages ------------*/  
      for (i=1; i<=imx; i++) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      for(m=2; (m<= maxwav); m++) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          anint[m][i]=9999;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;          s[m][i]=-1;
   }        }
   printf("Computing pij: result on file '%s' \n", filerespij);        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);          printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
            fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          s[m][i]=-1;
   /*if (stepm<=24) stepsize=2;*/        }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
   agelim=AGESUP;          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=stepsize*YEARM; /* Every year of age */          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]); 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          s[m][i]=-1;
         }
   /* hstepm=1;   aff par mois*/      }
     }
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    for (i=1; i<=imx; i++)  {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       k=k+1;      for(m=firstpass; (m<= lastpass); m++){
         fprintf(ficrespij,"\n#****** ");        if(s[m][i] >0){
         for(j=1;j<=cptcoveff;j++)          if (s[m][i] >= nlstate+1) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if(agedc[i]>0)
         fprintf(ficrespij,"******\n");              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                        agev[m][i]=agedc[i];
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              else {
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/                  fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
           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,"# Age");          else if(s[m][i] !=9){ /* Standard case, age in fractional
           for(i=1; i<=nlstate;i++)                                   years but with the precision of a
             for(j=1; j<=nlstate+ndeath;j++)                                   month */
               fprintf(ficrespij," %1d-%1d",i,j);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
           fprintf(ficrespij,"\n");            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
            for (h=0; h<=nhstepm; h++){              agev[m][i]=1;
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            else if(agev[m][i] <agemin){ 
             for(i=1; i<=nlstate;i++)              agemin=agev[m][i];
               for(j=1; j<=nlstate+ndeath;j++)              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            }
             fprintf(ficrespij,"\n");            else if(agev[m][i] >agemax){
              }              agemax=agev[m][i];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
           fprintf(ficrespij,"\n");            }
         }            /*agev[m][i]=anint[m][i]-annais[i];*/
     }            /*     agev[m][i] = age[i]+2*m;*/
   }          }
           else { /* =9 */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            agev[m][i]=1;
             s[m][i]=-1;
   fclose(ficrespij);          }
         }
         else /*= 0 Unknown */
   /*---------- Forecasting ------------------*/          agev[m][i]=1;
   if((stepm == 1) && (strcmp(model,".")==0)){      }
     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);    }
   }    for (i=1; i<=imx; i++)  {
   else{      for(m=firstpass; (m<=lastpass); m++){
     erreur=108;        if (s[m][i] > (nlstate+ndeath)) {
     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);          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,"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,"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");    /*for (i=1; i<=imx; i++){
   strcat(filerest,fileres);    for (m=firstpass; (m<lastpass); m++){
   if((ficrest=fopen(filerest,"w"))==NULL) {       printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
     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);    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");    free_vector(severity,1,maxwav);
   strcat(filerese,fileres);    free_imatrix(outcome,1,maxwav+1,1,n);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    free_vector(moisnais,1,n);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_vector(annais,1,n);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /* free_matrix(mint,1,maxwav,1,n);
   }       free_matrix(anint,1,maxwav,1,n);*/
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    free_vector(moisdc,1,n);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    free_vector(andc,1,n);
   
   strcpy(fileresv,"v");     
   strcat(fileresv,fileres);    wav=ivector(1,imx);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    dh=imatrix(1,lastpass-firstpass+1,1,imx);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    bh=imatrix(1,lastpass-firstpass+1,1,imx);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    mw=imatrix(1,lastpass-firstpass+1,1,imx);
   }     
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    /* Concatenates waves */
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   calagedate=-1;  
   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;    Tcode=ivector(1,100);
   for(cptcov=1;cptcov<=i1;cptcov++){    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    ncodemax[1]=1;
       k=k+1;    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
       fprintf(ficrest,"\n#****** ");        
       for(j=1;j<=cptcoveff;j++)    codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                   the estimations*/
       fprintf(ficrest,"******\n");    h=0;
     m=pow(2,cptcoveff);
       fprintf(ficreseij,"\n#****** ");   
       for(j=1;j<=cptcoveff;j++)    for(k=1;k<=cptcoveff; k++){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1; i <=(m/pow(2,k));i++){
       fprintf(ficreseij,"******\n");        for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
       fprintf(ficresvij,"\n#****** ");            h++;
       for(j=1;j<=cptcoveff;j++)            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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]);*/
       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);      /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
         codtab[1][2]=1;codtab[2][2]=2; */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /* for(i=1; i <=m ;i++){ 
       oldm=oldms;savm=savms;       for(k=1; k <=cptcovn; k++){
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
       if(popbased==1){       }
         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) ");    /* Calculates basic frequencies. Computes observed prevalence at single age
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       and prints on file fileres'p'. */
       fprintf(ficrest,"\n");  
       pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       epj=vector(1,nlstate+1);      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       for(age=bage; age <=fage ;age++){      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         if (popbased==1) {      oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
           for(i=1; i<=nlstate;i++)      
             prlim[i][i]=probs[(int)age][i][k];     
         }    /* For Powell, parameters are in a vector p[] starting at p[1]
               so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
         fprintf(ficrest," %4.0f",age);    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    if(mle>=1){ /* Could be 1 or 2 */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    }
           }      
           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++)    jk=1;
             vepp += vareij[i][j][(int)age];    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
         for(j=1;j <=nlstate;j++){    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    for(i=1,jk=1; i <=nlstate; i++){
         }      for(k=1; k <=(nlstate+ndeath); k++){
         fprintf(ficrest,"\n");        if (k != i) 
       }          {
     }            printf("%d%d ",i,k);
   }            fprintf(ficlog,"%d%d ",i,k);
 free_matrix(mint,1,maxwav,1,n);            fprintf(ficres,"%1d%1d ",i,k);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);            for(j=1; j <=ncovmodel; j++){
     free_vector(weight,1,n);              printf("%f ",p[jk]);
   fclose(ficreseij);              fprintf(ficlog,"%f ",p[jk]);
   fclose(ficresvij);              fprintf(ficres,"%f ",p[jk]);
   fclose(ficrest);              jk++; 
   fclose(ficpar);            }
   free_vector(epj,1,nlstate+1);            printf("\n");
              fprintf(ficlog,"\n");
   /*------- Variance limit prevalence------*/              fprintf(ficres,"\n");
           }
   strcpy(fileresvpl,"vpl");      }
   strcat(fileresvpl,fileres);    }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    if(mle==1){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* Computing hessian and covariance matrix */
     exit(0);      ftolhess=ftol; /* Usually correct */
   }      hesscov(matcov, p, npar, delti, ftolhess, func);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
   k=0;    printf("# Scales (for hessian or gradient estimation)\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1,jk=1; i <=nlstate; i++){
       k=k+1;      for(j=1; j <=nlstate+ndeath; j++){
       fprintf(ficresvpl,"\n#****** ");        if (j!=i) {
       for(j=1;j<=cptcoveff;j++)          fprintf(ficres,"%1d%1d",i,j);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf("%1d%1d",i,j);
       fprintf(ficresvpl,"******\n");          fprintf(ficlog,"%1d%1d",i,j);
                for(k=1; k<=ncovmodel;k++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            printf(" %.5e",delti[jk]);
       oldm=oldms;savm=savms;            fprintf(ficlog," %.5e",delti[jk]);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            fprintf(ficres," %.5e",delti[jk]);
     }            jk++;
  }          }
           printf("\n");
   fclose(ficresvpl);          fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
   /*---------- End : free ----------------*/        }
   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)
        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(pmmij,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(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(i=1,k=1;i<=npar;i++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      /*  if (k>nlstate) k=1;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          i1=(i-1)/(ncovmodel*nlstate)+1; 
            fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
   free_matrix(matcov,1,npar,1,npar);          printf("%s%d%d",alph[k],i1,tab[i]);
   free_vector(delti,1,npar);      */
   free_matrix(agev,1,maxwav,1,imx);      fprintf(ficres,"%3d",i);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      if(mle==1)
         printf("%3d",i);
   fprintf(fichtm,"\n</body>");      fprintf(ficlog,"%3d",i);
   fclose(fichtm);      for(j=1; j<=i;j++){
   fclose(ficgp);        fprintf(ficres," %.5e",matcov[i][j]);
          if(mle==1)
           printf(" %.5e",matcov[i][j]);
   if(erreur >0){        fprintf(ficlog," %.5e",matcov[i][j]);
     printf("End of Imach with error or warning %d\n",erreur);      }
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);      fprintf(ficres,"\n");
   }else{      if(mle==1)
    printf("End of Imach\n");        printf("\n");
    fprintf(ficlog,"End of Imach\n");      fprintf(ficlog,"\n");
   }      k++;
   printf("See log file on %s\n",filelog);    }
   fclose(ficlog);     
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
   /* 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);*/      fgets(line, MAXLINE, ficpar);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      puts(line);
   /*------ End -----------*/      fputs(line,ficparo);
     }
     ungetc(c,ficpar);
  end:  
 #ifdef windows    estepm=0;
   /* chdir(pathcd);*/    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
 #endif    if (estepm==0 || estepm < stepm) estepm=stepm;
  /*system("wgnuplot graph.plt");*/    if (fage <= 2) {
  /*system("../gp37mgw/wgnuplot graph.plt");*/      bage = ageminpar;
  /*system("cd ../gp37mgw");*/      fage = agemaxpar;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    }
  strcpy(plotcmd,GNUPLOTPROGRAM);     
  strcat(plotcmd," ");    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
  strcat(plotcmd,optionfilegnuplot);    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
  system(plotcmd);    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
 #ifdef windows    while((c=getc(ficpar))=='#' && c!= EOF){
   while (z[0] != 'q') {      ungetc(c,ficpar);
     /* chdir(path); */      fgets(line, MAXLINE, ficpar);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      puts(line);
     scanf("%s",z);      fputs(line,ficparo);
     if (z[0] == 'c') system("./imach");    }
     else if (z[0] == 'e') system(optionfilehtm);    ungetc(c,ficpar);
     else if (z[0] == 'g') system(plotcmd);    
     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);
   }    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);
 #endif    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
 }    printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
   Total number of observations=%d <br>\n
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
   <hr  size=\"2\" color=\"#EC5E5E\">
    <ul><li><h4>Parameter files</h4>\n
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
    - Log file of the run: <a href=\"%s\">%s</a><br>\n
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
      fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.50  
changed lines
  Added in v.1.81

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